Importing release version 322 from old repos

src/wsi/ra/chart2d/DArea.java

@@ -0,0 +1,726 @@
+/**
+ *  Filename: $RCSfile: DArea.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:41 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.chart2d;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.awt.*;
+import java.awt.image.BufferedImage;
+import javax.swing.*;
+import javax.swing.border.Border;
+import java.util.Vector;
+
+// zum Drucken:
+import java.awt.print.*;
+import wsi.ra.print.PagePrinter;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+/**
+ * DArea is the crossing of the <code>JComponent</code>s and the
+ * <code>DComponent</code>s. It's the <code>DParent</code> which can be added to
+ * <code>JComponent</code>s
+ */
+public class DArea extends JComponent implements DParent, Printable
+{
+  private static final boolean under_construction = false;
+
+  /**
+   * the default minimal rectangle which is shown
+   */
+  public static final DRectangle DEFAULT_MIN_RECT = new DRectangle(-1, -1, 2, 2);
+
+
+  /**
+   * the container in which all DElements of the area are contained except
+   * the grid
+   */
+  private DContainer container;
+
+  /**
+   * min_rectangle is set, when all elements are removed
+   * the intersection of visible_rect and max_rectangle is the currently visible
+   * rectangle
+   */
+  protected DRectangle min_rect     = DEFAULT_MIN_RECT,
+                       visible_rect = DEFAULT_MIN_RECT;
+
+  protected Double min_x, min_y, max_x, max_y;
+
+  /**
+   * the grid of the area
+   */
+  private DGrid grid;
+
+  private boolean auto_focus = false,
+                  auto_grid = false,
+                  grid_to_front = false;
+
+  /**
+   * maximal number of grid lines
+   */
+  private int max_grid = 10;
+
+  /**
+   * the measures of the area
+   * it calculates the coordinates
+   */
+  private DMeasures measures;
+
+
+  private DBorder dborder = new DBorder();
+
+  /**
+   * initializes the DArea with the initial capacity of 10 components
+   */
+  public DArea(){
+    this( 10 );
+  }
+
+  /**
+   * initializes the DArea with the specialized initial capacity of components
+   * (@see java.util.Vector)
+   *
+   * @param the initial capacity
+   */
+  public DArea( int initial_capacity ){
+    container = new DContainer();
+    container.setDParent( this );
+    grid = new DGrid( visible_rect, 1, 1 );
+    grid.setVisible( false );
+    grid.setDParent( this );
+    measures = new DMeasures( this );
+  }
+
+  /**
+   * returns the currently visible rectangle in DArea coordinates
+   *
+   * @return DRectangle the size and position of the visible area
+   */
+  public DRectangle getDRectangle(){
+    DRectangle rect = (DRectangle)visible_rect.clone();
+    if( min_x != null ) rect.x      = Math.max(rect.x,      getMinX()            );
+    if( min_y != null ) rect.y      = Math.max(rect.y,      getMinY()            );
+    if( max_x != null ) rect.width  = Math.min(rect.width,  getMaxX() - getMinX());
+    if( max_y != null ) rect.height = Math.min(rect.height, getMaxY() - getMinY());
+    return rect;
+  }
+
+  /**
+   * switches the auto focus of this DArea on or off
+   *
+   * @param b on or off
+   */
+  public void setAutoFocus( boolean b ){
+    boolean old = auto_focus;
+    auto_focus = b;
+    if( old != b ) repaint();
+  }
+
+  /**
+   * returns whether the DArea's auto focus is on or not
+   *
+   * @return <code>true</code> or <code>false</code>
+   */
+  public boolean isOnAutoFocus(){ return auto_focus; }
+
+  /**
+   * sets the visible rectangle to this size
+   *
+   * @param x the x coordinate of the left border
+   * @param y the y coordinate of the bottom border
+   * @param width the width of the area
+   * @param height the height of the area
+   */
+  public void setVisibleRectangle( double x, double y, double width, double height ){
+    //System.out.println("DArea.setVisibleRectangle(...)");
+    setVisibleRectangle( new DRectangle( x, y, width, height ) );
+  }
+
+  /**
+   * sets the visible rectangle
+   *
+   * @param rect the visible <code>DRectangle</code> in DArea coordinates
+   */
+  public void setVisibleRectangle( DRectangle rect ){
+    if( under_construction )System.out.println("DArea.setVisibleRectangle(DRectangle)");
+    if( rect.isEmpty() ) throw
+      new IllegalArgumentException(
+        "You shopuld never try to set an empty rectangle\n"
+        + "as the visible rectangle of an DArea" );
+
+    if( !rect.equals( visible_rect ) && rect.width > 0 && rect.height > 0 ){
+      auto_focus = false;
+      visible_rect = (DRectangle)rect.clone();
+      repaint();
+    }
+  }
+
+  /**
+   * sets the minimal rectangle
+   *
+   * @param x
+   * @param y
+   * @param width
+   * @param height
+   */
+  public void setMinRectangle( double x, double y, double width, double height ){
+    setMinRectangle( new DRectangle( x, y, width, height ) );
+  }
+
+  /**
+   * sets the minimal rectangle
+   *
+   * @param rect the visible <code>DRectangle</code> in DArea coordinates
+   */
+  public void setMinRectangle( DRectangle rect ){
+    if( rect.isEmpty() ) min_rect = DEFAULT_MIN_RECT;
+    else min_rect = (DRectangle)rect.clone();
+  }
+
+  /**
+   * method returns the minimal rectangle which is set as the visible when all
+   * elements are removed and the area is on auto focus
+   *
+   * @return the minmal rectangle
+   */
+  public DRectangle getMinRectangle(){
+    return (DRectangle)min_rect.clone();
+  }
+
+  /**
+   * method sets the maximal rectangle whioch can be viewed with the
+   * DArea. This method can be used if the area is used with scale functions
+   * which are not invertible on all reals
+   *
+   * @param x the minmal x value
+   * @param y the minmal y value
+   * @param width of the maximal rectangle
+   * @param height of the maximal rectangle
+   */
+  public void setMaxRectangle( double x, double y, double width, double height ){
+    setMaxRectangle( new DRectangle( x, y, width, height ) );
+  }
+
+
+  /**
+   * method sets the maximal rectangle whioch can be viewed with the
+   * DArea. This method can be used if the area is used with scale functions
+   * which are not invertible on all reals
+   *
+   * @param the rect maximal rectangle of the DArea
+   * @deprecated see setMinX, setMinY, setMaxX, setMaxY
+   */
+  public void setMaxRectangle( DRectangle rect ){
+    if( !rect.contains( min_rect ) ) throw
+      new IllegalArgumentException("Maximal rectangle does not contain minmal rectangle");
+
+    setMinX( rect.x );
+    setMinY( rect.y );
+    setMaxX( rect.x + rect.width );
+    setMaxY( rect.y + rect.height );
+  }
+
+  /**
+   * method returns the maximal rectangle of the area
+   *
+   * @return the maximal rectangle
+   * @deprecated see getMaxX, getMaxY, getMinX, getMinY
+   */
+  public DRectangle getMaxRectangle(){
+    return new DRectangle(min_x.doubleValue(),
+                          min_y.doubleValue(),
+                          max_x.doubleValue() - min_x.doubleValue(),
+                          max_y.doubleValue() - min_y.doubleValue() );
+  }
+
+  /**
+   * method sets the minimal x-value which can be displayed by the DArea
+   * might be helpful, if scale functions are used which are not defined overall
+   *
+   * @param mix the minimal x-value
+   */
+  public void setMinX( double mix ){
+    if( mix > min_rect.x ) throw
+      new IllegalArgumentException(
+        "Mimimal y-value axes intersects minmal rectangle.");
+    min_x = new Double( mix );
+  }
+
+  /**
+   * method resets the minimal x-value
+   */
+  public void releaseMinX(){
+    min_x = null;
+  }
+
+  /**
+   * method returns the minmal x-value which can be displayed in the DArea
+   *
+   * @return the minmal x-value
+   */
+  public double getMinX(){
+    if( min_x != null ) return min_x.doubleValue();
+    return 0;
+  }
+
+
+  /**
+   * method sets the minimal y-value which can be displayed by the DArea
+   * might be helpful, if scale functions are used which are not defined overall
+   *
+   * @param miy the minimal y-value
+   */
+  public void setMinY( double miy ){
+    if( miy > min_rect.y ) throw
+      new IllegalArgumentException(
+        "Mimimal y-value axes intersects minmal rectangle.");
+    min_y = new Double( miy );
+  }
+
+  /**
+   * method resets the minimal y-value
+   */
+  public void releaseMinY(){
+    min_y = null;
+  }
+
+  /**
+   * method returns the minmal y-value which can be displayed in the DArea
+   *
+   * @return the minmal y-value
+   */
+  public double getMinY(){
+    if( min_y != null ) return min_y.doubleValue();
+    return 0;
+  }
+
+
+
+  /**
+   * method sets the maximal x-value which can be displayed by the DArea
+   * might be helpful, if scale functions are used which are not defined overall
+   *
+   * @param max the maximal x-value
+   */
+  public void setMaxX( double max ){
+    if( max < min_rect.x + min_rect.width ) throw
+      new IllegalArgumentException(
+        "Maximal x-value axes intersects minmal rectangle.");
+    max_x = new Double( max );
+  }
+
+  /**
+   * method resets the maximal x-value
+   */
+  public void releaseMaxX(){
+    max_x = null;
+  }
+
+  /**
+   * method returns the maxmal x-value which can be displayed in the DArea
+   *
+   * @return the maxmal x-value
+   */
+  public double getMaxX(){
+    if( max_x != null ) return max_x.doubleValue();
+    return 0;
+  }
+
+
+
+  /**
+   * method sets the maximal y-values which can be displayed by the DArea
+   * might be helpful, if scale functions are used which are not defined overall
+   *
+   * @param may the maximal y-value
+   */
+  public void setMaxY( double may ){
+    if( may < min_rect.y + min_rect.height ) throw
+      new IllegalArgumentException(
+        "Maximal y-value axes intersects minmal rectangle.");
+    max_y = new Double( may );
+  }
+
+  /**
+   * method resets the maximal y-value
+   */
+  public void releaseMaxY(){
+    max_y = null;
+  }
+
+  /**
+   * method returns the maximal y-value which can be displayed in the DArea
+   *
+   * @return the maximal y-value
+   */
+  public double getMaxY(){
+    if( max_y != null ) return max_y.doubleValue();
+    return 0;
+  }
+
+
+  /**
+   * paints the DArea by a Graphics object
+   *
+   * @param g the java.awt.Graphics object
+   */
+  public void paint( Graphics g ){
+    if( under_construction ) System.out.println("DArea.paint(Graphics)");
+    if( auto_focus )  {
+      container.restore();
+      visible_rect = (DRectangle)container.getRectangle().clone();
+    }
+    if( visible_rect.isEmpty() )  visible_rect = (DRectangle)min_rect.clone();
+    super.paint( g );
+
+    measures.setGraphics( g );
+    if( grid.isVisible() && !grid_to_front ) paintGrid( measures );
+    container.paint( measures );
+    if( grid.isVisible() && grid_to_front ) paintGrid( measures );
+  }
+
+  /**
+   * repaints a part of the visible area
+   *
+   * @param r the rectangle to repaint
+   */
+  public void repaint( DRectangle r ){
+    if( under_construction ) System.out.println("DArea.repaint(DRectangle)"+r);
+    if( r == null ) throw
+      new IllegalArgumentException("Cannot repaint a null DRectangle");
+    if( r.isAll() || auto_focus ) repaint();
+    else{
+      Point p1 = measures.getPoint( r.x, r.y ),
+            p2 = measures.getPoint( r.x + r.width, r.y + r.height);
+      if( p1 == null || p2 == null ) repaint();
+      else {
+        DBorder b = getDBorder();
+        repaint( p1.x - b.left,
+                    p2.y - b.top,
+                    p2.x - p1.x + 1 + b.left + b.right,
+                    p1.y - p2.y + 1 + b.top + b.bottom );
+      }
+    }
+  }
+
+  /**
+   * adds a new component to the area
+   *
+   * @param e the new DElement
+   */
+  public void addDElement( DElement e ){
+    container.addDElement( e );
+  }
+
+  /**
+   * removes a certain element from the area
+   *
+   * @param e the element to remove
+   */
+  public boolean removeDElement( DElement e ){
+    return container.removeDElement( e );
+  }
+
+  /**
+   * removes all elements from the area
+   */
+  public void removeAllDElements()
+  {
+    visible_rect = (DRectangle)min_rect.clone();
+    container.removeAllDElements();
+  }
+
+  /**
+   * returnes all DElements in the container
+   *
+   * @return the elements of the container
+   */
+  public DElement[] getDElements(){
+    return container.getDElements();
+  }
+
+  /**
+   * method returns true, if the given element is contained in the container
+   *
+   * @param e the element
+   * @return if it is contained
+   */
+  public boolean contains( DElement e ){
+    return container.contains( e );
+  }
+
+
+  /**
+   * sets the grid visible or not
+   *
+   * @param aFlag visible or not
+   */
+  public void setGridVisible( boolean aFlag ){
+    if( under_construction ) System.out.println("DArea.setGridVisisble: "+aFlag);
+    grid.rectangle = getDRectangle();
+    grid.setVisible( aFlag );
+  }
+
+  /**
+   * returns if the grid is visible
+   * <code>true</code> if the grid is visible or <code>false</code> if not
+   *
+   * @return true or false
+   */
+  public boolean isGridVisible(){
+    return grid.isVisible();
+  }
+
+  /**
+   * sets the grid to the front
+   * that means that the grid is painted as last element
+   * default value is <code>false</code>
+   *
+   * @param aFlag grid t front or not
+   */
+  public void setGridToFront( boolean aFlag ){
+    boolean old = grid_to_front;
+    grid_to_front = aFlag;
+    if( old != aFlag && grid.isVisible() ) repaint();
+  }
+
+  /**
+   * sets the grid's horizontal and vertical distance
+   * that means that the grid's lines will have these distances
+   * in area coordinates
+   *
+   * @param hor_dist the horizontal distance
+   * @param ver_dist the vertical distance
+   */
+  public void setGrid( double hor_dist, double ver_dist ){
+    grid = new DGrid( visible_rect, hor_dist, ver_dist );
+    grid.setDParent( this );
+    auto_grid = false;
+    repaint();
+  }
+
+  /**
+   * sets the auto grid on or off
+   * if it's on, the grid's distances (@see #setGrid(double, double))
+   * are automatically calculated
+   *
+   * @param b auto grid on or not
+   */
+  public void setAutoGrid( boolean b ){
+    if( b ) {
+      grid.rectangle = getDRectangle();
+      grid.setVisible( true );
+    }
+    if( b == auto_grid ) return;
+    auto_grid = b;
+    repaint();
+  }
+
+  /**
+   * returns if the auto grid is switched on
+   *
+   * @return true if the grid is on, else false
+   */
+  public boolean hasAutoGrid(){ return auto_grid; }
+
+  /**
+   * sets the color of the grid
+   *
+   * @param java.awt.Color
+   */
+  public void setGridColor( Color color ){
+    grid.setColor( color );
+  }
+
+  /**
+   * sets the maximal number of grid lines
+   * default value is 10
+   *
+   * @param no maximal number of grid lines
+   */
+  public void setMaxGrid( int no ){
+    if( no < 1 ) return;
+    int old = max_grid;
+    max_grid = no;
+    if( old != no ) repaint();
+  }
+
+  /**
+   * prints the area and it's content
+   * @see java.awt.print.Printable and
+   * @see java.awt.print.PrintJob
+   *
+   * @param g  the Graphics object
+   * @param pf the @see java.awt.print.PageFormat
+   * @param pi the page index
+   *
+   * @return int @see java.awt.print.Printable
+   */
+  public int print( Graphics g, PageFormat pf, int pi ){
+    if( under_construction ) System.out.println("DArea.print(...)");
+    if( pi > 0 ) return Printable.NO_SUCH_PAGE;
+
+    Border sb = getBorder();
+    if( !(sb instanceof ScaledBorder) ) sb = null;
+    else ( (ScaledBorder)sb ).show_outer_border = false;
+    PagePrinter printer = new PagePrinter( this, g, pf );
+    int ret = printer.print();
+    if( sb != null ) ( (ScaledBorder)sb ).show_outer_border = true;
+    return ret;
+  }
+
+  /**
+   * sets a new scale function to the x-axis
+   * That means that not the standard linear scale is shown but the image
+   * of the linear scale under the given function
+   *
+   * @param x_s the scale function for the x-axis
+   */
+  public void setXScale( DFunction x_s ){
+    if( x_s == null && measures.x_scale == null ) return;
+    measures.x_scale = x_s;
+    repaint();
+  }
+
+
+  /**
+   * sets a new scale function to the y-axis
+   * That means that not the standard linear scale is shown but the image
+   * of the linear scale under the given function
+   *
+   * @param y_s the scale function for the y-axis
+   */
+  public void setYScale( DFunction y_s ){
+    if( y_s == null && measures.y_scale == null ) return;
+    measures.y_scale = y_s;
+    repaint();
+  }
+
+  /**
+   *  returns the measures of the DArea
+   *  The DMeasures object calculates the different coodinates and contains a
+   *  Graphics object to paint the DElements of the area
+   *
+   * @return the measures of the DArea
+   */
+  public DMeasures getDMeasures(){
+    return measures;
+  }
+
+  /**
+   * method 'adds' a certain border around the contained rectangle
+   * that means that it takes the old border
+   * and takes the maxima of the old and the new values
+   *
+   * @param clip the java.awt.Insets object of the new clip
+   */
+  public void addDBorder( DBorder b ){
+    dborder.insert(b);
+  }
+
+  /**
+   * method returns the current border around the rectangle
+   *
+   * @return the border
+   */
+  public DBorder getDBorder(){
+    return dborder;
+  }
+
+  public void restoreBorder(){
+    dborder = container.getDBorder();
+    if( under_construction ) System.out.println("DArea.restoreBorder -> "+dborder);
+  }
+
+  /**
+   * method paints the grid
+   * how the method paints the grid depends on whether the area is wrapped in a
+   * <code>ScaledBorder</code> or not and on the auto_grid option
+   */
+  private void paintGrid( DMeasures m ){
+    if( under_construction ) System.out.println("DArea.paintGrid(DMeasures)");
+    grid.rectangle = getDRectangle();
+    if( auto_grid ){
+      Border b = getBorder();
+      if( b instanceof ScaledBorder ){
+        ScaledBorder sb = (ScaledBorder)b;
+        paintGrid( sb, m );
+        return;
+      }
+      else{
+        grid.hor_dist = ScaledBorder.aBitBigger( grid.rectangle.width / max_grid );
+        grid.ver_dist = ScaledBorder.aBitBigger( grid.rectangle.height / max_grid );
+      }
+    }
+    grid.paint( m );
+  }
+
+
+  /**
+   * paints the grid when auto_grid is selected and the area is surrounded
+   * by an instance of ScaledBorder
+   *
+   * @param sb the ScaledBorder around the area
+   * @param m the measures of the area
+   */
+  private void paintGrid(ScaledBorder sb, DMeasures m){
+    if( under_construction ) System.out.println("DArea.paintGrid(ScaledBorder, DMeasures)");
+    Dimension d = getSize();
+    FontMetrics fm = m.getGraphics().getFontMetrics();
+    grid.hor_dist = sb.getSrcdX(fm, d);
+    grid.ver_dist = sb.getSrcdY(fm, d);
+
+    if( m.x_scale == null && m.y_scale == null ) grid.paint( m );
+
+    else{// selber malen
+      Graphics g = m.g;
+      g.setColor( grid.getColor() );
+
+      DRectangle rect = getDRectangle(),
+                 src_rect = m.getSourceOf( rect );
+
+      int x = (int)(src_rect.x / grid.hor_dist),
+          y = (int)(src_rect.y / grid.ver_dist);
+      if( x * grid.hor_dist < src_rect.x ) x++;
+      if( y * grid.ver_dist < src_rect.y ) y++;
+
+      DPoint min = new DPoint( rect.x, rect.y ),
+             max = new DPoint( min.x + rect.width, min.y + rect.height );
+
+      double pos;
+
+      for( ; (pos = x * grid.hor_dist) < src_rect.x + src_rect.width; x++ ){
+        if( m.x_scale != null ) pos = m.x_scale.getImageOf( pos );
+        Point p1 = m.getPoint( pos, min.y ),
+              p2 = m.getPoint( pos, max.y );
+        g.drawLine( p1.x, p1.y, p2.x, p2.y );
+      }
+
+      for( ; (pos = y * grid.ver_dist) < src_rect.y + src_rect.height; y++ ){
+        if( m.y_scale != null ) pos = m.y_scale.getImageOf( pos );
+        Point p1 = m.getPoint( min.x, pos ),
+              p2 = m.getPoint( max.x, pos );
+        g.drawLine( p1.x, p1.y, p2.x, p2.y );
+      }
+    }
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/chart2d/DArray.java

@@ -0,0 +1,205 @@
+package wsi.ra.chart2d;
+
+/**
+ * Title:
+ * Description:
+ * Copyright:    Copyright (c) 2001
+ * Company:
+ * @author
+ * @version 1.0
+ */
+
+/**
+ * This class stores an array of double values.
+ * It can be used as data stack for an DPointSet object.
+ * For that use, it is important to tell the DPoitSet object, when the data has
+ * been modified.
+ */
+public class DArray implements DIntDoubleMap{
+  private int initial_capacity, size;
+  private double capacity_multiplier = 2, max, min;
+  private double[] value;
+
+  /**
+   * Constructor for an DArray object with default values for the initial
+   * capacity (5) and the capacity multiplier (2).
+   */
+  public DArray(){
+    this(5, 2);
+  }
+
+  /**
+   * Constructor for an DArray object with default value for the capacity
+   * multiplier (2).
+   *
+   * @param initial_capacity the initial capacity of the array
+   */
+  public DArray(int initial_capacity){
+    this(initial_capacity, 2);
+  }
+
+  /**
+   * Constructor for an DArray object
+   *
+   * @param initial_capacity the initial capacity of the array
+   * @param capacity_multiplier the capacity multiplier when the array overflows
+   */
+  public DArray(int initial_capacity, double capacity_multiplier){
+    if( initial_capacity < 1 ) throw
+      new IllegalArgumentException("The initial capacity has to be at least 1");
+    if( capacity_multiplier <= 1 ) throw
+      new IllegalArgumentException("The capacity multiplier has to be bigger than 1");
+    this.initial_capacity = initial_capacity;
+    value = new double[initial_capacity];
+    this.capacity_multiplier = capacity_multiplier;
+  }
+
+  /**
+   * method sets the image value to the given source value
+   *
+   * @param source the source value
+   * @param image  the image value
+   */
+  public boolean setImage(int source, double image){
+    if(source<0 || source>=size) throw
+      new ArrayIndexOutOfBoundsException(source);
+    boolean min_max_changed = false, restore = false;
+    if( image < min ){ min = image; min_max_changed = true; }
+    else if( image > max ){ max = image; min_max_changed = true; }
+    if( value[source] == min || value[source] == max ) restore = true;
+    value[source] = image;
+    if( restore ) min_max_changed = restore() || min_max_changed;
+    return min_max_changed;
+  }
+
+  /**
+   * method returns the image value of the given source value
+   *
+   * @param source the source value
+   * @return the image value
+   */
+//  public double getImage(int source){
+//    if(source<0 || source>=size) throw
+//      new ArrayIndexOutOfBoundsException(source);
+//    return value[source];
+//  }
+    public double getImage(int source){
+    if(source<0) new ArrayIndexOutOfBoundsException(source);
+    if(source>=size && size > 1) return value[size-1];
+    return value[source];
+  }
+
+  /**
+   * the given image value becomes the image of (highest source value + 1)
+   *
+   * @param image the new image value
+   * @return <code>true<\code> when the minmal or the maximal image value
+   *          has been changed by this method call, else it returns
+   *          <code>false</code> @see #getMinImageValue(), #getMaxImageValue()
+   */
+  public boolean addImage(double image){
+    if( size >= value.length ){
+      int new_length = (int)(value.length * capacity_multiplier);
+      if( !(new_length > value.length) ) new_length++;
+      double[] new_val = new double[new_length];
+      System.arraycopy(value,0,new_val,0,value.length);
+      value = new_val;
+    }
+    boolean min_max_changed = false;
+    if( size == 0 ){ min = image; max = image; min_max_changed = true;}
+    else
+      if( image > max ) { max = image; min_max_changed = true; }
+      else if( image < min ) { min = image; min_max_changed = true; }
+    value[size++] = image;
+    return min_max_changed;
+  }
+
+  /**
+   * method returns the number of (source,image)-pairs stored in the array
+   *
+   * @return the size of the source value set
+   */
+  public int getSize(){
+    return size;
+  }
+
+  /**
+   * this method checks if the minimal and the maximal image value has changed
+   *
+   * @return <code>true</code> if one of them changed
+   */
+  public boolean restore(){
+    if( size == 0 ) return false;
+    double old_min = min, old_max = max;
+    min = value[0];
+    max = value[0];
+    for( int i=1; i<size; i++ )
+      if( value[i] < min ) min = value[i];
+      else if( value[i] > max ) max = value[i];
+    return (old_min != min) || (old_max != max);
+  }
+
+  /**
+   * throws all information away
+   */
+  public void reset(){
+    size = 0;
+    value = new double[initial_capacity];
+  }
+
+  /**
+   * returns the minmal image value
+   *
+   * @return the minmal image value
+   */
+  public double getMinImageValue(){
+    if( size == 0 ) throw
+      new IllegalArgumentException("DArray is empty. No minimal value exists");
+    return min;
+  }
+
+
+  /**
+   * returns the maxmal image value
+   *
+   * @return the maxmal image value
+   */
+  public double getMaxImageValue(){
+    if( size == 0 ) throw
+      new IllegalArgumentException("DArray is empty. No maximal value exists");
+    return max;
+  }
+
+  /**
+   * method checks if the given object is equal to this DArray object.
+   * It looks for differences in the stored image values
+   *
+   * @param o the object to compare with
+   * @return <code>true</code> when the object is an DArray object, containing
+   *          the same values
+   */
+  public boolean equals(Object o){
+    if( !(o instanceof DArray) ) return false;
+    DArray comp = (DArray)o;
+    if( comp.size != size ) return false;
+    if( comp.max != max ) return false;
+    if( comp.min != min ) return false;
+    for( int i=0; i<size; i++ )
+      if( comp.value[i] != value[i] ) return false;
+    return true;
+  }
+
+  public String toString(){
+    String text = "wsi.ra.chart2d.DArray[size:"+size;
+    if( size < 11 )
+      for( int i=0; i<size; i++ ) text += ", "+value[i];
+    text += "]";
+    return text;
+  }
+
+  public double[] toArray(double[] v){
+    if( v == null || v.length < size ) v = new double[size];
+    System.arraycopy(value,0,v,0,size);
+    return v;
+  }
+}

src/wsi/ra/chart2d/DBorder.java

@@ -0,0 +1,45 @@
+/**
+ *  Filename: $RCSfile: DBorder.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:41 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+package wsi.ra.chart2d;
+
+import java.awt.Insets;
+
+public class DBorder extends Insets{
+
+  public DBorder(){
+    this( 0, 0, 0, 0 );
+  }
+
+  public DBorder(int top, int left, int bottom, int right ){
+    super( top, left, bottom, right );
+  }
+
+  public boolean insert( DBorder b ){
+    boolean changed = false;
+    if( b.top    > top    ){ top    = b.top;    changed = true; }
+    if( b.bottom > bottom ){ bottom = b.bottom; changed = true; }
+    if( b.left   > left   ){ left   = b.left;   changed = true; }
+    if( b.right  > right  ){ right  = b.right;  changed = true; }
+    return changed;
+  }
+
+  public boolean equals( Object o ){
+    if( o instanceof DBorder )
+      return super.equals( o );
+    return false;
+  }
+
+  public String toString(){
+    return "wsi.ra.chart2d.DBorder[top="+top+",left="+left
+           +",bottom="+bottom+",right="+right+"]";
+  }
+}

src/wsi/ra/chart2d/DComponent.java

@@ -0,0 +1,159 @@
+/**
+ *  Filename: $RCSfile: DComponent.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:41 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.chart2d;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.awt.Color ;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+/**
+ * <code>DComponent</code> is the mother of all objects which can be displayed
+ * by a <code>DArea</code> object, even when it would be also enough to
+ * implement the <code>DElement</code> interface to an class
+ *
+ * DComponent is abstract because the paint method has to be overridden
+ */
+public abstract class DComponent implements DElement
+{
+  /**
+   * the color of the component
+   */
+  protected Color color;
+
+  /**
+   * the rectangle in which the component lies
+   */
+  protected DRectangle rectangle;
+
+  /**
+   * the parent of the component which is responsible for repainting
+   */
+  protected DParent parent;
+
+
+  private boolean visible = true;
+
+
+
+  /**
+   * this border respresents the additional space around the clip of the
+   * graphics context, which is calculated by the union of all DRectangles of
+   * the components. For example it is used by DPointIcons or DLabels.
+   */
+  private DBorder border = new DBorder();
+
+
+  /**
+   * this constructor is necessary to avoid infinite loops in constructing
+   * DRectangles
+   */
+  DComponent(boolean is_rect){}
+
+  public DComponent(){ rectangle = DRectangle.getEmpty(); }
+
+  /**
+   * returns the rectangle in which the object lies
+   */
+  public DRectangle getRectangle(){
+    return (DRectangle)rectangle.clone();
+  }
+
+
+  /**
+   * method sets a certain border around the contained rectangle
+   *
+   * @param b the new DBorder
+   */
+  public void setDBorder( DBorder b ){
+    if( parent != null ) {
+      if( border.insert(b) ) { parent.addDBorder( b ); repaint(); }
+      else { border = b; parent.restoreBorder(); }
+    }
+    else border = b;
+  }
+
+  /**
+   * method returns the current border around the rectangle
+   *
+   * @return the DBorder of the DComponent
+   */
+  public DBorder getDBorder(){
+    return border;
+  }
+
+  /**
+   * sets the parent of the component, which should take care of painting the
+   * component to the right time
+   */
+  public void setDParent( DParent parent ){
+    if( this.parent != null && this.parent != parent ){
+      this.parent.removeDElement( this );
+      this.parent.repaint( getRectangle() );
+    }
+    this.parent = parent;
+  }
+
+  /**
+   * returns the parent of the component
+   */
+  public DParent getDParent(){ return parent; }
+
+  /**
+   * invoces the parent to repaint the rectangle in which the component lies
+   */
+  public void repaint(){
+    //System.out.println("DComponent.repaint()");
+    if( parent != null ) parent.repaint( getRectangle() );
+  }
+
+  /**
+   * sets the color of the component
+   */
+  public void setColor( Color color ){
+    if( this.color == null || !this.color.equals( color ) ) {
+      this.color = color;
+      repaint();
+    }
+  }
+
+  /**
+   * returns the color of the component
+   */
+  public Color getColor(){ return color; }
+
+  /**
+   * sets the component visible or not
+   */
+  public void setVisible( boolean aFlag ){
+    boolean changed = ( aFlag != visible );
+    visible = aFlag;
+    if( changed ) repaint();
+  }
+
+  /**
+   * returns if the component should be visible when the parent shows the right
+   * area
+   */
+  public boolean isVisible(){ return visible; }
+
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/chart2d/DContainer.java

@@ -0,0 +1,223 @@
+/**
+ *  Filename: $RCSfile: DContainer.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:41 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.chart2d;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.util.Vector ;
+import java.awt.Color ;
+import java.awt.Graphics;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+public class DContainer extends DComponent implements DParent{
+  /**
+   * the elements of the container and their keys ( Strings )
+   */
+  protected Vector elements, keys;
+
+  public DContainer(){ this(10); }
+
+  public DContainer(int initial_capacity){
+    super();
+    elements = new Vector(initial_capacity);
+    keys = new Vector(initial_capacity);
+  }
+
+  public void repaint( DRectangle r ){
+    DParent parent = getDParent();
+    if( parent != null ) parent.repaint( r );
+  }
+
+  /**
+   * method adds a new DElement to the container
+   * if the container already contains this element, the method simply returns
+   * the method checks whether the DElement is an ancestor of the container
+   * itself. In that case it throws an IllegalArgumentException.
+   *
+   * @param e the new DElement to add
+   */
+  public void addDElement( DElement e ){
+    addDElement( null, e );
+  }
+
+
+  /**
+   * method adds a new DElement to the container by a certain key name
+   * if the container already contains this element, the method simply returns
+   * the method checks whether the DElement is an ancestor of the container
+   * itself. In that case it throws an IllegalArgumentException.
+   *
+   * @param key the name of the DElement in the container
+   * @param e   the new DElement to add
+   */
+  public void addDElement( String key, DElement e ){
+    if( elements.contains( e ) ) return;
+    if( e instanceof DParent ){
+      DParent he = (DParent)e, me = (DParent)this;
+      if( he == me ) throw new
+        IllegalArgumentException("Adding DParent to itself");
+      me = getDParent();
+      while( me != null ){
+        if( he == me )throw new
+          IllegalArgumentException("Adding DContainer's parent to itself");
+        if( me instanceof DElement )
+          me = ((DElement)me).getDParent();
+        else me = null;
+      }
+    }
+    elements.add( e );
+    addDBorder( e.getDBorder() );
+    keys.add( key );
+    e.setDParent( this );
+    DRectangle r = e.getRectangle();
+    rectangle.insert( r );
+    if( e.isVisible() ) repaint( r );
+  }
+
+  /**
+   * method removes a certain DElement from the container an returns whether it
+   * contained it before
+   *
+   * @param e the DElement to remove
+   * @return if this was possible
+   */
+  public boolean removeDElement( DElement e ){
+    int index = elements.indexOf( e );
+    if( index > -1 ){
+      elements.remove( index );
+      keys.remove( index );
+      repaint( e.getRectangle() );
+      restore();
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * method removes all DElements from the container
+   */
+  public void removeAllDElements()
+  {
+    elements.removeAllElements();
+    keys.removeAllElements();
+    rectangle = DRectangle.getEmpty();
+    repaint();
+  }
+
+  /**
+   * method returns all DElements of the container
+   *
+   * @return the elements of the container
+   */
+  public DElement[] getDElements(){
+    DElement[] es = new DElement[ elements.size() ];
+    elements.toArray(es);
+    return es;
+  }
+
+  /**
+   * method returns the first DElement of the contaioner belonging to
+   * the given key
+   *
+   * @param key the name of the DElement in the container
+   * @return the element when it could be found or null else
+   */
+  public DElement getDElement( String key ){
+    int index = -1;
+    for( int i=0; index == -1 && i < keys.size(); i++ )
+      if( ((String)keys.get(i)).equals( key ) ) index = i;
+    return (index<keys.size())? (DElement)elements.get(index):(DElement)null;
+  }
+
+// implementing DComponent:
+  /**
+   * method calls all currently visible DElements of the container to paint
+   * themselves by the given DMeasures object
+   *
+   * @param m the DMeasures object
+   */
+  public void paint( DMeasures m ){
+    DElement e;
+    for( int i=0; i<elements.size(); i++ ){
+      e = (DElement)elements.elementAt(i);
+      if( e.isVisible() && !m.getDRectangle().getIntersection( e.getRectangle() ).isEmpty()){
+        m.g.setColor( DEFAULT_COLOR );
+        e.paint( m );
+      }
+    }
+  }
+  /**
+   * method returns true, if the given element is contained in the container
+   *
+   * @param e the element
+   * @return if it is contained
+   */
+  public boolean contains( DElement e ){
+    return elements.contains( e );
+  }
+
+  /**
+   * method sets the given color to all contained DElements of the container
+   *
+   * @param c the new Color of the elements
+   */
+  public void setColor(Color c){
+    for( int i=0; i<elements.size(); i++ )
+      ((DElement)elements.get(i)).setColor(c);
+    super.setColor(c);
+  }
+
+  /**
+   * method adds the given border to the current border of the container
+   * that means, that if necessary it will enlarge it and tells it to its
+   * parent
+   *
+   * @param b the border to add
+   */
+  public void addDBorder(DBorder b){
+    if( getDBorder().insert(b) && parent != null ) parent.addDBorder(b);
+  }
+
+  public void restoreBorder(){
+    DBorder b = new DBorder();
+    for( int i=0; i<elements.size(); i++ )
+      b.insert( ((DElement)elements.get(i)).getDBorder() );
+    setDBorder( b );
+  }
+
+
+  /**
+   * restores the container, that means that the rectangle is completely new calculated
+   * this method is used after removing one of the elements
+   */
+  boolean restore(){
+    DRectangle old = (DRectangle)rectangle.clone();
+    rectangle = DRectangle.getEmpty();
+    setDBorder( new DBorder() );
+    for( int i=0; i<elements.size(); i++ ){
+      DElement elt = (DElement)elements.elementAt(i);
+      rectangle.insert(elt.getRectangle());
+      addDBorder( elt.getDBorder() );
+    }
+    return !old.equals( rectangle );
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/chart2d/DElement.java

@@ -0,0 +1,51 @@
+/**
+ *  Filename: $RCSfile: DElement.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:41 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.chart2d;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.awt.Color ;
+
+/*==========================================================================*
+ * INTERFACE DECLARATION
+ *==========================================================================*/
+
+/**
+ * some useful methods for objects which should be paintable in a scaled area
+ */
+public interface DElement
+{
+  Color DEFAULT_COLOR = Color.black;
+  DRectangle getRectangle();
+
+  void setDParent( DParent parent );
+  DParent getDParent();
+
+  void paint( DMeasures m );
+  void repaint();
+
+  void setVisible( boolean aFlag );
+  boolean isVisible();
+
+  void setColor( Color color );
+  Color getColor();
+
+  void setDBorder( DBorder b );
+  DBorder getDBorder();
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/chart2d/DFunction.java

@@ -0,0 +1,63 @@
+/**
+ *  Filename: $RCSfile: DFunction.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:41 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.chart2d;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.awt.Point ;
+import java.awt.Color ;
+import java.awt.Graphics ;
+
+/*==========================================================================*
+ * ABSTRACT CLASS DECLARATION
+ *==========================================================================*/
+
+public abstract class DFunction extends DComponent
+{
+  public DFunction(){
+    rectangle = DRectangle.getAll();
+  }
+
+  public abstract boolean isDefinedAt( double source );
+  public abstract boolean isInvertibleAt( double image );
+  public abstract double getSourceOf( double image ) throws IllegalArgumentException;
+  public abstract double getImageOf( double source ) throws IllegalArgumentException;
+
+  public void paint( DMeasures m ){
+    Graphics g = m.getGraphics();
+    if( color != null ) g.setColor( color );
+
+    DRectangle rect = m.getDRectangle(),
+               src_rect = m.getSourceOf( rect );
+    Point sw = m.getPoint( rect.x, rect.y ),
+          ne = m.getPoint( rect.x + rect.width, rect.y + rect.height );
+    int int_w = ne.x - sw.x;
+    Point last = null, next;
+    for( int i = 0; i < int_w; i++ ){
+      double x_val = src_rect.x + i / (double)int_w * src_rect.width ;
+      if( m.x_scale != null ) x_val = m.x_scale.getImageOf( x_val );
+      if( isDefinedAt( x_val ) ){
+        next = m.getPoint( x_val, getImageOf( x_val ) );
+        if( last != null ) g.drawLine( last.x, last.y, next.x, next.y );
+        last = next;
+      }
+      else last = null;
+    }
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/chart2d/DGrid.java

@@ -0,0 +1,115 @@
+/**
+ *  Filename: $RCSfile: DGrid.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:41 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.chart2d;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.awt.Color ;
+import java.awt.Graphics ;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+/**
+ * this class paints a grid with certain line distances on a DParent
+ */
+public class DGrid extends DComponent
+{
+  /**
+   * the distances between the lines
+   */
+  double hor_dist, ver_dist;
+
+  private Color DEFAULT_COLOR = Color.lightGray;
+
+  /**
+   * constructor with the size and position of the grid and the line distances
+   *
+   * @param rectangle the rectangle around the grid
+   * @param hor_dist the horizontal distance between the lines in D-coordinates,
+   *        not in pixel coordinates!
+   * @param ver_dist vertical distance between the lines in D-coordinates,
+   *        not in pixel coordinates!
+   */
+  public DGrid( DRectangle rectangle, double hor_dist, double ver_dist ){
+    this.rectangle = rectangle;
+    this.hor_dist = hor_dist;
+    this.ver_dist = ver_dist;
+    color = DEFAULT_COLOR;
+  }
+
+  /**
+   * constructor with the size and position of the grid and the line distances
+   *
+   * @param rectangle the rectangle around the grid
+   * @param hor_dist the horizontal distance between the lines in D-coordinates,
+   *        not in pixel coordinates!
+   * @param ver_dist the vertical distance between the lines in D-coordinates,
+   *        not in pixel coordinates!
+   * @param color the color of the grid
+   *        ( can also be set by setColor( java.awt.Color ) )
+   */
+  public DGrid( DRectangle rectangle, double hor_dist, double ver_dist, Color color ){
+    this.rectangle = rectangle;
+    this.hor_dist = hor_dist;
+    this.ver_dist = ver_dist;
+    this.color = color;
+  }
+
+  /**
+   * paints the grid...
+   *
+   * @param m the <code>DMeasures</code> object to paint the grid
+   */
+  public void paint( DMeasures m ){
+    Graphics g = m.getGraphics();
+    if( color != null ) g.setColor( color );
+    double minX, minY, pos;
+    DPoint p1, p2;
+    DLine l;
+
+    minX = (int)( rectangle.x / hor_dist );
+    if( minX * hor_dist <= rectangle.x ) minX++;
+    minX *= hor_dist;
+    minY = (int)( rectangle.y / ver_dist );
+    if( minY * ver_dist <= rectangle.y ) minY++;
+    minY *= ver_dist;
+
+    p1 = new DPoint( 0, rectangle.y );
+    p2 = new DPoint( 0, rectangle.y + rectangle.height );
+    for( pos = minX; pos<=rectangle.x + rectangle.width; pos += hor_dist ){
+      p1.x = p2.x = pos;
+      l = new DLine( p1, p2, color );
+      l.paint( m );
+    }
+
+    p1.x = rectangle.x;
+    p2.x = p1.x + rectangle.width;
+    for( pos = minY; pos<=rectangle.y + rectangle.height; pos += ver_dist ){
+      p1.y = p2.y = pos;
+      l = new DLine( p1, p2, color );
+      l.paint( m );
+    }
+  }
+
+  public String toString(){
+    return "chart2d.DGrid[ hor: "+hor_dist+", ver: "+ver_dist+" ]";
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/chart2d/DIntDoubleMap.java

@@ -0,0 +1,88 @@
+package wsi.ra.chart2d;
+
+/**
+ * Title:
+ * Description:
+ * Copyright:    Copyright (c) 2001
+ * Company:
+ * @author
+ * @version 1.0
+ */
+
+/**
+ * This interface is used by DPointSet to store values as images of integer
+ * values which can be displayed in a DArea. All modifications of the values can
+ * only be shown by the DArea, when the DPointSet.repaint method is
+ * called. This should be done in the implementation of the #setImage and
+ * #addImage method. To get the functionality of the DArea, the methods
+ * #getMaxImageValue and #getMinImageValue are necessary.
+ */
+public interface DIntDoubleMap {
+
+  /**
+   * implementation should change the map in that way, that from now the
+   * image of index is v
+   *
+   * @param source the preimage of the image
+   * @param image  the new image of the source value
+   * @return <code>true<\code> when the minmal or the maximal image value
+   *          has been changed by this method call, else it returns
+   *          <code>false</code> @see #getMinImageValue(), #getMaxImageValue()
+   */
+  boolean setImage(int source, double image);
+
+  /**
+   * implementation should return the image of source
+   *
+   * @param source the preimage
+   * @return the image value
+   */
+  double getImage(int source);
+
+  /**
+   * the image of the highest source value + 1 should be the given image value
+   *
+   * @param image the new image value
+   * @return <code>true<\code> when the minmal or the maximal image value
+   *          has been changed by this method call, else it returns
+   *          <code>false</code> @see #getMinImageValue(), #getMaxImageValue()
+   */
+  boolean addImage(double image);
+
+  /**
+   * implementation should return the number of source values
+   *
+   * @return the number of source values
+   */
+  int getSize();
+
+  /**
+   * returns the maximal image value
+   *
+   * @return the maximal image value
+   * @throw an IllegalArgumentException when it has no image values
+   */
+  double getMaxImageValue();
+
+  /**
+   * returns the minimal image value
+   *
+   * @return the minmal image value
+   * @throw an IllegalArgumentException when it has no image values
+   */
+  double getMinImageValue();
+
+  /**
+   * checks the minimal and the maximal image values and returns <code>true</code>
+   * when at least one of them has changed
+   *
+   * @return <code>true</code> when either the maximal image value or the
+   *         minmal image value has changed
+   */
+  boolean restore();
+
+  /**
+   * method removes all image values and sets the size to 0
+   */
+  void reset();
+}

src/wsi/ra/chart2d/DLine.java

@@ -0,0 +1,70 @@
+/**
+ *  Filename: $RCSfile: DLine.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:41 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.chart2d;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.awt.* ;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+public class DLine extends DComponent
+{
+  DPoint start, end;
+
+  public DLine( double x1, double y1, double x2, double y2 ){
+    this( new DPoint( x1, y1 ), new DPoint( x2, y2 ) );
+  }
+
+  public DLine( DPoint start, DPoint end ){
+    this.start = start;
+    this.end = end;
+  }
+  public DLine( double x1, double y1, double x2, double y2, Color color ){
+    this( new DPoint( x1, y1 ), new DPoint( x2, y2 ), color );
+  }
+
+  public DLine( DPoint start, DPoint end, Color color ){
+    this.start = start;
+    this.end = end;
+    this.color = color;
+  }
+
+  public DRectangle getRectangle(){
+    double x = start.x, y = start.y, width = end.x - x, height = end.y - y;
+    if( width < 0 ) { x += width; width *= -1; }
+    if( height < 0 ) { y += height; height *= -1; }
+    return new DRectangle( x, y, width, height );
+  }
+
+  public void paint( DMeasures m ){
+    //System.out.println("DLine.paint(Measures): "+this);
+    Graphics g = m.getGraphics();
+    if( color != null ) g.setColor( color );
+    Point p1 = m.getPoint( start ),
+          p2 = m.getPoint( end ) ;
+    g.drawLine( p1.x, p1.y, p2.x, p2.y );
+  }
+
+  public String toString(){
+    return "DLine[("+start.x+","+start.y+") --> ("+end.x+","+end.y+", color: "+color+"]";
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/chart2d/DMeasures.java

@@ -0,0 +1,274 @@
+/**
+ *  Filename: $RCSfile: DMeasures.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:41 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.chart2d;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.awt.Point ;
+import java.awt.Graphics ;
+import java.awt.Dimension ;
+import java.awt.Insets ;
+
+import java.awt.Component ;
+//import javax.swing.JComponent ;
+import java.io.Serializable;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+public class DMeasures implements Serializable
+{
+  /**
+	 * 
+	 */
+	private static final long serialVersionUID = 243092480517044848L;
+private boolean under_construction = false;
+  // when in use for a DArea:
+  Graphics g;
+  // when in use for a ScaledBorder:
+  ScaledBorder sb;
+  // for both:
+  DFunction x_scale, y_scale;
+  Component comp;
+  Insets insets;
+
+  /**
+   * package private constructor for the DMeasures object
+   * the object can be obtained by calling the method getDMeasures of an DArea
+   * object
+   *
+   * @param area the DArea object
+   */
+  DMeasures( DArea area ){
+    comp = area;
+  }
+
+  DMeasures( ScaledBorder sb ){
+    this.sb = sb;
+  }
+
+  /**
+   * method returns the pixel-point which belongs to the DPoint in the
+   * D-coordinates
+   * it says where to paint a certain DPoint
+   * returns <code>null</code> if the double coordinates do not belong to the
+   * image of the scale functions
+   *
+   * @param p the DPoint
+   * @return the coresponding pixel Point
+   */
+  public Point getPoint( DPoint p ){
+    //System.out.println("DMeasures.getPoint :"+org );
+    return getPoint( p.x, p.y );
+  }
+
+  /**
+   * method returns the pixel-point which belongs to the given D-coordinates
+   * it says where to paint a certain DPoint
+   * returns <code>null</code> if the double coordinates do not belong to the
+   * image of the scale functions
+   *
+   * @param x the double x D-coordinate
+   * @param y the double y D-coordinate
+   * @return the coresponding pixel Point
+   */
+  public Point getPoint( double x, double y ){
+    DRectangle rect = getSourceOf( getDRectangle() );
+    try{
+      if( x_scale != null ) x = x_scale.getSourceOf( x );
+      if( y_scale != null ) y = y_scale.getSourceOf( y );
+    }
+    catch( IllegalArgumentException e ){ return null; }
+    Point dp = new Point();
+    Dimension dim = getInner();
+    Insets insets = getInsets();
+    dp.x = (int)( dim.width * (x - rect.x)/(double)rect.width ) + insets.left;
+    dp.y = (int)( dim.height * (1 - (y - rect.y)/(double)rect.height)) + insets.top;
+    return dp;
+  }
+
+  /**
+   * method returns the point in D-coordinates which corresponds to the
+   * given pixel-point
+   * returns <code>null</code> if the given coordinates can not be calculated to
+   * the double coordinates, when they represent a point outside of the definition
+   * area of the scale functions
+   *
+   * @param p Point in pixel coordinates
+   * @return the coresponding DPoint
+   */
+  public DPoint getDPoint( Point p ){
+    return getDPoint( p.x, p.y );
+  }
+
+  /**
+   * method returns the point in D-coordinates which corresponds to the
+   * given pixel-coordinates
+   * returns <code>null</code> if the given coordinates can not be calculated to
+   * the double coordinates, when they represent a point outside of the definition
+   * area of the scale functions
+   *
+   * @param x x-pixel coordinate
+   * @param y y-pixel coordinate
+   * @return the coresponding DPoint
+   */
+  public DPoint getDPoint( int x, int y ){
+    DRectangle rect = getSourceOf( getDRectangle() );
+    Dimension dim = getInner();
+    Insets insets = getInsets();
+    x -= insets.left;
+    y -= insets.top;
+    double dx, dy;
+    dx = rect.x + rect.width * x/(double)dim.width;
+    dy = rect.y + rect.height * (1 - y/(double)dim.height );
+    try{
+      if( x_scale != null ) dx = x_scale.getImageOf( dx );
+      if( y_scale != null ) dy = y_scale.getImageOf( dy );
+    }
+    catch( IllegalArgumentException nde ){ return null; }
+    return new DPoint( dx, dy );
+  }
+
+  /**
+   * returns the visible rectangle in D-coordinates of the shown component
+   *
+   * return the visible rectangle
+   */
+  public DRectangle getDRectangle(){
+    if( under_construction ) System.out.println("DMeasures.getDRectangle");
+    if( sb != null ) return getImageOf( sb.src_rect );
+    return ((DArea)comp).getDRectangle();
+  }
+
+  /**
+   * returns the current Graphics object, which might be used by components to
+   * paint themselves
+   * the method sets the clipping area of the Graphics object to the currently
+   * visible rectangle
+   *
+   * @return the Graphics object ( or null if no object was set )
+   */
+  public Graphics getGraphics(){
+    if( under_construction ) System.out.println("DMeasures.getGraphics");
+    if( g != null ){
+      Dimension d = comp.getSize();
+      Insets insets = getInsets();
+      g.setClip( insets.left + 1, // dann sieht man noch was von der linken Achse
+                 insets.top,
+                 d.width - insets.left - insets.right,
+                 d.height - insets.top - insets.bottom);
+    }
+    return g;
+  }
+
+  /**
+   * used by DArea to set a new Graphics object
+   */
+  void setGraphics( Graphics g ){
+    if( under_construction ) System.out.println("DMeasures.setGraphics");
+    this.g = g;
+  }
+
+  /**
+   * used by ScaledBorder to update the DMeasures object
+   *
+   * @param c the parent component the border
+   */
+  void update( Component c, Insets insets ){
+    this.comp = c;
+    this.insets = insets;
+    x_scale = sb.x_scale;
+    y_scale = sb.y_scale;
+  }
+
+  private Dimension getInner(){
+    Dimension d = comp.getSize();
+    Insets insets = getInsets();
+    d.width -= insets.left + insets.right;
+    d.height -= insets.top + insets.bottom;
+    return d;
+  }
+
+
+  /**
+   * method returns the source rectangle of the given rectangle
+   * they differ if there are scale functions selected which are not the identity
+   * if the given rectangle does not belong to the image area of the scale
+   * functions, the method returns <code>null</code>
+   *
+   * @param rect the image rectangle
+   * @return the source of it
+   */
+  DRectangle getSourceOf( DRectangle rect ){
+    if( under_construction ) System.out.println("DMeasures.getSourceOf: "+rect);
+    if( !getDRectangle().contains( rect ) ) throw
+      new IllegalArgumentException("The rectangle lies not in the currently painted rectangle");
+    if( x_scale == null && y_scale == null ) return rect;
+    if( rect.isEmpty() ) return (DRectangle)rect.clone();
+    DPoint p1 = new DPoint( rect.x, rect.y ),
+           p2 = new DPoint( rect.x + rect.width, rect.y + rect.height );
+    try{
+      if( x_scale != null ){
+        p1.x = x_scale.getSourceOf( p1.x );
+        p2.x = x_scale.getSourceOf( p2.x );
+      }
+      if( y_scale != null ){
+        p1.y = y_scale.getSourceOf( p1.y );
+        p2.y = y_scale.getSourceOf( p2.y );
+      }
+    }
+    catch( IllegalArgumentException nde ){ return null; }
+    return new DRectangle( p1.x, p1.y, p2.x - p1.x, p2.y - p1.y );
+  }
+
+  /**
+   * method returns the image rectangle of the given rectangle
+   * they differ if there are scale functions selected which are not the identity
+   * if the given rectangle does not belong to the defintion area of the scale
+   * functions, the method returns <code>null</code>
+   *
+   * @param rect the source rectangle
+   * @return the source of it
+   */
+  DRectangle getImageOf( DRectangle rect ){
+    if( under_construction ) System.out.println("DMeasures.getImageOf: "+rect);
+    if( x_scale == null && y_scale == null ) return rect;
+    if( rect.isEmpty() ) return (DRectangle)rect.clone();
+    DPoint p1 = new DPoint( rect.x, rect.y ),
+           p2 = new DPoint( rect.x + rect.width, rect.y + rect.height );
+    try{
+      if( x_scale != null ){
+        p1.x = x_scale.getImageOf( p1.x );
+        p2.x = x_scale.getImageOf( p2.x );
+      }
+      if( y_scale != null ){
+        p1.y = y_scale.getImageOf( p1.y );
+        p2.y = y_scale.getImageOf( p2.y );
+      }
+    }
+    catch( IllegalArgumentException nde ){ return null; }
+    return new DRectangle( p1.x, p1.y, p2.x - p1.x, p2.y - p1.y );
+  }
+
+  private Insets getInsets(){
+    if( sb != null ) return insets;
+    return ((DArea)comp).getInsets();
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/chart2d/DParent.java

@@ -0,0 +1,34 @@
+/**
+ *  Filename: $RCSfile: DParent.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:41 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.chart2d;
+
+import java.awt.Graphics;
+
+/*==========================================================================*
+ * INTERFACE DECLARATION
+ *==========================================================================*/
+
+public interface DParent
+{
+  void addDElement( DElement e );
+  boolean removeDElement( DElement e );
+  void repaint( DRectangle r );
+  DElement[] getDElements();
+  boolean contains( DElement e );
+  void addDBorder( DBorder b );
+  void restoreBorder();
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/chart2d/DPoint.java

@@ -0,0 +1,99 @@
+/**
+ *  Filename: $RCSfile: DPoint.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:42 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.chart2d;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.awt.* ;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+public class DPoint extends DComponent
+{
+  public double x, y;
+  public String label;
+  protected DPointIcon icon = null;
+  public DPoint( ){
+  }
+  public void initpoint( double x, double y ){
+    this.x = x;
+    this.y = y;
+    rectangle = new DRectangle( x, y, 0, 0 );
+  }
+  public DPoint( double x, double y ){
+    this.x = x;
+    this.y = y;
+    rectangle = new DRectangle( x, y, 0, 0 );
+  }
+
+  public void paint( DMeasures m ){
+    Graphics g = m.getGraphics();
+    if( color != null ) g.setColor( color );
+    Point dp = m.getPoint( this );
+    if( label != null ){
+      FontMetrics fm = g.getFontMetrics();
+      g.drawString( label,
+                    dp.x - fm.stringWidth( label ) / 2,
+                    dp.y + fm.getAscent()
+      );
+    }
+    if( icon == null )
+      g.drawRect( dp.x, dp.y, 1, 1 );
+    else{
+      g.translate( dp.x, dp.y );
+      icon.paint( g );
+      g.translate( -dp.x, -dp.y );
+    }
+  }
+
+  /**
+   * method sets an icon for a better displaying of the point
+   *
+   * @param icon the DPointIcon
+   */
+  public void setIcon( DPointIcon icon ){
+    this.icon = icon;
+    if( icon == null ) setDBorder(new DBorder(1,1,1,1));
+    else setDBorder( icon.getDBorder() );
+  }
+
+  /**
+   * method returns the current icon of the point
+   *
+   * @return the DPointIcon
+   */
+  public DPointIcon getIcon(){
+    return icon;
+  }
+
+  public Object clone(){
+    DPoint copy = new DPoint( x, y );
+    copy.color = color;
+    return copy;
+  }
+
+  public String toString(){
+    String text = "DPoint[";
+    if( label != null ) text += label+", ";
+    text += "x: "+x+", y: "+y+", color: "+color+"]";
+    return text;
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/chart2d/DPointIcon.java

@@ -0,0 +1,38 @@
+package wsi.ra.chart2d;
+
+/**
+ *  Filename: $RCSfile: DPointIcon.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+import java.awt.Graphics;
+/**
+ * A simple interface which can be used to paint certain icons at DPoints
+ * ( @see chart2d.DPoint.setIcon or chart2d.DPointSet.setIcon ).
+ * Different points may be easier recognized in a complex graph.
+ * The container does not guarantee that the whole icon is visible in the graph
+ * because the icon does not concern the DRectangle of the DElement.
+ */
+
+public interface DPointIcon {
+
+  /**
+   * this method has to be overridden to paint the icon. The point itself lies
+   * at coordinates (0, 0)
+   */
+  void paint( Graphics g );
+
+  /**
+   * the border which is necessary to be paint around the DPoint that the whole
+   * icon is visible
+   *
+   * @return the border
+   */
+  DBorder getDBorder();
+}
+

src/wsi/ra/chart2d/DPointSet.java

@@ -0,0 +1,350 @@
+/**
+ *  Filename: $RCSfile: DPointSet.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:42 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.chart2d;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.awt.* ;
+import wsi.ra.tool.IntegerArrayList;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+public class DPointSet extends DComponent
+{
+  protected DPointIcon icon = null;
+
+  /*-------------------------------------------------------------------------*
+   * private member variables
+   *-------------------------------------------------------------------------*/
+
+  protected DIntDoubleMap x, y;
+  protected boolean connected;
+  protected Stroke stroke = new BasicStroke();
+  protected JumpManager jumper = new JumpManager();
+
+  /*-------------------------------------------------------------------------*
+   * constructor
+   *-------------------------------------------------------------------------*/
+  public DPointSet(){
+    this(10, 2);
+  }
+
+
+  public DPointSet( int initial_capacity ){
+    this(initial_capacity, 2);
+  }
+
+  public DPointSet( int initial_capacity, int length_multiplier ){
+    this( new DArray(initial_capacity, length_multiplier),
+          new DArray(initial_capacity, length_multiplier) );
+  }
+
+  public DPointSet(DIntDoubleMap x_values, DIntDoubleMap y_values){
+    if( x_values.getSize() != y_values.getSize() ) throw
+      new IllegalArgumentException(
+        "The number of x-values has to be the same than the number of y-values"
+      );
+    x = x_values;
+    y = y_values;
+    restore();
+    setDBorder(new DBorder(1,1,1,1));
+  }
+
+  /*-------------------------------------------------------------------------*
+   * public methods
+   *-------------------------------------------------------------------------*/
+
+  public void paint( DMeasures m ){
+    Graphics2D g = (Graphics2D)m.getGraphics();
+    g.setStroke(stroke);
+    if( color != null ) g.setColor( color );
+    int size = getSize();
+    if( connected && size > 1 ){
+      jumper.restore();
+      while( jumper.hasMoreIntervals() ){
+        int[] interval = jumper.nextInterval();
+        Point p1 = null, p2;
+        for( int i=interval[0]; i<interval[1]; i++ ){
+          p2 = m.getPoint( x.getImage(i), y.getImage(i) );
+          if( p1 != null)
+            g.drawLine( p1.x, p1.y, p2.x, p2.y );
+          if( icon != null ){
+            g.setStroke( new BasicStroke() );
+            g.translate(p2.x, p2.y);
+            icon.paint(g);
+            g.translate(-p2.x, -p2.y);
+            g.setStroke( stroke );
+          }
+          p1 = p2;
+        }
+      }
+    }
+    else{
+      Point p;
+      for( int i=0; i<size; i++ ){
+        p = m.getPoint( x.getImage(i), y.getImage(i) );
+        if( icon == null ){
+          g.drawLine(p.x - 1, p.y - 1, p.x + 1, p.y + 1);
+          g.drawLine(p.x + 1, p.y - 1, p.x - 1, p.y + 1);
+        }
+        else{
+          g.setStroke( new BasicStroke() );
+          g.translate(p.x, p.y);
+          icon.paint(g);
+          g.translate(-p.x, -p.y);
+        }
+      }
+    }
+    g.setStroke( new BasicStroke() );
+  }
+
+  public void addDPoint( DPoint p ){
+    x.addImage(p.x);
+    y.addImage(p.y);
+    rectangle.insert(p);
+    repaint();
+  }
+
+  public void addDPoint( double x, double y ){
+    addDPoint(new DPoint(x, y));
+  }
+
+  /**
+   * method causes the DPointSet to interupt the connected painting at the
+   * current position
+   */
+  public void jump(){
+    jumper.addJump();
+  }
+
+  /**
+   * method removes all jump positions
+   * if the DPointSet is connected, all points will be painted connected to
+   * their following point
+   */
+  public void removeJumps(){
+    jumper.reset();
+  }
+
+  /**
+   * method returns the DPoint at the given index
+   *
+   * @param index the index of the DPoint
+   * @return the DPoint at the given index
+   */
+  public DPoint getDPoint( int index ){
+    if( index >= x.getSize() ) {
+      System.out.println("getDPoint() index"+index);
+       System.out.println("x.getSize() "+x.getSize());
+      throw new ArrayIndexOutOfBoundsException(index);
+    }
+    DPoint p = new DPoint( x.getImage( index ), y.getImage( index ) );
+    p.setIcon( icon );
+    p.setColor( color );
+    return p;
+  }
+
+  /**
+   * method puts the given DPoint at the given position in the set
+   *
+   * @param index the index of the point
+   * @param p     the point to insert
+   */
+  public void setDPoint( int index, DPoint p ){
+    if( index >= x.getSize() ) throw new ArrayIndexOutOfBoundsException(index);
+    rectangle.insert(p);
+    x.setImage(index,p.x);
+    y.setImage(index,p.y);
+    restore();
+    repaint();
+  }
+
+  /**
+   * method sets an icon for a better displaying of the point set
+   *
+   * @param icon the DPointIcon
+   */
+  public void setIcon( DPointIcon icon ){
+    this.icon = icon;
+    if( icon == null ) setDBorder(new DBorder(1,1,1,1));
+    else setDBorder( icon.getDBorder() );
+  }
+
+  /**
+   * method returns the current icon of the point set
+   *
+   * @return the DPointIcon
+   */
+  public DPointIcon getIcon(){
+    return icon;
+  }
+
+  /**
+   *  method sets the stroke of the line
+   *  if the points were not connected, they now will be connected
+   *
+   * @param s the new stroke
+   */
+  public void setStroke( Stroke s ){
+    if( s == null ) s = new BasicStroke();
+    stroke = s;
+    repaint();
+  }
+
+  /**
+   * method returns the current stroke of the line
+   *
+   * @return the stroke
+   */
+  public Stroke getStroke(){
+    return stroke;
+  }
+
+  public void setConnected( boolean aFlag ){
+    boolean changed = !( aFlag == connected );
+    connected = aFlag;
+    if( changed ) repaint();
+  }
+
+  public void removeAllPoints(){
+    if( x.getSize() == 0 ) return;
+    x.reset();
+    y.reset();
+    jumper.reset();
+    repaint();
+    rectangle = DRectangle.getEmpty();
+  }
+
+  public String toString(){
+    String text = "wsi.ra.chart2d.DPointSet[size:"+getSize();
+    for( int i=0; i<x.getSize(); i++ )
+      text += ",("+x.getImage(i)+","+y.getImage(i)+")";
+    text += "]";
+    return text;
+  }
+
+  /**
+   * method returns the index to the nearest <code>DPoint</code> in this <code>DPointSet</code>.
+   *
+   * @return the index to the nearest <code>DPoint</code>. -1 if no nearest <code>DPoint</code> was found.
+   */
+  public int getNearestDPointIndex(DPoint point){
+    double minValue = Double.MAX_VALUE;
+    int    minIndex = -1;
+    for( int i=0; i<x.getSize(); i++ ){
+      double dx = point.x - x.getImage(i);
+      double dy = point.y - y.getImage(i);
+      double dummy = dx*dx + dy*dy;
+      if (dummy < minValue){
+        minValue = dummy;
+        minIndex = i;
+      }
+    }
+    return minIndex;
+  }
+
+  /**
+   * method returns the nearest <code>DPoint</code> in this <code>DPointSet</code>.
+   *
+   * @return the nearest <code>DPoint</code>
+   */
+  public DPoint getNearestDPoint(DPoint point){
+    int    minIndex = getNearestDPointIndex(point);
+
+    if(minIndex == -1) return null;
+    else return new DPoint(x.getImage(minIndex), y.getImage(minIndex));
+  }
+
+//  public int getSize(){
+//    int size = x.getSize();
+//    if( size != y.getSize() ) throw
+//      new ArrayStoreException(
+//        "The number of x-values is not equal to the number of y-values.\n"
+//        +"The size of the DPointSet isn<73>t clear."
+//      );
+//    return size;
+//  }
+  /**
+   *
+   */
+  public int getSize(){  // testhu
+    int size = x.getSize();
+    if( size <= y.getSize() )
+      return size;
+    return x.getSize();
+  }
+
+
+  protected void restore(){
+    if( getSize() == 0){
+      rectangle = DRectangle.getEmpty();
+      return;
+    }
+    double min_x = x.getMinImageValue(),
+           max_x = x.getMaxImageValue(),
+           min_y = y.getMinImageValue(),
+           max_y = y.getMaxImageValue();
+    rectangle = new DRectangle(min_x, min_y, max_x - min_x, max_y - min_y );
+  }
+
+  /**
+   * this class stores the jump positions (see this.jump)
+   */
+  class JumpManager{
+    protected IntegerArrayList jumps = new IntegerArrayList();
+    protected int index = -1;
+
+    public void addJump(){
+      jumps.add(getSize());
+    }
+
+    public int[] nextInterval(){
+      int no_jumps = jumps.size();
+      if( index >= no_jumps ) throw
+        new ArrayIndexOutOfBoundsException("No more intervals in JumpManager");
+
+      int[] inter = new int[2];
+
+      if( index == -1 ) inter[0] = 0;
+      else inter[0] = jumps.get(index);
+
+      index++;
+
+      if( index < no_jumps ) inter[1] = jumps.get(index);
+      else inter[1] = getSize();
+
+      return inter;
+    }
+
+    public boolean hasMoreIntervals(){
+      return index < jumps.size();
+    }
+
+    public void restore(){
+      index = -1;
+    }
+
+    public void reset(){
+      index = -1;
+      jumps.clear();
+    }
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/chart2d/DRectangle.java

@@ -0,0 +1,207 @@
+/**
+ *  Filename: $RCSfile: DRectangle.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:42 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.chart2d;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.awt.* ;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+public class DRectangle extends DComponent
+{
+  public double x, y, width, height;
+  public static final int PART = 0, ALL = 1, EMPTY = 2;
+  protected int status;
+  protected Color fillColor;
+
+  private DRectangle( int status ){
+    super(true);
+    this.status = status;
+  }
+
+  public DRectangle( double x, double y, double width, double height ){
+    super(true);
+    this.x = x;
+    this.y = y;
+    if( width < 0 ) throw
+      new IllegalArgumentException("Width of a DRectangle has to be >= 0");
+    this.width = width;
+    if( height < 0 ) throw
+      new IllegalArgumentException("Height of a DRectangle has to be >= 0");
+    this.height = height;
+    status = PART;
+  }
+
+  public DRectangle getRectangle(){ return this; }
+
+  public void paint( DMeasures m ){
+    if( isEmpty() ) return;
+    Graphics g = m.getGraphics();
+    Color old_color = g.getColor();
+    DRectangle rect = m.getDRectangle();
+    rect = rect.getIntersection( this );
+    Point p1 = m.getPoint( rect.x, rect.y ),
+          p2 = m.getPoint( rect.x + rect.width, rect.y + rect.height );
+    if( fillColor != null ){
+      g.setColor( fillColor );
+      g.fillRect( p1.x, p2.y, p2.x - p1.x, p1.y - p2.y );
+    }
+    if( !isAll() ){
+      if( color != null ) g.setColor( color );
+      else g.setColor( DEFAULT_COLOR );
+      g.drawRect( p1.x, p2.y, p2.x - p1.x, p1.y - p2.y );
+    }
+    g.setColor( old_color );
+  }
+
+  public boolean contains( DPoint p ){
+    if( status == ALL ) return true;
+    if( status == EMPTY ) return false;
+    if( p.x < x ) return false;
+    if( p.y < y ) return false;
+    if( p.x > x + width ) return false;
+    if( p.y > y + height ) return false;
+    return true;
+  }
+
+  public boolean contains( DRectangle rect ){
+    if( status == ALL || rect.isEmpty() ) return true;
+    if( status == EMPTY || rect.isAll() ) return false;
+    if( !contains( new DPoint( rect.x, rect.y ) ) ) return false;
+    if( !contains( new DPoint( rect.x + rect.width, rect.y + rect.height ) ) ) return false;
+    return true;
+  }
+
+  public DRectangle getIntersection( DRectangle r ){
+    if( status == ALL ) return (DRectangle)r.clone();
+    if( status == EMPTY ) return DRectangle.getEmpty();
+    if( r.status == ALL ) return (DRectangle)clone();
+    if( r.status == EMPTY ) return DRectangle.getEmpty();
+    DRectangle s = (DRectangle)this.clone();
+    if( s.x < r.x ){
+      s.x = r.x;
+      s.width -= r.x - s.x;
+    }
+    if( s.y < r.y ){
+      s.y = r.y;
+      s.height -= r.y - s.y;
+    }
+    if( s.x + s.width > r.x + r.width )
+      s.width = r.x + r.width - s.x;
+    if( s.y + s.height > r.y + r.height )
+      s.height = r.y + r.height - s.y;
+    if( s.width < 0 || s.height < 0 ) return DRectangle.getEmpty();
+    else return s;
+  }
+
+  /**
+   * method resizes the rectangle to insert p
+   *
+   * @param the dPoint p to insert
+   * @return true when the size of the rectangle changed
+   */
+  public boolean insert( DPoint p ){
+    if( p.x == Double.NaN || p.y == Double.NaN ) return false;
+    if( isAll() ) return false;
+    if( contains( p ) ) return false;
+    if( isEmpty() ){
+      x = p.x; y = p.y; width = height = 0;
+      status = PART;
+      return true;
+    }
+    if( p.x < x ) {
+      width += x - p.x;
+      x = p.x;
+    }
+    else if( p.x > x + width ) width = p.x - x;
+    if( p.y < y ) {
+      height += y - p.y;
+      y = p.y;
+    }
+    else if( p.y > y + height ) height = p.y - y;
+    return true;
+  }
+
+  /**
+   * method inserts the given rectangle to this instance of it
+   * and returns true when the size changed
+   *
+   * @param rect the rectangle to inserts
+   * @return true if the size changed
+   */
+  public boolean insert( DRectangle rect ){
+    if( isAll() || rect.isEmpty() ) return false;
+    if( rect.isAll() ){ status = ALL; return true; }
+    if( isEmpty() ){
+      x = rect.x; y = rect.y; width = rect.width; height = rect.height;
+      status = PART;
+      return true;
+    }
+    boolean changed = false;
+    changed = insert( new DPoint( rect.x, rect.y ) );
+    changed = insert( new DPoint( rect.x + rect.width, rect.y + rect.height ) )? true : changed;
+    return changed;
+  }
+
+  public Object clone(){
+    DRectangle copy = new DRectangle( x, y, width, height );
+    copy.status = status;
+    if( color != null ) copy.color = new Color( color.getRGB() );
+    return copy;
+  }
+
+  public String toString(){
+    String text = "DRectangle[ ";
+    switch( status ){
+      case ALL   : text += "all"; break;
+      case EMPTY : text += "empty"; break;
+      case PART  : text += x+", "+y+", "+width+", "+height;
+    }
+    text += " ]";
+    return text;
+  }
+
+  public boolean equals( DRectangle r ){
+    if( r.status != status ) return false;
+    if( r.x != x ) return false;
+    if( r.y != y ) return false;
+    if( r.width != width ) return false;
+    if( r.height != height ) return false;
+    return true;
+  }
+
+  public void setFillColor( Color fill_color ){
+    if( fillColor == null || !fillColor.equals( fill_color ) ){
+      fillColor = fill_color;
+      repaint();
+    }
+  }
+
+  public Color getFillColor(){
+    return fillColor;
+  }
+
+  public static DRectangle getAll(){ return new DRectangle( ALL ); }
+  public boolean isAll(){ return status == ALL; }
+  public static DRectangle getEmpty(){ return new DRectangle( EMPTY ); }
+  public boolean isEmpty(){ return status == EMPTY; }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/chart2d/ScaledBorder.java

@@ -0,0 +1,493 @@
+/**
+ *  Filename: $RCSfile: ScaledBorder.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:42 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+
+
+package wsi.ra.chart2d;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.awt.* ;
+import javax.swing.BorderFactory;
+import javax.swing.border.* ;
+import java.awt.geom.AffineTransform ;
+import java.text.NumberFormat;
+import java.text.DecimalFormat;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+/**
+ * ScaledBorder puts an border around Components
+ * ( especially around DrawingAreas ) with scaled and labeled axes
+ */
+public class ScaledBorder implements Border 
+{
+  private boolean under_construction = false;
+
+  /**
+   * length of the distance markers on the axes in pixels
+   */
+  int marker_length = 2;
+
+  /**
+   * length in pixels of the arrows at the ends of the axes
+   */
+  int arrow_length = 10;
+
+  /**
+   * a flag if the arrows should be visible
+   */
+  public boolean show_arrows = true;
+
+  /**
+   * distance between the x-values in digits
+   */
+  int x_value2value = 2;
+
+  /**
+   * distance between y-label and y-values in digit width
+   */
+  int y_label2values = 1;
+
+  /**
+   * distance between y-values and y-axis markers in parts of the digit width
+   */
+  int y_values2marker = 2;
+
+  /**
+   * distance between values and arrows in pixels
+   */
+  int x_values2arrow = 10,
+      y_values2arrow = 10;
+
+  /**
+   * distance between arrows and outer border
+   */
+  int axis2border = 4;
+
+  /**
+   * distance between labels and the border in pixels
+   */
+  public int x_label2border = 6,
+             y_label2border = 6;
+
+  /**
+   * the size of the source rectangle
+   * that means before the values are mdified by scale functions
+   */
+  DRectangle src_rect;
+
+  /**
+   * the minimal increment of the scales
+   */
+  public double minimal_increment;
+
+  /**
+   * the  displayed labels
+   */
+  public String x_label, y_label;
+
+  /**
+   * foreground and background colors
+   */
+  public Color foreground, background;
+
+  /**
+   * the border which is shown around the scaled border
+   */
+  Border outer_border;
+
+  /**
+   * flag if the outer border should be displayed
+   */
+  boolean show_outer_border = true;
+
+  /**
+   * scale functions if, for example, an logarithmic function is needed instead
+   * of a linear.
+   */
+  public DFunction x_scale, y_scale;
+
+  /**
+   * formatters of the x- and y-axis numbers
+   * @see java.text.NumberFormat
+   */
+  public NumberFormat format_x = new DecimalFormat(),
+                      format_y = new DecimalFormat();
+
+  private double src_dX = -1, src_dY = -1;
+
+  private boolean do_refresh,
+                  auto_scale_x = true,
+                  auto_scale_y = true;
+
+  private Insets old_insets;
+
+  private DMeasures m;
+
+  /**
+   * constructor creates a default ScaledBorder inside of a lowered BevelBorder
+   */
+  public ScaledBorder(){
+    this(
+      BorderFactory.createBevelBorder(
+        BevelBorder.LOWERED,
+        Color.white,
+        Color.lightGray,
+        Color.black,
+        Color.lightGray
+      )
+    );
+  }
+  /**
+   * constructor creates a new <code>ScaledBorder<code/>
+   * surrounded by the specified <code>Border<code/>
+   */
+  public ScaledBorder( Border outer ){
+    outer_border = outer;
+    m = new DMeasures( this );
+  }
+
+  /**
+   * method tells the border to calculate the differences between displayed
+   * x-values by itself
+   */
+  public void setAutoScaleX(){ auto_scale_x = true; }
+
+  /**
+   * method tells the border to calculate the differences between displayed
+   * y-values by itself
+   */
+  public void setAutoScaleY(){ auto_scale_y = true; }
+
+  /**
+   * method sets the differences between source x-values of the displayed values
+   * @see setAutoScaleX().
+   * If scale functions are used there might be a difference between the shown values
+   * and the source values
+   */
+  public void setSrcdX(double dX){
+    auto_scale_x = false;
+    src_dX = dX;
+  }
+
+  /**
+   * method sets the differences between source y-values of the displayed values
+   * @see setAutoScaleY().
+   * If scale functions are used there might be a difference between the shown values
+   * and the source values
+   */
+  public void setSrcdY(double dY){
+    auto_scale_y = false;
+    src_dY = dY;
+  }
+
+  public void paintBorder(Component c, Graphics g, int x, int y, int width, int height){
+    if( under_construction ) System.out.println("ScaledBorder.paintBorder()");
+    if( foreground == null ) foreground = c.getForeground();
+    if( background == null ) background = c.getBackground();
+    Color old_color = g.getColor();
+    g.setColor( background );
+    g.fillRect( x, y, width, height );
+    g.setColor( old_color );
+
+    Insets outer_insets = new Insets( 0, 0, 0, 0);// insets of the outer border
+    if( show_outer_border ) {
+      outer_border.paintBorder( c, g, x, y, width, height );
+      outer_insets = outer_border.getBorderInsets( c );
+    }
+
+    do_refresh = true;
+    Insets inner_insets = getBorderInsets(c);
+
+    Dimension d = c.getSize(),
+              cd = new Dimension( d.width - inner_insets.left - inner_insets.right,
+                                  d.height - inner_insets.top - inner_insets.bottom );
+    FontMetrics fm = g.getFontMetrics();
+    int fontAsc = fm.getAscent();
+    do_refresh = false;
+
+    m.update(c, inner_insets);
+
+    // axes
+    g.setColor( foreground );
+    g.drawLine( inner_insets.left, inner_insets.top,
+                inner_insets.left, inner_insets.top + cd.height );
+    g.drawLine( inner_insets.left, inner_insets.top + cd.height,
+                inner_insets.left + cd.width, inner_insets.top + cd.height );
+
+    if( show_arrows ){
+      g.drawLine( inner_insets.left, inner_insets.top,
+                  inner_insets.left, inner_insets.top - y_values2arrow );
+      g.drawLine( inner_insets.left - marker_length, inner_insets.top - y_values2arrow,
+                  inner_insets.left, inner_insets.top - y_values2arrow - arrow_length );
+      g.drawLine( inner_insets.left + marker_length, inner_insets.top - y_values2arrow,
+                  inner_insets.left, inner_insets.top - y_values2arrow - arrow_length);
+      g.drawLine( inner_insets.left - marker_length, inner_insets.top - y_values2arrow,
+                  inner_insets.left + marker_length, inner_insets.top - y_values2arrow );
+
+      g.drawLine( inner_insets.left + cd.width , inner_insets.top + cd.height,
+                  inner_insets.left + cd.width + x_values2arrow, inner_insets.top + cd.height );
+      g.drawLine( inner_insets.left + cd.width + x_values2arrow,
+                  inner_insets.top + cd.height - marker_length,
+                  inner_insets.left + cd.width + x_values2arrow + arrow_length,
+                  inner_insets.top + cd.height );
+      g.drawLine( inner_insets.left + cd.width + x_values2arrow,
+                  inner_insets.top + cd.height + marker_length,
+                  inner_insets.left + cd.width + x_values2arrow + arrow_length,
+                  inner_insets.top + cd.height );
+      g.drawLine( inner_insets.left + cd.width + x_values2arrow,
+                  inner_insets.top + cd.height - marker_length,
+                  inner_insets.left + cd.width + x_values2arrow,
+                  inner_insets.top + cd.height + marker_length );
+    }
+
+    if( y_label != null ) {
+      Dimension yld = new Dimension(fm.getAscent()+fm.getDescent(), fm.stringWidth(y_label));
+      AffineTransform T = new AffineTransform(0, -1, 1, 0, 0, 0);
+      Font old = g.getFont(), f = old.deriveFont( T );
+      g.setFont( f );
+      g.drawString( y_label, y_label2border + fm.getAscent(), inner_insets.top + ( cd.height + yld.height )/ 2 );
+      g.setFont( old );
+    }
+
+    if( x_label != null )
+      g.drawString(
+        x_label, inner_insets.left + ( cd.width - fm.stringWidth( x_label ) ) / 2,
+        d.height - outer_insets.bottom - x_label2border - fm.getDescent() );
+
+    if( src_rect.x == 0 && src_rect.y == 0 ){
+      int v2m = fm.stringWidth("0") / y_values2marker;
+      g.drawString( "0", inner_insets.left - fm.stringWidth( "0" ) - v2m - marker_length,
+                         inner_insets.top + cd.height + fontAsc );
+      g.drawLine( inner_insets.left, inner_insets.top + cd.height + fm.getAscent(),
+                  inner_insets.left, inner_insets.top + cd.height);
+      g.drawLine( inner_insets.left, inner_insets.top + cd.height,
+                  inner_insets.left - fm.stringWidth( "0" ) - v2m - marker_length,
+                  inner_insets.top + cd.height );
+    }
+
+    drawYValues( g, inner_insets, cd );
+    drawXValues( g, inner_insets, cd );
+
+    g.setColor( old_color );
+  }
+
+  private void drawYValues( Graphics g, Insets insets, Dimension cd ){
+    if( under_construction ) System.out.println("ScaledBorder.drawYValues()");
+
+    FontMetrics fm = g.getFontMetrics();
+    int n, fontAsc = fm.getAscent(), v2m = fm.stringWidth("0") / y_values2marker;
+    n = (int)( src_rect.y / src_dY );
+    if( n * src_dY < src_rect.y || ( src_rect.x == 0 && src_rect.y == 0 ) ) n++;
+
+
+    double v, minx = src_rect.x;
+    if( x_scale != null ) minx = x_scale.getImageOf( minx );
+    for(; (v = n * src_dY) <= src_rect.y + src_rect.height; n++ ){
+      if( y_scale != null ) v = y_scale.getImageOf( v );
+      String text = format_y.format(v);
+      try{ v = format_y.parse(text).doubleValue(); }
+      catch( java.text.ParseException ex ){ }
+      Point p = m.getPoint( minx, v );
+      if( p != null ){
+        g.drawString( text,
+                      insets.left - fm.stringWidth( text ) - v2m - marker_length,
+                      p.y  + fontAsc / 2 );
+        g.drawLine( insets.left - marker_length, p.y, insets.left, p.y );
+      }
+    }
+  }
+
+  public double getSrcdY( FontMetrics fm, Dimension cd ){
+    if( under_construction ) System.out.println("ScaledBorder.getSrcdY()");
+    if( (!do_refresh && src_dY != -1) || !auto_scale_y ) return src_dY;
+    int max = cd.height / fm.getHeight();
+    double minsrc_dY = 2 * src_rect.height / (double)max; // die 2 einfach mal so eingesetzt   <--------------------------
+    src_dY = aBitBigger( minsrc_dY );
+    if( src_dY < minimal_increment ) src_dY = minimal_increment;
+    return src_dY;
+  }
+
+  private void drawXValues( Graphics g, Insets insets, Dimension cd ){
+    if( under_construction ) System.out.println("ScaledBorder.drawXValues()");
+
+    FontMetrics fm = g.getFontMetrics();
+    double mx = cd.width / src_rect.width;
+    int n, labelX,
+        xnull = insets.left + (int)( - src_rect.x * mx );
+
+    n = (int)( src_rect.x / src_dX );
+    if( n * src_dX < src_rect.x || ( src_rect.x == 0 && src_rect.y == 0 ) ) n++;
+
+    int fontAsc = fm.getAscent(), xLineY = insets.top + cd.height;
+    labelX = xnull + (int)(n * src_dX * mx);
+    while( n * src_dX <= src_rect.x + src_rect.width ){
+      double v = n * src_dX;
+      if( x_scale != null ) v = x_scale.getImageOf(v);
+      String text = format_x.format(v);
+      try{ v = format_x.parse(text).doubleValue(); }
+      catch( java.text.ParseException ex ){ }
+      int strW = fm.stringWidth( text );
+      g.drawString( text, labelX - strW / 2, xLineY + fontAsc );
+      g.drawLine( labelX, xLineY, labelX, xLineY + marker_length );
+      n++;
+      labelX = xnull + (int)( n * src_dX * mx);
+    }
+  }
+
+  public double getSrcdX( FontMetrics fm, Dimension cd ){
+    if( under_construction ) System.out.println("ScaledBorder.getSrcdX()");
+    if( (!do_refresh && src_dX != - 1) || !auto_scale_x ) return src_dX;
+    int digit_width = fm.stringWidth("0"),
+        max = cd.width / ( digit_width * ( x_value2value + 1 ) );
+    src_dX = src_rect.width / (double)max;
+    int n, labelX, olsrc_dX;
+
+    boolean ok = false;
+    while( !ok ){
+      src_dX = aBitBigger( src_dX );
+
+      n = (int)( src_rect.x / src_dX );
+      if( n * src_dX < src_rect.x ) n++;
+
+      olsrc_dX = 0;
+
+      boolean suits = true, first = true;
+      while( suits && n * src_dX <= src_rect.x + src_rect.width ){
+        double v = n * src_dX;
+        if( x_scale != null ) v = x_scale.getImageOf( v );
+        String text = format_x.format(v);
+        int strW = fm.stringWidth( text );
+        labelX = (int)((( n * src_dX - src_rect.x ) / src_rect.width ) * cd.width ) - strW / 2;
+        if( !first && labelX <= olsrc_dX + digit_width * x_value2value ) suits = false;
+        else{
+          olsrc_dX = labelX + strW;
+          n++;
+        }
+        first = false;
+      }
+      if( !suits ) ok = false;
+      else ok = true;
+    }
+    if( src_dX < minimal_increment ) src_dX = minimal_increment;
+    return src_dX;
+  }
+
+  /**
+   * method returns to a certain minimal value the next higher value which can be
+   * displayed, which looks a bit nicer
+   * it returns values like ... 0.05, 0.1, 0.2, 0.5, 1, 2, 5, 10, ...
+   *
+   * @param the double value next to which the displayable value should be found
+   * @return the displayable value
+   */
+  public static double aBitBigger( double min ){
+    if( min <= 0 ) return 1;
+    double d = 1;
+    if( min < d ){
+      while( d * .5 > min ) {
+        d *= .5;
+        if( d * .4 > min ) d *= .4;
+        if( d * .5 > min ) d *= .5;
+      }
+    }
+    else{
+      while( d <= min ) {
+        d *= 2;
+        if( d <= min ) d *= 2.5;
+        if( d <= min ) d *= 2;
+      }
+    }
+    return d;
+  }
+
+  public boolean isBorderOpaque(){
+    return outer_border.isBorderOpaque();
+  }
+//
+//  private String stringOf( double v ){
+//    if( (int)v == v ) return String.valueOf( (int)v );
+//    return String.valueOf( v );
+//  }
+
+  public Insets getBorderInsets(Component c){
+    if( under_construction ) System.out.println("ScaledBorder.getBorderInsets()");
+    if( !do_refresh && old_insets != null ) return old_insets;
+
+    Graphics g = c.getGraphics();
+
+    Insets insets = new Insets(0, 0, 0, 0);
+    if( show_outer_border ) insets = outer_border.getBorderInsets( c );
+
+    if( g == null ) return insets;
+
+    FontMetrics fm = g.getFontMetrics();
+//    int fontAsc = fm.getAscent();
+    int fontHeight = fm.getHeight(),
+        digit_width = fm.stringWidth("0");
+
+    if( c instanceof DArea ){
+      DArea area = (DArea)c;
+      DMeasures m = area.getDMeasures();
+      DRectangle rect = m.getSourceOf( area.getDRectangle() );
+      src_rect = (DRectangle)rect.clone();
+      x_scale = area.getDMeasures().x_scale;
+      y_scale = area.getDMeasures().y_scale;
+    }
+
+    // left:
+    if( y_label != null ) insets.left += fm.getAscent() + fm.getDescent();
+    insets.left += y_label2values * digit_width;
+    getSrcdY( fm, c.getSize() );
+    int n, maxWidth = 0;
+    n = (int)( src_rect.y / src_dY );
+    if( n * src_dY < src_rect.y ) n++;
+    while( n * src_dY <= src_rect.y + src_rect.height ){
+    	// TODO here might be a bug for mean values
+      double v = n * src_dY;
+      if( y_scale != null ) v = y_scale.getImageOf( v );
+      int w = fm.stringWidth( format_y.format(v) );
+      if( w > maxWidth ) maxWidth = w;
+      n++;
+    }
+    insets.left += 1 + y_label2border + maxWidth + digit_width / y_values2marker + marker_length;
+
+    // bottom:
+    insets.bottom += 1 + fontHeight + x_label2border;
+    if( x_label != null ) insets.bottom += fontHeight;
+
+    // top:
+    if( show_arrows ) insets.top += y_values2arrow + arrow_length;
+    insets.top += axis2border;
+
+    // right:
+    if( show_arrows ) insets.right += x_values2arrow + arrow_length;
+    insets.right += axis2border;
+    getSrcdX( fm, c.getSize() );
+    n = (int)( src_rect.x + src_rect.width / src_dX );
+    if( n < 0 ) n ++;
+    int w = fm.stringWidth( format_x.format(n * src_dX) );
+    if( w / 2 > insets.right ) insets.right = w / 2;
+
+    old_insets = insets;
+    return insets;
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/diagram/ColorBarCalculator.java

@@ -0,0 +1,156 @@
+/**
+ *  Filename: $RCSfile: ColorBarCalculator.java,v $
+ *  Purpose:  Calculates the color values for a legend-style color bar.
+ *  Language: Java
+ *  Compiler: JDK 1.2
+ *  Authors:  Badreddin Abolmaali, Fred Rapp, Simon Wiest
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:41 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.diagram;
+
+/*============================================================================
+ * IMPORTS
+ *============================================================================*/
+
+import java.awt.*;
+import java.awt.geom.*;
+import java.awt.image.*;
+import javax.swing.*;
+
+import wsi.ra.math.*;
+
+/*============================================================================
+ * CLASS DECLARATION
+ *============================================================================*/
+
+/**
+ * Calculates the color values for a legend-style color bar.
+ */
+public class ColorBarCalculator
+{
+  /*--------------------------------------------------------------------------
+   * static public final member variables
+   *--------------------------------------------------------------------------*/
+
+  static public final int BLUE_TO_RED         = 0;
+  static public final int GREY_SCALE          = 1;
+  static public final int BLUE_SCALE          = 2;
+  static public final int ALL_COLORS          = 3;
+  // GREY_SCALE returns luminance values in [0.1;0.9], GREY_EXTENDED_SCALE in [0.0;1.0]
+  static public final int GREY_EXTENDED_SCALE = 4;
+
+  /*--------------------------------------------------------------------------
+   * private member variables
+   *--------------------------------------------------------------------------*/
+
+  private int color_scale = BLUE_TO_RED;
+  private boolean inverseScale = false;
+
+  /*--------------------------------------------------------------------------
+   * constructor
+   *--------------------------------------------------------------------------*/
+
+  public ColorBarCalculator(int color_scale)
+  {
+    this.color_scale = color_scale;
+  }
+
+  /*--------------------------------------------------------------------------
+   * public methods
+   *--------------------------------------------------------------------------*/
+
+  public void setColorScale(int color_scale) { this.color_scale = color_scale; }
+
+  /**
+   * Returns color for the given float-value, which must be in the range from 0 to 1.
+   * Warning: Creates new color object, better use the method 'getRGB' if possible.
+   */
+  public Color getColor(float value)
+  {
+    return new Color( getRGB(value) );
+  }
+
+  /**
+   * Returns color RGB-value for the given float-value, which must be in the range from 0 to 1.
+   */
+  public int getRGB(float value)
+  {
+    int rgbValue = 0;
+    if(inverseScale) {
+      value = 1 - value;
+    }
+    switch (color_scale)
+    {
+      case BLUE_TO_RED:
+        float hue = value * (value + value * 0.8F) / 2.65F - 1F;
+        rgbValue = Color.HSBtoRGB(hue, 0.6F, 1F);
+        break;
+
+      case GREY_SCALE:
+        rgbValue = Color.HSBtoRGB(0F, 0F, (value * 0.8F) + 0.1F);
+        break;
+
+      case BLUE_SCALE:
+        int rg = (int) (value * 0.95F * 256);
+        int b  = (int) ((value/2.0F + 0.45F) * 256);
+        rgbValue = rg * 0x10000 + rg * 0x100 + b;
+        break;
+
+      case ALL_COLORS:
+        rgbValue = Color.HSBtoRGB(value, 0.6F, 1F);
+        break;
+
+      case GREY_EXTENDED_SCALE:
+        rgbValue = Color.HSBtoRGB(0F, 0F, value );
+        break;
+    }
+    return rgbValue;
+  }
+
+  /**
+   * Reverts color scale (e.g. black will be white and vice versa).
+   * @param isInverse Color scale is inverted, if <code>isInverse</code> is set to true.
+   */
+  public void setInverseScale(boolean isInverse) {
+    inverseScale = isInverse;
+  }
+
+  /**
+   * Returns current scale mode.
+   * @return <code>true</code> if scale is inverted, else <code>false</code>.
+   */
+  public boolean isInverseScale() {
+   return inverseScale;
+  }
+
+  /*--------------------------------------------------------------------------
+   * static public methods
+   *--------------------------------------------------------------------------*/
+
+  /**
+   * Returns color for the given float-value, which must be in the range from 0 to 1.
+   * Warning: Creates new color object, better use the method 'getRGB' if possible.
+   */
+  static public Color getDefaultColor(float value)
+  {
+    return new Color( getDefaultRGB(value) );
+  }
+
+  /**
+   * Returns color RGB-value for the given float-value, which must be in the range from 0 to 1.
+   */
+  static public int getDefaultRGB(float value)
+  {
+    float hue = value * (value + value * 0.8F) / 2.65F - 1F;
+    return Color.HSBtoRGB(hue, 0.6F, 1F);
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/
+

src/wsi/ra/jproxy/ComAdapter.java

@@ -0,0 +1,639 @@
+package wsi.ra.jproxy;
+
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.3 $
+ *            $Date: 2004/04/28 07:50:32 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.net.MalformedURLException;
+import java.rmi.Naming;
+import java.rmi.NotBoundException;
+import java.rmi.RemoteException;
+import java.rmi.registry.Registry;
+import java.util.ArrayList;
+import java.util.Properties;
+import java.util.StringTokenizer;
+
+import javaeva.tools.Serializer;
+
+/**
+ *
+ */
+public class ComAdapter {
+	static final public boolean TRACE = false;
+	static final public int PORT = 1099;
+	static final public String SEP = "_";
+	static protected ComAdapter m_instance = null;
+
+	public Registry m_Registry = null;
+	private ArrayList<RMIConnection> m_Connections = new ArrayList<RMIConnection>();
+	private String m_ownHostName;
+	private ArrayList<String> m_HostNameList = new ArrayList<String>();
+	private ArrayList<String> m_AvailableHostNameList = new ArrayList<String>();
+//	private String m_RemoteAdapterName;
+	private String m_UserName;
+	private int m_ownHostIndex = 0;
+	protected RMIServer m_RMIServer;
+	private String serverListSeparator = ",";
+	private boolean gettingRegistry;
+
+	/**
+	 *
+	 */
+	public static ComAdapter getInstance() {
+		if (m_instance != null)
+			return m_instance;
+		m_instance = new ComAdapter();
+		return m_instance;
+	}
+
+	/**
+	 *
+	 */
+	protected ComAdapter() {
+		if (TRACE) System.out.println("constructor ComAdapter");
+		m_UserName = System.getProperty("user.name");
+		
+		m_ownHostName = "localhost"; //"192.168.0.1";
+
+		System.setProperty("java.security.policy", "server.policy");
+		launchRMIRegistry(false);
+		if (!m_HostNameList.contains("localhost")) {
+			// make sure localhost is in the list
+			m_HostNameList.add("localhost");
+		}
+	}
+	
+	/**
+	 * Parse a string of server names. The comma "," must be used as separator.
+	 * 
+	 * @param serverList
+	 */
+	public void addServersFromString(String serverList) {
+		if (serverList != null) {
+			// parse the servernames
+			StringTokenizer st = new StringTokenizer(serverList, serverListSeparator);
+
+			while (st.hasMoreTokens()) {
+				String current = st.nextToken().trim();
+				if (!m_HostNameList.contains(current)) {
+					if (TRACE) System.out.println("adding server " + current);
+					m_HostNameList.add(current);
+				} else {
+					if (TRACE) System.out.println("server " + current + " was already in list");
+				}
+			}
+		}
+	}
+	
+	/**
+	 * Add a server list from a Properties instance. The key used is "ServerList".
+	 * 
+	 * @param props
+	 */
+	public void addServersFromProperties(Properties props) {
+		String servs = props.getProperty("ServerList");
+		addServersFromString(servs);
+	}
+	
+	/**
+	 * Set the separator for the server list string.
+	 * 
+	 * @return
+	 */
+	public void setServerListSeparator(String sep) {
+		serverListSeparator = sep;
+	}
+		
+	/**
+	 * The separator for the server list string.
+	 * 
+	 * @return
+	 */
+	public String getServerListSeparator() {
+		return serverListSeparator;
+	}
+	
+	/**
+	 *
+	 * @param c
+	 * @param host
+	 * @return
+	 */
+	public void setServerList(String[] server){
+		m_HostNameList.clear();
+		for (int i=0;i<server.length;i++)
+			m_HostNameList.add(server[i]);
+
+	}
+	/**
+	 *
+	 *
+	 */
+	public RMIInvocationHandler getRMIHandler(Object c, String host) {
+		System.out.println("ComAdapter.getRMIHandler() for host " + host);
+		m_ownHostName = host;
+		RMIInvocationHandler ret = null;
+		while (ret == null) {
+			ret = getConnection(m_ownHostName).getRMIHandler(c);
+			if (ret == null)
+				System.out.println("Error in getRMIHandler");
+		}
+		return ret;
+	}
+
+	/**
+	 *
+	 *
+	 */
+	public RMIThreadInvocationHandler getRMIThreadHandler(Object c, String host) {
+		if (TRACE)
+			System.out.println("ComAdapter.getRMIThreadHandler()");
+		m_ownHostName = host;
+		RMIThreadInvocationHandler ret = null;
+		while (ret == null) {
+			ret = getConnection(m_ownHostName).getRMIThreadHandler(c);
+			if (ret == null)
+				System.err.println("Error in getRMIThreadHandler");
+		}
+		return ret;
+	}
+
+	/**
+	 *
+	 *
+	 */
+	public RMIThreadInvocationHandler getRMIThreadHandler(Object c) {
+		if (TRACE)
+			System.out.println("RMIThreadInvokationHandler getRMIThreadHandler");
+		RMIThreadInvocationHandler ret = null;
+		if (m_AvailableHostNameList.size() == 0) {
+			evalAvailableHostNameList();
+			m_ownHostIndex = 0;
+		}
+		m_ownHostIndex++;
+		if (m_ownHostIndex >= m_AvailableHostNameList.size())
+			m_ownHostIndex = 0;
+		m_ownHostName = (String) m_AvailableHostNameList.get(m_ownHostIndex);
+		ret = getRMIThreadHandler(c, m_ownHostName);
+		return ret;
+	}
+
+	/**
+	 *
+	 *
+	 */
+	public RMIInvocationHandler getRMIHandler(Object c) {
+		if (TRACE)
+			System.out.println("RMIThreadInvokationHandler getRMIHandler");
+		RMIInvocationHandler ret = null;
+		while (m_AvailableHostNameList.size() == 0) {
+			evalAvailableHostNameList();
+			if (m_AvailableHostNameList.size() == 0)
+				System.err.println("no host availabe waiting !!");
+			m_ownHostIndex = 0;
+		}
+		m_ownHostIndex++;
+		if (m_ownHostIndex >= m_AvailableHostNameList.size())
+			m_ownHostIndex = 0;
+		m_ownHostName = (String) m_AvailableHostNameList.get(m_ownHostIndex);
+		ret = getRMIHandler(c, m_ownHostName);
+		return ret;
+	}
+
+//	/**
+//	 *
+//	 */
+//	public String getLoad() {
+//		if (TRACE)
+//			System.out.println("ComAdapter.getLoad()");
+//		String Load = null;
+//		Load = getConnection(m_ownHostName).getExecOutput("rup " + m_ownHostName);
+//		if (TRACE)
+//			System.out.println("Load of Modules on Server !! :" + Load);
+////		if (m_LogPanel != null)
+////		m_LogPanel.logMessage("Load of Modules on Server !! :" + Load);
+//		return Load;
+//	}
+
+//	/**
+//	*
+//	*/
+//	public String gettokens() {
+//	if (TRACE)
+//	System.out.println("ComAdapter.gettokens()");
+//	String Tokens = null;
+//	Tokens = getConnection(m_ActualHostName).getExecOutput("tokens");
+//	if (TRACE)
+//	System.out.println("tokens on Server !! :" + Tokens);
+//	Tokens = getConnection(m_ActualHostName).getExecOutput(
+//	"klog -principal ulmerh -password ");
+//	if (TRACE)
+//	System.out.println("KLOG !!! !! :" + Tokens);
+//	Tokens = getConnection(m_ActualHostName).getExecOutput("tokens");
+//	if (TRACE)
+//	System.out.println("tokens on Server !! :" + Tokens);
+//	return Tokens;
+//	}
+
+	/**
+	 *
+	 */
+	public void evalAvailableHostNameList() {
+		long time = System.currentTimeMillis();
+		if (TRACE)
+			System.out.println("ComAdapter.getAvailableHostNameList()");
+		m_AvailableHostNameList.clear();
+		for (int i = 0; i < m_HostNameList.size(); i++) {
+			if (rmiPing((String) m_HostNameList.get(i)) == true)
+				m_AvailableHostNameList.add((String) m_HostNameList.get(i));
+			String testurl = (String) m_HostNameList.get(i);
+			for (int j = 1; j < 3; j++) {
+				if (rmiPing(testurl + "_" + j) == true) {
+					if (TRACE) System.out.println("found EvAServer on: " + testurl);
+					m_AvailableHostNameList.add(testurl + "_" + j);
+				}
+			}
+		}
+		time = System.currentTimeMillis() - time;
+		if (TRACE) System.out.println("getAvailableHostNameList: " + m_AvailableHostNameList.size() + " found time " + time);
+
+	}
+
+	/**
+	 *
+	 */
+	public String[] getAvailableHostNameList() {
+		if (m_AvailableHostNameList.size() == 0)
+			evalAvailableHostNameList();
+		String[] ret = new String[m_AvailableHostNameList.size()];
+		m_AvailableHostNameList.toArray(ret);
+		return ret;
+	}
+
+	/**
+	 *
+	 */
+	public String[] getHostNameList() {
+		String[] x = new String[m_HostNameList.size()];
+		m_HostNameList.toArray(x);
+		return x;
+	}
+
+	/**
+	 *
+	 */
+	public String getHostName() {
+		return m_ownHostName;
+	}
+
+	/**
+	 *
+	 */
+	public void setHostName(String newHost) {
+		m_ownHostName = newHost;
+		Serializer.storeString("hostname.ser", m_ownHostName);
+	}
+
+
+	/**
+	 *  Creates a RMI-MainAdapter to host.
+	 *  @return
+	 */
+	protected MainAdapter createRMIMainConnect(String HostToConnect) {
+		if (TRACE)
+			System.out.println("RMIMainConnect.RMIMainConnect() =" + HostToConnect);
+		int len = HostToConnect.indexOf(SEP);
+		String Host = HostToConnect;
+		String Number = SEP + "0";
+		if (len != -1) {
+			StringTokenizer st = new StringTokenizer(HostToConnect, SEP);
+			Host = st.nextToken().trim();
+			Number = SEP + st.nextToken().trim();
+		}
+		String MainAdapterName = m_UserName + MainAdapterImpl.MAIN_ADAPTER_NAME + Number; // attention
+		
+		logInfo(" RMIConnect to " + HostToConnect);
+		MainAdapter MainRemoteObject = null;
+		try {
+			try {
+				try {
+					//System.out.println("--> ComAdapter: "+"rmi://"+Host+":"+MainAdapterImpl.PORT+"/"+MainAdapterName);
+//					String[] list = Naming.list("rmi://" + Host + ":" +
+//							MainAdapterImpl.PORT);
+					//for (int i=0;i<list.length;i++)
+					//  System.out.println("RMIName: "+list[i]);
+					//m_NumberOfVM = getNumberOfVM(list);
+					if (TRACE) System.out.println("getMain:" + "rmi://" + Host + ":" +
+							MainAdapterImpl.PORT + "/" + MainAdapterName);
+					RMIInvocationHandler invocHandler = (RMIInvocationHandler) Naming.lookup(
+							"rmi://" + Host + ":" + MainAdapterImpl.PORT + "/" +
+							MainAdapterName);
+					//System.out.println(" x ="+x.getClass().getName());
+					MainRemoteObject = getMainAdapter(invocHandler);
+
+					//MainRemoteObject = (MainAdapter)Naming.lookup("rmi://"+HostToConnect+":"+MainAdapterImpl.PORT+"/"+MainAdapterImpl.MAIN_ADAPTER_NAME);
+					//MainRemoteObject = (MainAdapter)LogProxy.newInstance(MainRemoteObject);
+					MainRemoteObject.setBuf("Ok.");
+					logInfo(" RMIConnect " + MainRemoteObject.getBuf());
+				} catch (MalformedURLException ex) {
+					System.err.println("MalformedURLException: Error while looking up " +
+							ex.getMessage());
+				}
+			} catch (NotBoundException ex) {
+				System.err.println("NotBoundException: Error while looking up " +
+						ex.getMessage());
+				ex.printStackTrace();
+
+			}
+			if (TRACE)
+				System.out.println("Connect to " + HostToConnect + " works fine");
+		} catch (RemoteException e) {
+			logInfo("Error while connecting Host: " + HostToConnect +
+					" \n ERROR: " + e.getMessage());
+			System.err.println("Error while connecting Host: " + HostToConnect +
+					" \n ERROR: " + e.getMessage());
+			return null;
+		}
+		return MainRemoteObject;
+	}
+
+	protected MainAdapter getMainAdapter(RMIInvocationHandler invocHandler) throws RemoteException {
+		return (MainAdapter) invocHandler.getWrapper();
+	}
+
+	protected void logInfo(String msg) {
+		System.out.println("ComAdapter-Log: " + msg);
+	}
+
+	/**
+	 *
+	 */
+	protected int getNumberOfServersonHost(String testurl) {
+//		String MainAdapterName = m_UserName + MainAdapterImpl.MAIN_ADAPTER_NAME;
+		String[] list = null;
+		try {
+			list = Naming.list("rmi://" + testurl + ":" + MainAdapterImpl.PORT);
+		} catch (Exception e) {
+			//if (TRACE && m_LogPanel!=null) m_LogPanel.logMessage ("No connecting to : "+testurl  );
+			//if (TRACE) System.out.println ("No connecting to : "+testurl  );
+			System.err.println ("Exception : "+testurl  );
+			return 0;
+		}
+		int ret = 0;
+		for (int i = 0; i < list.length; i++) {
+			if (list[i].indexOf(MainAdapterImpl.MAIN_ADAPTER_NAME) != -1)
+				ret++;
+		}
+		System.err.println("error in ComAdapter.getNumberOfServersonHost");
+		//System.out.println(" ret ===        "+ret);
+		return ret;
+	}
+
+	/**
+	 *
+	 */
+	private boolean rmiPing(String testurl) {
+		if (TRACE)
+			System.out.println("ComAdapter.rmiPing " + testurl);
+		MainAdapter Test = null;
+//		String Load = null;
+		int len = testurl.indexOf(SEP);
+		String Host = testurl;
+		String Number = "_0";
+		if (len != -1) {
+			StringTokenizer st = new StringTokenizer(testurl, SEP);
+			Host = st.nextToken().trim();
+			Number = SEP + st.nextToken().trim();
+		}
+		String MainAdapterName = m_UserName + MainAdapterImpl.MAIN_ADAPTER_NAME +
+		Number;
+		try {
+			if (TRACE)
+				System.out.println("ping:" + "rmi://" + Host + ":" +
+						MainAdapterImpl.PORT + "/" + MainAdapterName);
+			RMIInvocationHandler x = (RMIInvocationHandler) Naming.lookup("rmi://" +
+					Host + ":" + MainAdapterImpl.PORT + "/" + MainAdapterName); // attention !!
+			Test = (MainAdapter) x.getWrapper();
+//			if (Test != null) {
+//				Load = Test.getExecOutput("rup " + testurl);
+//			}
+		} catch (Exception e) {
+			if (TRACE) {
+				logInfo("No connection to : " + testurl);
+				System.out.println("ComAdapter.rmiPing false " + e.getMessage());
+			}
+			return false;
+		}
+		if (Test != null) {
+			if (TRACE) logInfo("ping succeeded");
+		}
+		if (TRACE)
+			System.out.println("ComAdapter.rmiPing true");
+		return true;
+	}
+
+	/**
+	 *
+	 */
+	public void killServer(String ServerToKill) {
+		if (TRACE)
+			System.out.println("ComAdapter.Killing Server :" + ServerToKill);
+		RMIConnection myConnection = getConnection(ServerToKill);
+		myConnection.killServer();
+		this.m_Connections.remove(myConnection);
+	}
+
+	/**
+	 *
+	 */
+	public void killAllServers() {
+		if (TRACE)
+			System.out.println("ComAdapter.Killing All Servers :");
+		for (int i = 0; i < m_AvailableHostNameList.size(); i++) {
+			RMIConnection myConnection = getConnection((String)
+					m_AvailableHostNameList.get(i));
+			myConnection.killServer();
+			this.m_Connections.remove(myConnection);
+		}
+	}
+
+	/**
+	 *
+	 */
+	public void restartServerAllServer() {
+		if (TRACE) System.out.println("ComAdapter.restartServerAllServer :");
+		for (int i = 0; i < m_AvailableHostNameList.size(); i++) {
+			RMIConnection myConnection = getConnection((String)
+					m_AvailableHostNameList.get(i));
+			myConnection.restartServer();
+			m_Connections.remove(myConnection);
+		}
+	}
+
+	/**
+	 *
+	 */
+	public void restartServer(String host) {
+		m_ownHostName = host;
+		restartServer();
+	}
+
+	/**
+	 *
+	 */
+	public void restartServer() {
+		if (TRACE)
+			System.out.println("ComAdapter.restartServer");
+		if (TRACE)
+			System.out.println("m_ActualHostName = " + m_ownHostName);
+//		System.out.println("m_ActualHostName = " + m_ActualHostName);
+		if (m_ownHostName.equals("localhost")) { // TODO whats this?
+			return;
+		}
+		if (TRACE == true)
+			System.out.println("ComAdapter.restartServer Server :" + m_ownHostName);
+		RMIConnection x = getConnection(m_ownHostName);
+		x.restartServer();
+		m_Connections.remove(x);
+		try {
+			Thread.sleep(3000);
+		} catch (Exception e) {
+			System.err.println("Error in sleep of ExitThread");
+		}
+	}
+
+	public void setRMIRegistry(Registry reg) {
+		m_Registry = reg;
+		gettingRegistry = false;
+	}
+	
+	/**
+	 * Install RMIregistry on default port !!
+	 */
+	protected void launchRMIRegistry(boolean ownThread) {
+		if (ownThread) {
+			Thread t = new Thread(new RMIRegistration(this));
+			gettingRegistry = true;
+			t.start();
+		} else {
+			RMIRegistration rmiReg = new RMIRegistration(this);
+			gettingRegistry = true;
+			rmiReg.run();
+		}
+	}
+	/**
+	 *
+	 */
+	public void setLocalRMIServer(RMIServer Server) {
+		m_RMIServer = Server;
+	}
+
+	/**
+	 * Just the main for testing the class.
+	 */
+	public static void main(String[] args) {
+		ComAdapter TestApp = ComAdapter.getInstance();
+		TestApp.evalAvailableHostNameList();
+		TestApp.killAllServers();
+		//TestApp.restartServerAllServer();
+	}
+
+	/**
+	 *
+	 */
+	protected RMIConnection getConnection(String Host) {
+		if (TRACE) System.out.println("ComAdapter.getConnection for host :" + Host);
+		for (int i = 0; i < this.m_Connections.size(); i++) {
+			// search for an already established connection to the given host
+			// and return it if found
+			RMIConnection ret = (RMIConnection) m_Connections.get(i);
+			if (Host.equals(ret.getHostName())) return ret;
+		}
+		// else create and add new RMIConnection
+		RMIConnection ret = null;
+		if (Host.equals("localhost") && m_RMIServer != null) {
+			// this uses rmi on the localhost
+			ret = createRMIConnection(Host, m_RMIServer.getMainRemoteObject(),
+					new MainAdapterClientImpl("localhost"));
+		} else {
+			MainAdapter Adapter = (MainAdapter)createRMIMainConnect(Host);
+			if (Adapter != null)
+				ret = createRMIConnection(Host, Adapter,
+						(MainAdapterClient) RMIProxyLocal.newInstance(new MainAdapterClientImpl(Host)));
+		}
+		if (ret != null) m_Connections.add(ret);
+		else System.err.println("Warning no valid connection !!");
+		return ret;
+	}	
+	
+	protected RMIConnection createRMIConnection(String Host, MainAdapter mainRemoteObject, MainAdapterClient client) { 
+		return new RMIConnection(Host, mainRemoteObject, client);
+	}
+	
+//	private RMIConnection getConnection(String Host) {
+//		if (TRACE == true) System.out.println("ComAdapter.getConnection for host :" + Host);
+//		RMIConnection ret = null;
+//		for (int i = 0; i < this.m_Connections.size(); i++) {
+//			ret = (RMIConnection) m_Connections.get(i);
+//			if (Host.equals(ret.getHostName()) == true)
+//				return ret;
+//		}
+//		// create and add new RMIConnection
+//		if (Host.equals("localhost") && (m_RMIServer != null)) {
+//			ret = new RMIConnection(Host, m_RMIServer.getMainRemoteObject(),
+//					new MainAdapterClientImpl());
+//		} else {
+//			MainAdapter Adapter = createRMIMainConnect(Host);
+//			if (Adapter != null)
+//				ret = new RMIConnection(Host, Adapter,
+//						(MainAdapterClient)
+//						RMIProxyLocal.newInstance(new MainAdapterClientImpl()));
+//		}
+//		if (ret != null) m_Connections.add(ret);
+//		else System.err.println("Warning no valid connection !!");
+//		return ret;
+//	}
+}
+
+class RMIRegistration implements Runnable {
+	ComAdapter comAd = null;
+	private boolean TRACE = false;
+	Registry reg = null;
+	
+	public RMIRegistration(ComAdapter comAdapter) {
+		comAd = comAdapter;
+	}
+
+	public void run() {
+		if (TRACE)
+			System.out.println("LaunchRMIRegistry on Client on PORT " + ComAdapter.PORT);
+		try {
+			reg = java.rmi.registry.LocateRegistry.createRegistry(ComAdapter.PORT);
+		}
+		catch (Throwable e) {
+			if (TRACE) System.out.println("Registry notcreated !!" + e.getMessage());
+			reg = null;
+		}
+		if (reg == null) {
+			if (TRACE) System.out.println("Try to get registry with getRegistry on PORT " + ComAdapter.PORT);
+			try {
+				reg = java.rmi.registry.LocateRegistry.getRegistry(ComAdapter.PORT);
+			}
+			catch (Throwable e) {
+				if (TRACE) System.out.println("registry not created !!" + e.getMessage());
+				reg = null;
+			}
+		}
+		if (reg != null && TRACE) System.out.println("--> got RMIREGISTRY");
+		comAd.setRMIRegistry(reg);
+	}
+	
+}

src/wsi/ra/jproxy/JProxyRemoteThread.java

@@ -0,0 +1,113 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.1 $
+ *            $Date: 2004/04/15 09:12:29 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.lang.reflect.InvocationHandler;
+import java.lang.reflect.Method;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Proxy;
+import java.io.Serializable;
+import java.util.ArrayList;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+/**
+ *
+ */
+public class JProxyRemoteThread implements InvocationHandler,
+        Serializable {
+  private static ComAdapter m_ComAdapter;
+  private Object m_Object;
+  private RMIThreadInvocationHandler m_RMIThreadHandler;
+  private String m_ObjectName;
+  /**
+   *
+   */
+  public static Object newInstance(Serializable object, String host) throws NO_RMIServerAvailable {
+    return Proxy.newProxyInstance(
+            object.getClass().getClassLoader(),
+            object.getClass().getInterfaces(),
+            new JProxyRemoteThread(object, host));
+  }
+
+  /**
+   *
+   */
+  public static Object newInstance(Serializable object) throws NO_RMIServerAvailable {
+    return Proxy.newProxyInstance(
+            object.getClass().getClassLoader(),
+            object.getClass().getInterfaces(),
+            new JProxyRemoteThread(object));
+  }
+
+  /**
+   *
+   * @param c
+   * @return
+   */
+  public static String[] getServerList() {
+    if (m_ComAdapter == null) {
+      //try {
+      m_ComAdapter = ComAdapter.getInstance();
+//      } catch (NO_RMIServerAvailable ex) {
+//        ex.printStackTrace();
+//
+//      }
+    }
+    m_ComAdapter.evalAvailableHostNameList();
+    return m_ComAdapter.getAvailableHostNameList();
+
+  }
+
+  /**
+   *
+   */
+  public static void setComAdaper(ComAdapter x) {
+    m_ComAdapter = x;
+  }
+
+
+  /**
+   *
+   */
+  private JProxyRemoteThread(Serializable object, String host) throws NO_RMIServerAvailable {
+    if (m_ComAdapter == null)
+      m_ComAdapter = ComAdapter.getInstance();
+    m_RMIThreadHandler = m_ComAdapter.getRMIThreadHandler(object, host);
+  }
+
+  /**
+   *
+   */
+  private JProxyRemoteThread(Serializable object) throws NO_RMIServerAvailable {
+    if (m_ComAdapter == null)
+      m_ComAdapter = ComAdapter.getInstance();
+    m_RMIThreadHandler = m_ComAdapter.getRMIThreadHandler(object);
+  }
+
+  /**
+   *
+   */
+  public Object invoke(Object proxy, Method method, Object[] args) throws Throwable {
+    Object ret = null;
+    if (method.getName().equals("getServerName")) {
+      ret = m_RMIThreadHandler.getServerName();
+    } else {
+      ret = m_RMIThreadHandler.invoke(method.getName(), args);
+    }
+
+    //long finish = System.currentTimeMillis();
+    //System.out.println("Calling :"+m.getName()+" of "+m_ObjectName+ " time :"+(finish-start));
+    return ret;
+  }
+}

src/wsi/ra/jproxy/MainAdapter.java

@@ -0,0 +1,31 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.1 $
+ *            $Date: 2004/04/15 09:12:29 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+/*==========================================================================*
+* INTERFACE DECLARATION
+*==========================================================================*/
+/**
+ *
+ */
+public interface MainAdapter {
+  public String getExecOutput(String command);
+  public void setBuf(String s);
+  public void killServer();
+  public void restartServer();
+  public String getBuf();
+  public RMIInvocationHandler getRMIHandler(Object obj);
+  public RMIThreadInvocationHandler getRMIThreadHandler(Object obj);
+  public void setRemoteThis (MainAdapter x);
+}
+

src/wsi/ra/jproxy/MainAdapterClient.java

@@ -0,0 +1,25 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.1 $
+ *            $Date: 2004/04/15 09:12:30 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+/*==========================================================================*
+* INTERFACE DECLARATION
+*==========================================================================*/
+/**
+ *
+ */
+public interface MainAdapterClient {
+  public RMIInvocationHandler getRMIHandler(Object obj);
+  public RMIThreadInvocationHandler getRMIThreadHandler(Object obj);
+  public String getHostName();
+}

src/wsi/ra/jproxy/MainAdapterClientImpl.java

@@ -0,0 +1,76 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.1 $
+ *            $Date: 2004/04/15 09:12:30 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.net.InetAddress;
+/*==========================================================================*
+* CLASS DECLARATION
+*==========================================================================*/
+/**
+ *
+ */
+public class MainAdapterClientImpl implements MainAdapterClient {
+  static final public String MAIN_ADAPTER_CLIENT_NAME = "Main_Remote_Object_Client_Name";
+  static public boolean TRACE = false;
+  private String m_HostName = "not__defined__";
+  /**
+   *
+   */
+  public MainAdapterClientImpl() {
+    try {
+      m_HostName  =  InetAddress.getLocalHost().getHostName();
+    } catch (Exception e) {
+      System.out.println("ERROR getting HostName MainAdapterClientImpl "+e.getMessage());
+    }
+  }
+
+  /**
+  *
+  */
+ public MainAdapterClientImpl(String hostName) {
+	 m_HostName = hostName;
+ }
+  
+  /**
+   *
+   */
+  public RMIInvocationHandler getRMIHandler(Object obj) {
+    if (TRACE) System.out.println("MainAdapterClientImpl.getRMIHandler");
+    RMIInvocationHandler ret = null;
+    try {
+      ret = new RMIInvocationHandlerImpl(obj);
+    } catch (Exception e) {
+      System.out.println(" Error  ret= new RMIInvokationHandlerImpl(obj);"+e.getMessage());
+    }
+    return ret;
+  }
+  /**
+   *
+   */
+  public RMIThreadInvocationHandler getRMIThreadHandler(Object obj) {
+    if (TRACE) System.out.println("MainAdapterClientImpl.getRMIThreadHandler");
+    RMIThreadInvocationHandler ret = null;
+    try {
+      ret = new RMIThreadInvocationHandlerImpl(obj);
+    } catch (Exception e) {
+      System.out.println(" Error  ret= new getRMIThreadHandler(obj);"+e.getMessage());
+    }
+    return ret;
+  }
+  /**
+   *
+   */
+  public String getHostName () {
+    return m_HostName;
+  }
+}

src/wsi/ra/jproxy/MainAdapterImpl.java

@@ -0,0 +1,154 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.1 $
+ *            $Date: 2004/04/15 09:12:30 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+
+/*==========================================================================*
+* CLASS DECLARATION
+*==========================================================================*/
+/**
+ *
+ */
+public class MainAdapterImpl implements MainAdapter {
+  static final public String MAIN_ADAPTER_NAME = "MainRemoteObjectName";
+  static final public int PORT = 1099;
+  static public boolean TRACE = false;
+  private String m_Buf = "";
+  private MainAdapter m_RemoteThis;
+  /**
+   *
+   */
+  public MainAdapterImpl() {
+    if (TRACE) System.out.println("Constructor MainAdapterImpl !!!!!!");
+    m_RemoteThis = this;
+  }
+  /**
+   *
+   */
+  public void setBuf(String s) {
+    if (TRACE) System.out.println("MainAdapterImpl.setBuf:"+s);
+    m_Buf = s;
+  }
+  /**
+   *
+   */
+  public void restartServer() {
+    System.out.println("Received message to restartServer !!!!");
+    try {
+      String Out ="";
+      String command = "java -cp .:../lib/jdom.jar:../lib/log4j.jar javaeva.server.EvAServer &";
+
+      System.out.println("Calling the command:"+"java javaeva.server.EvAServer");
+      Process pro =  Runtime.getRuntime().exec(command);
+      BufferedReader in = new  BufferedReader ( new InputStreamReader (pro.getInputStream()));
+//      String line = null;
+//      while((line = in.readLine()) != null ) {
+//        System.out.println(line);
+//        Out = Out + line;
+//      }
+      System.out.println("command="+command);
+    } catch (Exception e) {
+      System.out.println("Error in calling the command:"+e.getMessage());
+    }
+    killServer();
+  }
+  /**
+   *
+   */
+  public void killServer() {
+    //Mail.SendMail("Received message to kill EvAServer");
+    System.out.println("Received message to kill EvAServer !!!!");
+    KillThread x = new KillThread();
+    x.start();
+    return;
+  }
+
+  /**
+   *
+   */
+  public String getBuf() {
+    return m_Buf;
+  }
+  /**
+   *
+   */
+  public String getExecOutput(String command) {
+    String Out= new String();
+    try {
+      BufferedReader in = null;
+      Process pro = null;
+      if (TRACE) System.out.println("Calling the command:"+command);
+      pro = Runtime.getRuntime().exec(command);
+      in = new  BufferedReader ( new InputStreamReader (pro.getInputStream()));
+      String line = null;
+      while((line = in.readLine()) != null ) {
+    	  if (TRACE) System.out.println(line);
+        Out = Out + line;
+      }
+    } catch (Exception e) {
+      System.err.println("Error in calling the command:"+e.getMessage());
+    }
+    return Out;
+  }
+  /**
+   *
+  */
+  public RMIInvocationHandler getRMIHandler(Object obj) {
+    System.out.println("getRMIHandler");
+    RMIInvocationHandler ret = null;
+    try {
+      ret = new RMIInvocationHandlerImpl(obj);
+    }
+    catch (Exception e) {
+      System.out.println("Error: RMIInvokationHandler getRMIHandler");
+    }
+    return ret;
+  }
+   /**
+   *
+  */
+  public RMIThreadInvocationHandler getRMIThreadHandler(Object obj) {
+    if (TRACE) System.out.println("getRMIThreadHandler");
+    RMIThreadInvocationHandler ret = null;
+    try {
+
+      ret = new RMIThreadInvocationHandlerImpl(obj);
+    }
+    catch (Exception e) {
+      System.out.println("Error: RMIThreadInvokationHandler getRMIThreadHandler");
+    }
+    return ret;
+  }
+  /**
+   *
+   */
+  public void setRemoteThis (MainAdapter x) {
+    m_RemoteThis = x;
+  }
+}
+/**
+ *
+ */
+class KillThread extends Thread {
+  /**
+   *
+   */
+  public void run() {
+    try {sleep(3000);}
+    catch(Exception e) {
+      System.out.println("Error in sleep");
+    }
+    System.exit(-1);
+  }
+}

src/wsi/ra/jproxy/NO_RMIServerAvailable.java

@@ -0,0 +1,24 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.1 $
+ *            $Date: 2004/04/15 09:12:30 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+/**
+ * This exception will be thrown when no
+ * RMIServer con be found by the ComAdapter.
+ */
+public class NO_RMIServerAvailable extends Exception {
+  NO_RMIServerAvailable() {
+    printStackTrace();
+  }
+
+}

src/wsi/ra/jproxy/RMIConnection.java

@@ -0,0 +1,98 @@
+package wsi.ra.jproxy;
+
+
+/**
+ *
+ */
+public class RMIConnection {
+  public static boolean TRACE = false;
+  private String m_HostName;
+  protected MainAdapter m_MainAdapter;
+  protected MainAdapterClient m_MainAdapterClient;
+  /**
+   *
+   */
+  public RMIConnection(String HostName, MainAdapter Adapter,
+                       MainAdapterClient AdapterClient) {
+    m_MainAdapter = Adapter;
+    m_HostName = HostName;
+    m_MainAdapterClient = AdapterClient;
+  }
+
+  /**
+   *
+   */
+  public String getHostName() {
+    return m_HostName;
+  }
+
+  /**
+   *
+   */
+  public MainAdapter getMainAdapter() {
+    return m_MainAdapter;
+  }
+
+  /**
+   *
+   */
+  public void killServer() {
+    try {
+      m_MainAdapter.killServer();
+    } catch (Exception e) {
+      System.out.println("Error while killing server: " + e.getMessage());
+    }
+  }
+
+  /**
+   *
+   */
+  public void restartServer() {
+    try {
+      m_MainAdapter.restartServer();
+    } catch (Exception e) {
+      System.out.println("Error while restartServer server: " + e.getMessage());
+    }
+  }
+
+  /**
+   *
+   */
+  public RMIInvocationHandler getRMIHandler(Object c) {
+    RMIInvocationHandler ret = null;
+    try {
+      ret = m_MainAdapter.getRMIHandler(c);
+    } catch (Exception e) {
+      System.out.println("Error while getRMIHandler server: " + e.getMessage());
+      e.printStackTrace();
+    }
+    return ret;
+  }
+
+  /**
+   *
+   */
+  public RMIThreadInvocationHandler getRMIThreadHandler(Object c) {
+    RMIThreadInvocationHandler ret = null;
+    try {
+      ret = m_MainAdapter.getRMIThreadHandler(c);
+    } catch (Exception e) {
+      System.out.println("Error while RMIThreadInvokationHandler server: " +
+                         e.getMessage());
+    }
+    return ret;
+  }
+
+  /**
+   *
+   */
+  public String getExecOutput(String command) {
+    String ret = null;
+    try {
+      ret = m_MainAdapter.getExecOutput(command);
+    } catch (Exception e) {
+      System.out.println("Error while getExecOutput server: " + e.getMessage());
+    }
+    return ret;
+  }
+}

src/wsi/ra/jproxy/RMIInvocationHandler.java

@@ -0,0 +1,27 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.1 $
+ *            $Date: 2004/04/15 09:12:30 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.rmi.Remote;
+import java.rmi.RemoteException;
+/*==========================================================================*
+* INTERFACE DECLARATION
+*==========================================================================*/
+/**
+ *
+ */
+public interface RMIInvocationHandler extends Remote {
+  public Object invoke (String m, Object[] args)throws RemoteException;
+  public Object getWrapper () throws RemoteException;
+  public void setWrapper(Object Wrapper)  throws RemoteException;
+}

src/wsi/ra/jproxy/RMIInvocationHandlerImpl.java

@@ -0,0 +1,128 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.2 $
+ *            $Date: 2004/07/31 20:02:09 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import wsi.ra.math.RNG;
+import java.rmi.RemoteException;
+import java.rmi.Naming;
+import java.rmi.server.UnicastRemoteObject;
+import java.lang.reflect.Method;
+import java.lang.reflect.InvocationTargetException;
+/*==========================================================================*
+* CLASS DECLARATION
+*==========================================================================*/
+/**
+ *
+ */
+public class RMIInvocationHandlerImpl extends UnicastRemoteObject implements RMIInvocationHandler {
+  public static final boolean TRACE = false;
+  private Object m_Object;
+  private String m_AdapterName;
+  private Object m_Wrapper;
+  private Method[] m_list;// m_Object.getClass().getMethods();
+  /**
+   *
+   */
+  public RMIInvocationHandlerImpl(Object obj)  throws RemoteException {
+    if (TRACE) System.out.println("RMIInvokationHandlerImpl");
+    m_AdapterName = obj.getClass().getName()+"_"+RNG.randomInt(0,10000);
+    try {
+      m_Object = obj;
+      m_list = m_Object.getClass().getMethods();
+      if (TRACE) System.out.println(" --> rebind : "+m_AdapterName+" RMIInvokationHandlerImpl of object "+obj.getClass().getName());
+      Naming.rebind(m_AdapterName,this);
+    } catch (Exception e) {
+      System.err.println(" Naming.rebind --> ERROR" + e.getMessage());
+      e.printStackTrace();
+    }
+  }
+  /**
+   *
+   */
+  public RMIInvocationHandlerImpl(Object obj,String AdapterName)  throws RemoteException {
+    m_AdapterName = AdapterName;
+    try {
+      m_Object = obj;
+       m_list = m_Object.getClass().getMethods();
+      if (TRACE) System.out.println(" -----> rebind : "+m_AdapterName+" "+this.getClass().getName()+" of object "+obj.getClass().getName());
+      Naming.rebind(m_AdapterName,this);
+    } catch (Exception e) {
+      System.err.println(" Naming.rebind --> ERROR " + obj + " " + e.getMessage());
+      e.printStackTrace();
+    }
+  }
+  /**
+   *
+   */
+  public void setWrapper(Object Wrapper)  throws RemoteException {
+    m_Wrapper = Wrapper;
+  }
+  /**
+   *
+   */
+  public Object getWrapper () throws RemoteException {
+    return m_Wrapper;
+  }
+
+  /**
+   *
+   */
+  public Object invoke (String m, Object[] args) throws RemoteException {
+    Object ret=null;
+    String Name = "";
+    //System.out.println("calling "+m);
+    if (TRACE) Name = Thread.currentThread().getName();
+    try {
+      if (TRACE) System.out.println( Name+" Before invoke on server :" +m);
+      //Method[] list = m_Object.getClass().getMethods();
+      boolean invoked = false;
+      for (int i=0;i<m_list.length;i++) {
+        if (TRACE)  System.out.println(Name+" list[i].getName() "+m_list[i].getName());
+
+//        if (m.equals("free")==true) {
+//          System.out.println("called free !!!!!!!!!!!!!!!!!!!!!!!!!"+m_AdapterName);
+//          String[] list = Naming.list("rmi://localhost:" + MainAdapterImpl.PORT);
+//          System.out.println("-->list :"+list.length);
+//          for (int j = 0; j < list.length; j++){
+//            System.out.println("list="+list[j]+"--"+m_AdapterName);
+//            if (list[j].lastIndexOf(m_AdapterName)!=-1) {
+//              System.out.println("unbind !!!!!!!!!!!!!!!!!!!!!!!!!!");
+//              Naming.unbind(list[j]);
+//
+//              return null;
+//            }
+//          }
+//          System.out.println("Object not found !!!!!");
+//          return null;
+//        }
+        if (m.equals(m_list[i].getName())==true) {
+          if (TRACE)  System.out.println(Name+" find "+m);
+          //if (args==null) System.out.println(Name+" args==null ");
+          ret = m_list[i].invoke(m_Object,args);
+          invoked= true;
+          break;
+        }
+      }
+      if (invoked==false) System.out.println(Name+ " No memberfunction found !!!!!!!!!!!!!!!!!");
+    }
+    catch ( InvocationTargetException e) {
+      e.printStackTrace();
+      System.out.println(Name+" RMIInvokationHandlerImpl  InvocationTargetException "+e.getMessage());
+    }
+    catch (Exception e) {
+      e.printStackTrace();
+      System.out.println(Name+" Exception :"+e.getMessage());
+    }
+    return ret;
+  }
+}

src/wsi/ra/jproxy/RMIProxyLocal.java

@@ -0,0 +1,111 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.2 $
+ *            $Date: 2004/04/15 12:28:34 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.io.Serializable;
+import java.lang.reflect.InvocationHandler;
+import java.lang.reflect.Method;
+import java.lang.reflect.Proxy;
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+/**
+ *
+ */
+public class RMIProxyLocal implements InvocationHandler, Serializable {
+	private RMIInvocationHandler m_RMIHandler;
+	public static boolean TRACE = false;
+	private Class originalClass = null;
+	/**
+	 *
+	 */
+	public static Object newInstance (Object c, String RMIName) {
+		if (TRACE) System.out.println("RMIProxyLocal:"+c.getClass().getName());
+		RMIProxyLocal proxyLocal = new RMIProxyLocal(c,RMIName);
+		Object ret = java.lang.reflect.Proxy.newProxyInstance (
+				c.getClass().getClassLoader(),
+				c.getClass().getInterfaces(),
+				proxyLocal);
+		proxyLocal.setWrapper(ret); 
+		proxyLocal.setOriginalClass(c.getClass());
+		if (TRACE) System.out.println(" --> " + ret.getClass());
+		return ret;
+	}
+	/**
+	 *
+	 */
+	public static Object newInstance (Object c) {
+		if (TRACE) System.out.println("RMIProxyLocal:"+c.getClass().getName());
+		RMIProxyLocal proxyLocal = new RMIProxyLocal(c);
+		Object ret = java.lang.reflect.Proxy.newProxyInstance (
+				c.getClass().getClassLoader(),
+				c.getClass().getInterfaces(),
+				proxyLocal);
+		proxyLocal.setWrapper(ret);
+		proxyLocal.setOriginalClass(c.getClass());
+		if (TRACE) System.out.println(" --> " + ret.getClass());
+		return ret;
+	}
+	/**
+	 *
+	 */
+	private RMIProxyLocal (Object c) {
+		if (TRACE) System.out.println("RMIProxyLocal:"+c.getClass().getName());
+		try {
+			m_RMIHandler = new RMIInvocationHandlerImpl(c);
+		} catch (Exception e) {
+			System.err.println("Error in m_RMIHandler = new RMIInvokationHandlerImpl(c)");
+			e.printStackTrace();
+		}
+	}
+	/**
+	 *
+	 */
+	private RMIProxyLocal (Object c,String RMIName) {
+		try {
+			m_RMIHandler = new RMIInvocationHandlerImpl(c,RMIName);
+		} catch (Exception e) {
+			System.out.println("Error in m_RMIHandler = new RMIInvokationHandlerImpl(c)");
+			e.printStackTrace();
+		}
+	}
+	/**
+	 *
+	 */
+	public void setWrapper(Object Wrapper) {
+		try {
+			m_RMIHandler.setWrapper(Wrapper);
+		} catch (Exception e) {
+			System.out.println("Error in setWrapper "+e.getMessage());
+		}
+	}
+
+	/**
+	 *
+	 */
+	public Object invoke (Object proxy, Method m, Object[] args) throws Throwable {
+		return m_RMIHandler.invoke(m.getName(),args);
+	}
+	/**
+	 * @return the originalClass
+	 */
+	public Class getOriginalClass() {
+		return originalClass;
+	}
+	/**
+	 * @param originalClass the originalClass to set
+	 */
+	public void setOriginalClass(Class originalClass) {
+		if (TRACE) System.out.println("setting original proxy class "+originalClass.getName());
+		this.originalClass = originalClass;
+	}
+}

src/wsi/ra/jproxy/RMIProxyLocalThread.java

@@ -0,0 +1,116 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.1 $
+ *            $Date: 2004/04/15 09:12:30 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.io.Serializable;
+import java.lang.reflect.InvocationHandler;
+import java.lang.reflect.Method;
+ /*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+/**
+ *
+ */
+public class RMIProxyLocalThread implements InvocationHandler,Serializable {
+  private RMIInvocationHandler m_RMIHandler;
+  private final static boolean TRACE = true; 
+  /**
+   *
+   */
+  public static Object newInstance (Object c,String RMIName) {
+    //System.out.println("RMIProxyLocal.newInstance !!!!!!!!!!!!!!!");
+    RMIProxyLocalThread Proxy = new RMIProxyLocalThread(c,RMIName);
+    Object ret = java.lang.reflect.Proxy.newProxyInstance (
+      c.getClass().getClassLoader(),
+      c.getClass().getInterfaces(),
+      Proxy);
+    Proxy.setWrapper(ret);
+    if (TRACE) System.out.println("RMIProxyLocalThread "+c.getClass() + " ret " + ret.getClass());
+    return ret;
+  }
+  /**
+   *
+   */
+  public static Object newInstance (Object c) {
+    RMIProxyLocalThread Proxy = new RMIProxyLocalThread(c);
+    Object ret = java.lang.reflect.Proxy.newProxyInstance (
+      c.getClass().getClassLoader(),
+      c.getClass().getInterfaces(),
+      Proxy);
+    Proxy.setWrapper(ret);
+    if (TRACE) System.out.println("RMIProxyLocalThread "+c.getClass() + " ret " + ret.getClass());
+    return ret;
+  }
+  /**
+   *
+   */
+  private RMIProxyLocalThread (Object c) {
+     System.out.println("RMIProxyLocal:"+c.getClass().getName());
+    try {
+      m_RMIHandler = new RMIInvocationHandlerImpl(ThreadProxy.newInstance(c));
+    } catch (Exception e) {
+      System.out.println("Error in m_RMIHandler = new RMIInvokationHandlerImpl(c)");
+      e.printStackTrace();
+    }
+  }
+  /**
+   *
+   */
+  private RMIProxyLocalThread (Object c,String RMIName) {
+    System.out.println("RMIProxyLocal:"+RMIName);
+    System.out.println("RMIProxyLocal:"+c.getClass().getName());
+
+    try {
+      m_RMIHandler = new RMIInvocationHandlerImpl(ThreadProxy.newInstance(c),RMIName);
+    } catch (Exception e) {
+      System.out.println("Error in m_RMIHandler = new RMIInvokationHandlerImpl(c)");
+       e.printStackTrace();
+    }
+  }
+  /**
+   *
+   */
+  public void setWrapper(Object Wrapper) {
+    try {
+      m_RMIHandler.setWrapper(Wrapper);
+    } catch (Exception e) {
+      System.out.println("Error in setWrapper "+e.getMessage());
+    }
+  }
+
+  /**
+   *
+   */
+   public Object invoke (Object proxy, Method m, Object[] args) throws Throwable {
+    //long start = System.currentTimeMillis();
+    //System.out.println("Before invoke:" +m.getName());
+    //Object ret = m_RMIHandler.invoke(m.getName(),args);
+    //long finish = System.currentTimeMillis();
+    //System.out.println("Calling :"+m.getName()+" of "+m_ObjectName+ " time :"+(finish-start));
+    //return ret;
+    return m_RMIHandler.invoke(m.getName(),args);
+  }
+  /**
+   *
+   */
+  public static void main(String[] args) {
+      //
+    //Doit x = new DoitImpl();
+//    Doit xx = (Doit) RMIProxyRemote.newInstance(x,"primergy4.informatik.uni-tuebingen.de");
+//    Doit2 yy = (Doit2) RMIProxyLocal.newInstance(new Doit2Impl());
+//    System.out.println(" jhdfjldf");
+//    yy.doit();
+//    yy.doit();
+
+//    xx.newdoit(yy);
+  }
+}

src/wsi/ra/jproxy/RMIProxyRemote.java

@@ -0,0 +1,116 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.1 $
+ *            $Date: 2004/04/15 09:12:30 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.io.Serializable;
+import java.lang.reflect.InvocationHandler;
+import java.lang.reflect.Method;
+ /*==========================================================================*
+* CLASS DECLARATION
+*==========================================================================*/
+/**
+ *
+ */
+
+public class RMIProxyRemote implements InvocationHandler,Serializable {
+  private static ComAdapter m_Adapter;
+  private static boolean TRACE = true;
+  private Object m_Object;
+  private String m_ObjectName;
+  private RMIInvocationHandler m_RMIHandler=null;
+  private long m_counter=0;
+  /**
+   *
+   */
+  public static Object newInstance (Object c,MainAdapterClient Client) {
+    return java.lang.reflect.Proxy.newProxyInstance (
+      c.getClass().getClassLoader(),
+      c.getClass().getInterfaces(),
+      new RMIProxyRemote(c,Client));
+  }
+  /**
+   *
+   */
+  public static Object newInstance (Object c,String host) {
+    return java.lang.reflect.Proxy.newProxyInstance (
+      c.getClass().getClassLoader(),
+      c.getClass().getInterfaces(),
+      new RMIProxyRemote(c,host));
+  }
+  /**
+   *
+   */
+  public static Object newInstance (Object c) {
+    return java.lang.reflect.Proxy.newProxyInstance (
+      c.getClass().getClassLoader(),
+      c.getClass().getInterfaces(),
+      new RMIProxyRemote(c));
+  }
+  /**
+   *
+   */
+  public static void setComAdaper(ComAdapter x) {
+    m_Adapter = x;
+  }
+  /**
+   *
+   */
+  private RMIProxyRemote (Object c, String host) {
+    m_ObjectName = c.getClass().getName();
+    if (m_Adapter==null) m_Adapter = ComAdapter.getInstance();
+    m_RMIHandler = m_Adapter.getRMIHandler(c,host);
+    if (TRACE) System.out.println("creating RMIProxyRemote " + c.getClass() + " " + host);
+  }
+  /**
+   *
+   */
+  private RMIProxyRemote (Object c, MainAdapterClient Client) {
+    m_ObjectName = c.getClass().getName();
+    try {
+      m_RMIHandler = Client.getRMIHandler(c);
+    } catch (Exception e) {
+      System.out.println("RMIProxyRemote error ex "+e.getMessage());
+      e.printStackTrace();
+    }
+    if (TRACE) System.out.println("creating RMIProxyRemote " + c.getClass() + " " + Client.getClass());
+  }
+  /**
+   *
+   */
+  private RMIProxyRemote (Object c) {
+    m_ObjectName = c.getClass().getName();
+    if (m_Adapter==null) m_Adapter = ComAdapter.getInstance();
+    m_RMIHandler = m_Adapter.getRMIHandler(c);
+  }
+  /**
+   *
+   */
+   public Object invoke (Object proxy, Method m, Object[] args) throws Throwable {
+    long start = System.currentTimeMillis();
+    ++m_counter;
+    //System.out.println("Before invoke:" +m.getName());
+    Object ret = m_RMIHandler.invoke(m.getName(),args);
+    long finish = System.currentTimeMillis();
+    //System.out.println("Calling :"+m.getName()+" of "+m_ObjectName+ " time :"+(finish-start));
+    return ret;
+  }
+  /**
+   *
+   */
+//  public static void main(String[] args) {
+//    Doit remotex = (Doit) RMIProxyRemote.newInstance(new DoitImpl(),"primergy4.informatik.uni-tuebingen.de");
+//    remotex.doit();
+//    remotex.doit();
+//    remotex.doit();
+//    remotex.doit();
+//  }
+}

src/wsi/ra/jproxy/RMIProxyRemoteThread.java

@@ -0,0 +1,136 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.2 $
+ *            $Date: 2004/04/28 07:50:33 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.io.Serializable;
+import java.lang.reflect.InvocationHandler;
+import java.lang.reflect.Method;
+/*==========================================================================*
+* CLASS DECLARATION
+*==========================================================================*/
+/**
+ *
+ */
+public class RMIProxyRemoteThread implements InvocationHandler,
+                                             Serializable {
+  private static ComAdapter m_Adapter;
+  private Object m_Object;
+  private String m_ObjectName;
+  private RMIThreadInvocationHandler m_RMIThreadHandler;
+  /**
+   *
+   */
+  public static Object newInstance (Object c,MainAdapterClient Client) {
+    return java.lang.reflect.Proxy.newProxyInstance (
+      c.getClass().getClassLoader(),
+      c.getClass().getInterfaces(),
+      new RMIProxyRemoteThread(c,Client));
+  }
+  /**
+   *
+   */
+  public static Object newInstance (Object c,String host) {
+    return java.lang.reflect.Proxy.newProxyInstance (
+      c.getClass().getClassLoader(),
+      c.getClass().getInterfaces(),
+      new RMIProxyRemoteThread(c,host));
+  }
+  /**
+   *
+   * @param c
+   * @return
+   */
+  public static String[] getServerList() {
+    if (m_Adapter==null) m_Adapter = ComAdapter.getInstance();
+      m_Adapter.evalAvailableHostNameList();
+    return m_Adapter.getAvailableHostNameList();
+
+  }
+  public static void setServerList(String[] servers ) {
+    if (m_Adapter==null) m_Adapter = ComAdapter.getInstance();
+
+    m_Adapter.setServerList(servers);
+     m_Adapter.evalAvailableHostNameList();
+
+  }
+
+  /**
+   *
+   */
+  public static Object newInstance (Object c) {
+    return java.lang.reflect.Proxy.newProxyInstance (
+      c.getClass().getClassLoader(),
+      c.getClass().getInterfaces(),
+      new RMIProxyRemoteThread(c));
+  }
+  /**
+   *
+   */
+  public static void setComAdaper(ComAdapter x) {
+    m_Adapter = x;
+  }
+  /**
+   *
+   */
+  private RMIProxyRemoteThread (Object c, String host) {
+    m_ObjectName = c.getClass().getName();
+    if (m_Adapter==null) m_Adapter = ComAdapter.getInstance();
+    m_RMIThreadHandler = m_Adapter.getRMIThreadHandler(c,host);
+  }
+  /**
+   *
+   */
+  private RMIProxyRemoteThread (Object c, MainAdapterClient Client) {
+    m_ObjectName = c.getClass().getName();
+    try {
+      m_RMIThreadHandler = Client.getRMIThreadHandler(c);
+    } catch (Exception e) {
+      System.out.println("RMIProxyRemoteThreaderror ex "+e.getMessage());
+      e.printStackTrace();
+    }
+  }
+  /**
+   *
+   */
+  private RMIProxyRemoteThread (Object c) {
+    m_ObjectName = c.getClass().getName();
+    if (m_Adapter==null) m_Adapter = ComAdapter.getInstance();
+    m_RMIThreadHandler = m_Adapter.getRMIThreadHandler(c);
+  }
+  /**
+   *
+   */
+   public Object invoke (Object proxy, Method m, Object[] args) throws Throwable {
+    //long start = System.currentTimeMillis();
+    //System.out.println("Before invoke:" +m.getName());
+    Object ret = null;
+    if (m.getName().equals("getServerName")) {
+      ret = m_RMIThreadHandler.getServerName();
+    } else {
+      ret = m_RMIThreadHandler.invoke(m.getName(), args);
+    }
+    //long finish = System.currentTimeMillis();
+    //System.out.println("Calling :"+m.getName()+" of "+m_ObjectName+ " time :"+(finish-start));
+    return ret;
+  }
+  /**
+   *
+   */
+//  public static void main(String[] args) {
+//    Doit remotex = (Doit) RMIProxyRemoteThread.newInstance(new DoitImpl(),
+//      "ranode1.informatik.uni-tuebingen.de");
+//    remotex.doit();
+//    remotex.doit();
+//    remotex.doit();
+//    remotex.doit();
+//  }
+}

src/wsi/ra/jproxy/RMIServer.java

@@ -0,0 +1,194 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.1 $
+ *            $Date: 2004/04/15 09:12:31 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.net.InetAddress;
+import java.net.MalformedURLException;
+import java.net.UnknownHostException;
+import java.rmi.Naming;
+import java.rmi.RemoteException;
+import java.rmi.registry.Registry;
+///////////////////////////////////////////////////////////////
+// -Xrunhprof:cpu=times
+// -Djava.security.policy=server.policy
+///////////////////////////////////////////////////////////////
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+/**
+ *
+ */
+public class RMIServer {
+  /* Version string of the server application. */
+  public static boolean TRACE = false;
+//  public static Registry m_Registry;
+  protected static RMIServer m_instance;
+  /* Name of host on which the server is running. */
+  private String m_MyHostName = "undefined";
+  /* IP of host on which the server is running. */
+  private String m_MyHostIP = "undefined";
+  /* MainAdapterImp object. This is need for the first
+    connection between the server and the client program.  */
+  public MainAdapter m_MainRemoteObject;
+  /* String describing the properties of the enviroment. */
+//  private ComAdapter m_ComAdapter;
+  public static String m_UserName;
+  public static int m_NumberOfVM = 0;
+  Registry m_Registry = null;
+  
+  /**
+   *
+   */
+  public static RMIServer getInstance() {
+	  if (m_instance == null) {
+		  m_instance = new RMIServer();
+	  }
+	  return m_instance;
+  }
+  /**
+   * Constructor of EvAServer.
+   * Calls RMIConnection().
+   */
+  protected RMIServer() {
+    m_UserName = System.getProperty("user.name");
+    //System.out.println(EVAHELP.getSystemPropertyString());
+    initConnection();
+//    m_ComAdapter = ComAdapter.getInstance();
+  }
+
+  /**
+   * Main method of this class.
+   * Is the starting point of the server application.
+   */
+  static public void main(String[] args) {
+    System.out.println("Start RMIServer !");
+    RMIServer Application = RMIServer.getInstance();
+  }
+
+
+  /**
+   * Launchs the RMIRegistry and makes the registration
+   * of the MainAdapterImpl class at the rmiregistry.
+   * @param
+   */
+  private void initConnection() {
+    String MainAdapterName = m_UserName + MainAdapterImpl.MAIN_ADAPTER_NAME;
+    System.setProperty("java.security.policy", "server.policy");
+    launchRMIRegistry();
+    try {
+        m_MyHostIP = InetAddress.getLocalHost().getHostAddress();
+        m_MyHostName = InetAddress.getLocalHost().getHostName();
+    } catch (Exception e) {
+      System.out.println("ERROR getting HostName (RMIServer.initConnection)" + e.getMessage());
+    }
+    System.out.println("Start of EvA RMI-Server on host " + m_MyHostName + " = " + m_MyHostIP);
+//    Object test = null;
+    try {
+      try {
+        String[] list =
+                Naming.list("rmi://localhost:" + MainAdapterImpl.PORT);
+//        System.out.println("-->list");
+//        for (int i = 0; i < list.length; i++)
+//          System.out.println("-->RMIName" + list[i]);
+        m_NumberOfVM = getNumberOfVM(list);
+      } catch (RemoteException e) {
+    	  System.err.println("no RMI registry available yet...");
+        if (TRACE)
+          System.out.println(
+                  "RemoteException OK IAM the first server for this rmiregistry: "
+                  + e.getMessage());
+      }
+    } catch (MalformedURLException ex) {
+      System.out.println(
+              "MalformedURLException: Error while looking up "
+              + ex.getMessage());
+    }
+    createMainRemoteObject(MainAdapterName);
+    
+    System.out.println("End of RMI-Server Initialisation");
+    System.out.println(" --> OK on Host: " + m_MyHostName + " = " + m_MyHostIP + ", adapter name is " + MainAdapterName);
+    System.out.println("Waiting for a client ..............");
+  }
+
+  protected void createMainRemoteObject(String mainAdapterName) {
+	  try {
+		  m_MainRemoteObject = new MainAdapterImpl();
+		  m_MainRemoteObject =
+			  (MainAdapter) RMIProxyLocal.newInstance(m_MainRemoteObject,mainAdapterName + "_" + m_NumberOfVM);
+		  m_MainRemoteObject.setRemoteThis(m_MainRemoteObject);
+	  } catch (Exception e) {
+		  e.printStackTrace();
+	  }
+  }
+  
+  /**
+   *
+   */
+  public MainAdapter getMainRemoteObject() {
+    return m_MainRemoteObject;
+  }
+
+  /**
+   * Install RMIregistry on default port !!
+   */
+  private void launchRMIRegistry() {
+    if (TRACE)
+      System.out.println(
+              "LaunchRMIRegistry on Server on PORT " + MainAdapterImpl.PORT);
+    try {
+      m_Registry =
+              java.rmi.registry.LocateRegistry.createRegistry(
+              MainAdapterImpl.PORT);
+    } catch (Throwable e) {
+      if (TRACE)
+        System.out.println("Registry not created !!" + e.getMessage());
+      m_Registry = null;
+    }
+    if (m_Registry == null) {
+      System.out.println(
+              "Try to get registry with getRegistry on PORT "
+              + MainAdapterImpl.PORT);
+      try {
+        m_Registry =
+                java.rmi.registry.LocateRegistry.getRegistry(
+                MainAdapterImpl.PORT);
+        if (TRACE)
+          System.out.println(
+                  "m_Registry.REGISTRY_PORT=" + m_Registry.REGISTRY_PORT);
+      } catch (Throwable e) {
+        if (TRACE)
+          System.out.println(
+                  "registry notcreated !!" + e.getMessage());
+        m_Registry = null;
+      }
+    }
+    if (m_Registry == null) {
+    	System.err.println("--> got no RMIREGISTRY");
+    } else if (TRACE) System.out.println("--> got RMIREGISTRY");
+  }
+  
+  /**
+   *
+   */
+  private int getNumberOfVM(String[] list) {
+    int ret = 0;
+    for (int i = 0; i < list.length; i++) {
+      if (list[i].indexOf(MainAdapterImpl.MAIN_ADAPTER_NAME) != -1)
+        ret++;
+    }
+    if (TRACE)
+      System.out.println(" getNumberOfVM()  NumberOfVM =" + ret);
+    return ret;
+  }
+}
+
+

src/wsi/ra/jproxy/RMIThreadInvocationHandler.java

@@ -0,0 +1,27 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.1 $
+ *            $Date: 2004/04/15 09:12:31 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.rmi.Remote;
+import java.rmi.RemoteException;
+/*==========================================================================*
+* INTERFACE DECLARATION
+*==========================================================================*/
+/**
+ *
+ */
+public interface RMIThreadInvocationHandler extends Remote {
+  public Object invoke (String m, Object[] args)throws RemoteException;
+  public Object getWrapper () throws RemoteException;
+  public void setWrapper(Object Wrapper)  throws RemoteException;
+  public String getServerName()throws RemoteException;
+}

src/wsi/ra/jproxy/RMIThreadInvocationHandlerImpl.java

@@ -0,0 +1,147 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.2 $
+ *            $Date: 2004/04/15 12:28:34 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.net.InetAddress;
+import java.rmi.Naming;
+import java.rmi.RemoteException;
+import java.rmi.server.UnicastRemoteObject;
+
+import wsi.ra.math.RNG;
+/*==========================================================================*
+* CLASS DECLARATION
+*==========================================================================*/
+/**
+ *
+ */
+public class RMIThreadInvocationHandlerImpl extends UnicastRemoteObject implements RMIThreadInvocationHandler {
+  public static final boolean TRACE = false;
+  private Object m_Object;
+  private String m_AdapterName;
+  private Object m_Wrapper;
+  private Method[] m_list;
+  private String m_hostname;
+  /**
+   *
+   * @return
+   */
+  public String getServerName() {
+    return m_hostname;
+  }
+  /**
+   *
+   */
+  public RMIThreadInvocationHandlerImpl(Object obj)  throws RemoteException {
+    try {
+      m_hostname = InetAddress.getLocalHost().getHostName();
+    }
+    catch (Exception e) {
+      System.out.println("ERROR getting HostName (RMIThreadInvokationHandlerImpl(obj))" + e.getMessage());
+    }
+
+    m_AdapterName = obj.getClass().getName()+"_"+RNG.randomInt(0,10000);
+    try {
+      m_Object = ThreadProxy.newInstance(obj);
+      m_list = m_Object.getClass().getMethods();
+       if (TRACE) System.out.println(" --> rebind : "+m_AdapterName+" RMIThreadInvokationHandlerImpl of object "+obj.getClass().getName());
+      Naming.rebind(m_AdapterName,this);
+    } catch (Exception e) {
+      System.out.println(" Naming.rebind --> ERROR" + e.getMessage());
+      e.printStackTrace();
+    }
+  }
+  /**
+   *
+   */
+  public RMIThreadInvocationHandlerImpl(Object obj,String AdapterName)  throws RemoteException {
+    try {
+      m_hostname = InetAddress.getLocalHost().getHostName();
+    }
+    catch (Exception e) {
+      System.out.println("ERROR getting HostName (RMIThreadInvokationHandlerImpl(obj,adapt))" + e.getMessage());
+    }
+
+    m_AdapterName = AdapterName;
+    try {
+       m_Object = ThreadProxy.newInstance(obj);
+       m_list = m_Object.getClass().getMethods();
+      if (TRACE) System.out.println(" -----> rebind : "+m_AdapterName+" "+this.getClass().getName()+" of object "+obj.getClass().getName());
+      Naming.rebind(m_AdapterName,this);
+    } catch (Exception e) {
+      System.out.println(" Naming.rebind --> ERROR" + e.getMessage());
+    }
+  }
+  /**
+   *
+   */
+  public void setWrapper(Object Wrapper)  throws RemoteException {
+    m_Wrapper = Wrapper;
+  }
+  /**
+   *
+   */
+  public Object getWrapper () throws RemoteException {
+    return m_Wrapper;
+  }
+  /**
+   *
+   */
+  public Object invoke (String m, Object[] args) throws RemoteException {
+    Object ret=null;
+    String Name = "";
+    if (TRACE) Name = Thread.currentThread().getName();
+    try {
+      if (TRACE) System.out.println( Name+" Before invoke on server :" +m);
+      //Method[] list = m_Object.getClass().getMethods();
+      boolean invoked = false;
+      for (int i=0;i<m_list.length;i++) {
+        //if (TRACE)  System.out.println(Name+" list[i].getName() "+list[i].getName());
+        if (m.startsWith("free") == true) {
+//          System.out.println("called free !!!!!!!!!!!!!!!!!!!!!!!!!" + m_AdapterName);
+          String[] list = Naming.list("rmi://localhost:" + MainAdapterImpl.PORT);
+//          System.out.println("-->list :" + list.length);
+          for (int j = 0; j < list.length; j++) {
+//            System.out.println("list=" + list[j] + "--" + m_AdapterName);
+            if (list[j].lastIndexOf(m_AdapterName) != -1) {
+//              System.out.println("unbind !!!!!!!!!!!!!!!!!!!!!!!!!!");
+              Naming.unbind(list[j]);
+              return null;
+            }
+
+          }
+          System.out.println("Object not found !!!!!");
+          return null;
+        }
+
+        if (m.equals(m_list[i].getName())==true) {
+          //if (TRACE)System.out.println(Name+" find "+m);
+          //if (args==null) System.out.println(Name+" args==null ");
+          ret = m_list[i].invoke(m_Object,args);
+          invoked= true;
+          break;
+        }
+      }
+      if (invoked==false) System.out.println(Name+ " No memberfunction found !!!!!!!!!!!!!!!!!");
+    }
+    catch ( InvocationTargetException e) {
+      e.printStackTrace();
+      System.out.println(Name+" RMIThreadInvokationHandlerImpl InvocationTargetException "+e.getMessage());
+    }
+    catch (Exception e) {
+      e.printStackTrace();
+      System.out.println(Name+" Exception :"+e.getMessage());
+    }
+    return ret;
+  }
+}

src/wsi/ra/jproxy/RemoteStateListener.java

@@ -0,0 +1,27 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.1 $
+ *            $Date: 2004/04/15 09:12:30 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+/*==========================================================================*
+* INTERFACE DECLARATION
+*==========================================================================*/
+
+/**
+ *
+ */
+public interface RemoteStateListener {
+  public void performedStop();
+  public void performedStart(String infoString);
+  public void performedRestart(String infoString);
+  public void updateProgress(final int percent);
+}

src/wsi/ra/jproxy/ThreadProxy.java

@@ -0,0 +1,96 @@
+package wsi.ra.jproxy;
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.2 $
+ *            $Date: 2004/04/28 07:50:33 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.io.Serializable;
+import java.lang.reflect.InvocationHandler;
+import java.lang.reflect.Method;
+import java.lang.reflect.Proxy;
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+/**
+ *
+ */
+public class ThreadProxy implements InvocationHandler,
+                                    Serializable {
+  private Object m_Object;
+  private ThreadWrapper m_ThreadWrapper;
+  private int m_maxthreads = 8;
+ /**
+   *
+   */
+  public static Object newInstance (Object obj) {
+      return Proxy.newProxyInstance(
+          obj.getClass().getClassLoader(),
+          obj.getClass().getInterfaces(),
+          new ThreadProxy(obj));
+  }
+  /**
+   *
+   */
+  public static Object newInstance (Object obj,int maxthreads) {
+      return Proxy.newProxyInstance(
+          obj.getClass().getClassLoader(),
+          obj.getClass().getInterfaces(),
+          new ThreadProxy(obj,maxthreads));
+  }
+
+  /**
+   *
+   */
+  public ThreadProxy (Object obj) {
+    m_Object = obj;
+  }
+  /**
+   *
+   */
+  public ThreadProxy (Object obj,int maxthreads) {
+    m_Object = obj;
+    m_maxthreads = maxthreads;
+  }
+
+  /**
+   *
+   */
+   public Object invoke (Object proxy,Method method,Object[] args) throws Throwable {
+    Class rettype = method.getReturnType();
+    if (rettype.equals(Void.TYPE)== true) {
+      if (m_ThreadWrapper == null) {
+        m_ThreadWrapper = new ThreadWrapper(m_maxthreads);
+      }
+      else {
+        m_ThreadWrapper.pleasewait();
+      }
+      m_ThreadWrapper.invoke(m_Object,method,args);
+      return null;
+    }
+    Object ret = null;
+    try {
+      if (method.getName().equals("isAlive")) {
+
+        if (m_ThreadWrapper != null) {
+          Boolean rret = new Boolean(m_ThreadWrapper.isAlive());
+          // System.out.println("calling is alive" +rret);
+          return rret;
+        }
+      }
+      if (m_ThreadWrapper != null)
+        m_ThreadWrapper.pleasewait();
+      ret = method.invoke(m_Object, args);
+    } catch (Exception e) {
+      System.out.println("ERROR +" + e.getMessage());
+      e.printStackTrace();
+    }
+    return ret;
+  }
+}

src/wsi/ra/jproxy/ThreadWrapper.java

@@ -0,0 +1,83 @@
+package wsi.ra.jproxy;
+
+/**
+ * Title:        The JProxy Framework
+ * Description:  API for distributed and parallel computing.
+ * Copyright:    Copyright (c) 2004
+ * Company:      University of Tuebingen
+ * @version:  $Revision: 1.2 $
+ *            $Date: 2004/04/28 07:50:33 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.lang.reflect.Method;
+import java.util.ArrayList;
+import java.io.Serializable;
+
+/*
+ *  ==========================================================================*
+ *  CLASS DECLARATION
+ *  ==========================================================================
+ */
+public class ThreadWrapper extends ArrayList {
+  private int m_counter = 0;
+  private ArrayList m_ThreadContainer = new ArrayList();
+  private static int m_numberofMAXThreads = 4;
+  /**
+   *
+   */
+  public ThreadWrapper(int number) {
+    m_numberofMAXThreads = number;
+  }
+
+  /**
+   *
+   */
+  public ThreadWrapper() {
+  }
+
+  /**
+   *
+   */
+  public synchronized void invoke(Object x, String Method, Object[] Para) {
+    m_ThreadContainer.add(XThread.getXThread(x, Method, Para, m_numberofMAXThreads));
+//    System.out.println("ADDED to THREADWRAPPER LIST" + m_ThreadContainer.size());
+  }
+
+  /**
+   *
+   */
+  public synchronized void invoke(Object x, Method m, Object[] Para) {
+    m_ThreadContainer.add(XThread.getXThread(x, m, Para, m_numberofMAXThreads));
+//  System.out.println("ADDED to THREADWRAPPER LIST" + m_ThreadContainer.size());
+  }
+
+  /**
+   *
+   */
+  public synchronized void pleasewait() {
+    for (int i = 0; i < m_ThreadContainer.size(); i++) {
+      try {
+        ((Thread) m_ThreadContainer.get(i)).join();
+        m_ThreadContainer.remove(i); // testhu
+      } catch (InterruptedException e) {
+        e.printStackTrace();
+        System.out.println("Error");
+      }
+    }
+  }
+
+  /**
+   *
+   */
+  public synchronized boolean isAlive() {
+    for (int i = 0; i < m_ThreadContainer.size(); i++) {
+      boolean alive = ((Thread) m_ThreadContainer.get(i)).isAlive();
+      if (alive == true)
+        return true;
+    }
+    return false;
+  }
+}

src/wsi/ra/jproxy/XThread.java

@@ -0,0 +1,257 @@
+package wsi.ra.jproxy;
+
+import java.lang.reflect.Method;
+import java.util.ArrayList;
+import java.io.Serializable;
+
+/*
+ *  ==========================================================================*
+ *  CLASS DECLARATION
+ *  ==========================================================================
+ */
+public class XThread extends Thread implements Serializable {
+  private Object m_Object;
+  private volatile Method m_Method;
+  private volatile Object[] m_Para;
+  //private static byte m_instances = 0;
+  private static XThread[] m_Instances;
+  private static int m_MAXinstances = 10;
+  private static int m_index = 0;
+
+  public static void init(int x) {
+    m_MAXinstances = x;
+    m_Instances = new XThread[m_MAXinstances];
+    m_index = 0;
+  }
+
+//  private static void instup() {
+//    m_instances++;
+//  }
+//
+//  private static void instdown() {
+//    m_instances--;
+//  }
+
+  public static int get() {
+    int ret =0;
+    if (m_Instances==null) return ret;
+    for (int i=0;i<m_Instances.length;i++) {
+      if (m_Instances[i]==null) continue;
+      if (m_Instances[i].isAlive() == true)
+        ret++;
+    }
+    return ret;
+  }
+
+  /**
+   *
+   */
+  public static XThread getXThread(Object x, Method m, Object[] Para, int MAXinstances) {
+System.out.println("getXThread2 CALLLED");
+    //System.out.println("waiting "+m_instances+ " on "+x.hashCode()+ " m "+m.getName()+" m_MAXinstances " +MAXinstances);
+    XThread ret = null;
+    if (m_Instances == null)
+      init(MAXinstances);
+    if (m_index >= m_Instances.length)
+      m_index = 0;
+    if (m_Instances[m_index] == null) {
+      ret = new XThread(x, m, Para);
+      m_Instances[m_index] = ret;
+      m_index++;
+      return ret;
+    }
+    int w = 1;
+    while (true) {
+      for (int i = 0; i < m_Instances.length; i++) {
+        if (m_Instances[i] == null) {
+          m_index = i;
+          ret = new XThread(x, m, Para);
+          m_Instances[m_index] = ret;
+          m_index++;
+          return ret;
+        }
+        if (m_Instances[i].isAlive() == false) {
+          m_index = i;
+          ret = new XThread(x, m, Para);
+          m_Instances[m_index] = ret;
+          m_index++;
+          return ret;
+
+        }
+      }
+      try {
+        Thread.sleep(w);
+        w = 2 * w; //System.out.println(""+i);
+      } catch (Exception e) {
+        System.out.println("Error in sleep of XThread");
+      }
+
+    } // end of while true
+
+//    int i=1;
+//    while (m_instances >= MAXinstances) {
+//    //      if (i>200)
+//    //     System.out.println(i+ " waiting "+m_instances+ " on "+x.hashCode()+ " m "+m.getName()+" m_MAXinstances " +MAXinstances);
+//    //       pleasewait();
+//      try {
+//        Thread.sleep(i);
+//        i=2*i; //System.out.println(""+i);
+//      } catch (Exception e) {
+//        System.out.println("Error in sleep of XThread");
+//      }
+//    }
+//    instup();//m_instances++;
+//    if (
+//    XThread ret = new XThread(x, m, Para);
+//    //     m_ThreadContainer.add(ret);
+//    return ret;
+
+  }
+
+  /**
+   *
+   */
+  public static XThread getXThread(Object x, String m, Object[] Para, int MAXinstances) {
+    System.out.println("getXThread1 CALLLED");
+//    while (m_instances >= MAXinstances) {
+//      //System.out.println("waiting "+m_instances);
+//      //pleasewait();
+//      try {
+//        Thread.sleep(50);
+//      } catch (Exception e) {
+//        System.out.println("Error in sleep of XThread");
+//      }
+//    }
+//    instup(); //m_instances++;
+//    //System.out.println("XThread ++"+m_instances+" m_MAXinstances " +m_MAXinstances);
+//    XThread ret = new XThread(x, Method, Para);
+//    //    m_ThreadContainer.add(ret);
+//    return ret;
+    XThread ret = null;
+     if (m_Instances == null)
+       init(MAXinstances);
+     if (m_index >= m_Instances.length)
+       m_index = 0;
+     if (m_Instances[m_index] == null) {
+       ret = new XThread(x, m, Para);
+       m_Instances[m_index] = ret;
+       m_index++;
+       return ret;
+     }
+     int w = 1;
+     while (true) {
+       for (int i = 0; i < m_Instances.length; i++) {
+         if (m_Instances[i] == null) {
+           m_index = i;
+           ret = new XThread(x, m, Para);
+           m_Instances[m_index] = ret;
+           m_index++;
+           return ret;
+         }
+         if (m_Instances[i].isAlive() == false) {
+           m_index = i;
+           ret = new XThread(x, m, Para);
+           m_Instances[m_index] = ret;
+           m_index++;
+           return ret;
+
+         }
+       }
+       try {
+         Thread.sleep(w);
+         w = 2 * w; //System.out.println(""+i);
+       } catch (Exception e) {
+         System.out.println("Error in sleep of XThread");
+       }
+
+     } // end of while true
+
+  }
+
+  /**
+   *
+   */
+//  public static synchronized void pleasewait() {
+//    for (int i = 0; i < m_ThreadContainer.size(); i++) {
+//      try {
+//        if (((Thread) m_ThreadContainer.get(i)).isAlive()==false)
+//          m_ThreadContainer.remove(i);
+//      } catch (InterruptedException e) {
+//        e.printStackTrace();
+//        System.out.println("Error");
+//      }
+//    }
+//  }
+
+  private void removemyself() {
+    for (int i = 0; i < m_Instances.length; i++) {
+      System.out.println("TRYING TO REMOVE");
+      if (this.m_Instances[i] == this) {
+        this.m_Instances[i] = null;
+        System.out.println("REMOVED");
+        return;
+      }
+    }
+    System.out.println("DANGER!!!!!!!!! XTHREAD ->NOT<- REMOVED");
+  }
+  /**
+   *
+   */
+  private XThread(Object object, Method method, Object[] Para) {
+    System.out.println("XTHREAD INSTANZIERT");
+    m_Object = object;
+    m_Para = Para;
+    m_Method = method;
+    start();
+  }
+
+  /**
+   *
+   */
+  private XThread(Object x, String method, Object[] Para) {
+    System.out.println("XTHREAD INSTANZIERT");
+    m_Object = x;
+    m_Para = Para;
+    try {
+      Method[] methods = x.getClass().getDeclaredMethods();
+      for (int i = 0; i < methods.length; i++) {
+        if (methods[i].getName().equals(method) == true) {
+          m_Method = methods[i];
+          break;
+        }
+      }
+    } catch (Exception e) {
+      System.out.println(" ERROR in XTHREAD +" + e.getMessage());
+      e.printStackTrace();
+    }
+    start();
+  }
+
+  /**
+   *
+   */
+  public void run() {
+   System.out.println("XTHREAD CALLED RUN");
+    if (m_Method != null) {
+      //setPriority(Thread.MAX_PRIORITY);
+      try {
+        System.out.println("XTHREAD calling m_Method"+m_Method.getName());
+        //System.out.print("--->");
+        //this.setPriority(Thread.MAX_PRIORITY);
+        m_Method.invoke(m_Object, m_Para);
+
+        //instdown(); //m_instances--;
+        //System.out.println("<--");
+        //System.out.println("XThread --"+m_instances+" m_MAXinstances " +m_MAXinstances);
+      } catch (Exception e) {
+        System.out.println("ERROR +" + e.getMessage());
+        e.printStackTrace();
+      }
+    } else {
+      System.out.println("Warning Method == null !!!!! in ThreadWrapper");
+    }
+    removemyself();
+  }
+
+
+}

src/wsi/ra/math/Jama/CholeskyDecomposition.java

@@ -0,0 +1,182 @@
+package wsi.ra.math.Jama;
+
+   /** Cholesky Decomposition.
+   <P>
+   For a symmetric, positive definite matrix A, the Cholesky decomposition
+   is an lower triangular matrix L so that A = L*L'.
+   <P>
+   If the matrix is not symmetric or positive definite, the constructor
+   returns a partial decomposition and sets an internal flag that may
+   be queried by the isSPD() method.
+   */
+
+public class CholeskyDecomposition implements java.io.Serializable {
+
+/* ------------------------
+   Class variables
+ * ------------------------ */
+
+   /** Array for internal storage of decomposition.
+   @serial internal array storage.
+   */
+   private double[][] L;
+
+   /** Row and column dimension (square matrix).
+   @serial matrix dimension.
+   */
+   private int n;
+
+   /** Symmetric and positive definite flag.
+   @serial is symmetric and positive definite flag.
+   */
+   private boolean isspd;
+
+/* ------------------------
+   Constructor
+ * ------------------------ */
+
+   /** Cholesky algorithm for symmetric and positive definite matrix.
+   @param  A   Square, symmetric matrix.
+   @return     Structure to access L and isspd flag.
+   */
+
+   public CholeskyDecomposition (Matrix Arg) {
+      // Initialize.
+      double[][] A = Arg.getArray();
+      n = Arg.getRowDimension();
+      L = new double[n][n];
+      isspd = (Arg.getColumnDimension() == n);
+      // Main loop.
+      for (int j = 0; j < n; j++) {
+         double[] Lrowj = L[j];
+         double d = 0.0;
+         for (int k = 0; k < j; k++) {
+            double[] Lrowk = L[k];
+            double s = 0.0;
+            for (int i = 0; i < k; i++) {
+               s += Lrowk[i]*Lrowj[i];
+            }
+            Lrowj[k] = s = (A[j][k] - s)/L[k][k];
+            d = d + s*s;
+            isspd = isspd & (A[k][j] == A[j][k]);
+         }
+         d = A[j][j] - d;
+         isspd = isspd & (d > 0.0);
+         L[j][j] = Math.sqrt(Math.max(d,0.0));
+         for (int k = j+1; k < n; k++) {
+            L[j][k] = 0.0;
+         }
+      }
+   }
+
+
+
+//   \** Right Triangular Cholesky Decomposition.
+//   <P>
+//   For a symmetric, positive definite matrix A, the Right Cholesky
+//   decomposition is an upper triangular matrix R so that A = R'*R.
+//   This constructor computes R with the Fortran inspired column oriented
+//   algorithm used in LINPACK and MATLAB.  In Java, we suspect a row oriented,
+//   lower triangular decomposition is faster.  We have temporarily included
+//   this constructor here until timing experiments confirm this suspicion.
+//   *\
+
+
+   private transient double[][] R;
+
+
+
+   public CholeskyDecomposition (Matrix Arg, int rightflag) {
+      // Initialize.
+      double[][] A = Arg.getArray();
+      n = Arg.getColumnDimension();
+      R = new double[n][n];
+      isspd = (Arg.getColumnDimension() == n);
+      // Main loop.
+      for (int j = 0; j < n; j++) {
+         double d = 0.0;
+         for (int k = 0; k < j; k++) {
+            double s = A[k][j];
+            for (int i = 0; i < k; i++) {
+               s = s - R[i][k]*R[i][j];
+            }
+            R[k][j] = s = s/R[k][k];
+            d = d + s*s;
+            isspd = isspd & (A[k][j] == A[j][k]);
+         }
+         d = A[j][j] - d;
+         isspd = isspd & (d > 0.0);
+         R[j][j] = Math.sqrt(Math.max(d,0.0));
+         for (int k = j+1; k < n; k++) {
+            R[k][j] = 0.0;
+         }
+      }
+   }
+
+
+   public Matrix getR () {
+      return new Matrix(R,n,n);
+   }
+
+
+   /** Is the matrix symmetric and positive definite?
+   @return     true if A is symmetric and positive definite.
+   */
+
+   public boolean isSPD () {
+      return isspd;
+   }
+
+   /** Return triangular factor.
+   @return     L
+   */
+
+   public Matrix getL () {
+      return new Matrix(L,n,n);
+   }
+
+   /** Solve A*X = B
+   @param  B   A Matrix with as many rows as A and any number of columns.
+   @return     X so that L*L'*X = B
+   @exception  IllegalArgumentException  Matrix row dimensions must agree.
+   @exception  RuntimeException  Matrix is not symmetric positive definite.
+   */
+
+   public Matrix solve (Matrix B) {
+      if (B.getRowDimension() != n) {
+         throw new IllegalArgumentException("Matrix row dimensions must agree.");
+      }
+      if (!isspd) {
+         throw new RuntimeException("Matrix is not symmetric positive definite.");
+      }
+
+      // Copy right hand side.
+      double[][] X = B.getArrayCopy();
+      int nx = B.getColumnDimension();
+
+      // Solve L*Y = B;
+      for (int k = 0; k < n; k++) {
+         for (int i = k+1; i < n; i++) {
+            for (int j = 0; j < nx; j++) {
+               X[i][j] -= X[k][j]*L[i][k];
+            }
+         }
+         for (int j = 0; j < nx; j++) {
+            X[k][j] /= L[k][k];
+         }
+      }
+
+      // Solve L'*X = Y;
+      for (int k = n-1; k >= 0; k--) {
+         for (int j = 0; j < nx; j++) {
+            X[k][j] /= L[k][k];
+         }
+         for (int i = 0; i < k; i++) {
+            for (int j = 0; j < nx; j++) {
+               X[i][j] -= X[k][j]*L[k][i];
+            }
+         }
+      }
+      return new Matrix(X,n,nx);
+   }
+}

src/wsi/ra/math/Jama/EigenvalueDecomposition.java

@@ -0,0 +1,956 @@
+package wsi.ra.math.Jama;
+import  wsi.ra.math.Jama.util.Maths;
+
+
+/** Eigenvalues and eigenvectors of a real matrix.
+<P>
+    If A is symmetric, then A = V*D*V' where the eigenvalue matrix D is
+    diagonal and the eigenvector matrix V is orthogonal.
+    I.e. A = V.times(D.times(V.transpose())) and
+    V.times(V.transpose()) equals the identiCty matrix.
+<P>
+    If A is not symmetric, then the eigenvalue matrix D is block diagonal
+    with the real eigenvalues in 1-by-1 blocks and any complex eigenvalues,
+    lambda + i*mu, in 2-by-2 blocks, [lambda, mu; -mu, lambda].  The
+    columns of V represent the eigenvectors in the sense that A*V = V*D,
+    i.e. A.times(V) equals V.times(D).  The matrix V may be badly
+    conditioned, or even singular, so the validity of the equation
+    A = V*D*inverse(V) depends upon V.cond().
+**/
+
+public class EigenvalueDecomposition implements java.io.Serializable {
+
+/* ------------------------
+   Class variables
+ * ------------------------ */
+
+   /** Row and column dimension (square matrix).
+   @serial matrix dimension.
+   */
+   private int n;
+
+   /** Symmetry flag.
+   @serial internal symmetry flag.
+   */
+   private boolean issymmetric;
+
+   /** Arrays for internal storage of eigenvalues.
+   @serial internal storage of eigenvalues.
+   */
+   private double[] d, e;
+
+   /** Array for internal storage of eigenvectors.
+   @serial internal storage of eigenvectors.
+   */
+   private double[][] V;
+
+   /** Array for internal storage of nonsymmetric Hessenberg form.
+   @serial internal storage of nonsymmetric Hessenberg form.
+   */
+   private double[][] H;
+
+   /** Working storage for nonsymmetric algorithm.
+   @serial working storage for nonsymmetric algorithm.
+   */
+   private double[] ort;
+
+/* ------------------------
+   Private Methods
+ * ------------------------ */
+
+   // Symmetric Householder reduction to tridiagonal form.
+
+   private void tred2 () {
+
+   //  This is derived from the Algol procedures tred2 by
+   //  Bowdler, Martin, Reinsch, and Wilkinson, Handbook for
+   //  Auto. Comp., Vol.ii-Linear Algebra, and the corresponding
+   //  Fortran subroutine in EISPACK.
+
+      for (int j = 0; j < n; j++) {
+         d[j] = V[n-1][j];
+      }
+
+      // Householder reduction to tridiagonal form.
+
+      for (int i = n-1; i > 0; i--) {
+
+         // Scale to avoid under/overflow.
+
+         double scale = 0.0;
+         double h = 0.0;
+         for (int k = 0; k < i; k++) {
+            scale = scale + Math.abs(d[k]);
+         }
+         if (scale == 0.0) {
+            e[i] = d[i-1];
+            for (int j = 0; j < i; j++) {
+               d[j] = V[i-1][j];
+               V[i][j] = 0.0;
+               V[j][i] = 0.0;
+            }
+         } else {
+
+            // Generate Householder vector.
+
+            for (int k = 0; k < i; k++) {
+               d[k] /= scale;
+               h += d[k] * d[k];
+            }
+            double f = d[i-1];
+            double g = Math.sqrt(h);
+            if (f > 0) {
+               g = -g;
+            }
+            e[i] = scale * g;
+            h = h - f * g;
+            d[i-1] = f - g;
+            for (int j = 0; j < i; j++) {
+               e[j] = 0.0;
+            }
+
+            // Apply similarity transformation to remaining columns.
+
+            for (int j = 0; j < i; j++) {
+               f = d[j];
+               V[j][i] = f;
+               g = e[j] + V[j][j] * f;
+               for (int k = j+1; k <= i-1; k++) {
+                  g += V[k][j] * d[k];
+                  e[k] += V[k][j] * f;
+               }
+               e[j] = g;
+            }
+            f = 0.0;
+            for (int j = 0; j < i; j++) {
+               e[j] /= h;
+               f += e[j] * d[j];
+            }
+            double hh = f / (h + h);
+            for (int j = 0; j < i; j++) {
+               e[j] -= hh * d[j];
+            }
+            for (int j = 0; j < i; j++) {
+               f = d[j];
+               g = e[j];
+               for (int k = j; k <= i-1; k++) {
+                  V[k][j] -= (f * e[k] + g * d[k]);
+               }
+               d[j] = V[i-1][j];
+               V[i][j] = 0.0;
+            }
+         }
+         d[i] = h;
+      }
+
+      // Accumulate transformations.
+
+      for (int i = 0; i < n-1; i++) {
+         V[n-1][i] = V[i][i];
+         V[i][i] = 1.0;
+         double h = d[i+1];
+         if (h != 0.0) {
+            for (int k = 0; k <= i; k++) {
+               d[k] = V[k][i+1] / h;
+            }
+            for (int j = 0; j <= i; j++) {
+               double g = 0.0;
+               for (int k = 0; k <= i; k++) {
+                  g += V[k][i+1] * V[k][j];
+               }
+               for (int k = 0; k <= i; k++) {
+                  V[k][j] -= g * d[k];
+               }
+            }
+         }
+         for (int k = 0; k <= i; k++) {
+            V[k][i+1] = 0.0;
+         }
+      }
+      for (int j = 0; j < n; j++) {
+         d[j] = V[n-1][j];
+         V[n-1][j] = 0.0;
+      }
+      V[n-1][n-1] = 1.0;
+      e[0] = 0.0;
+   }
+
+   // Symmetric tridiagonal QL algorithm.
+
+   private void tql2 () {
+
+   //  This is derived from the Algol procedures tql2, by
+   //  Bowdler, Martin, Reinsch, and Wilkinson, Handbook for
+   //  Auto. Comp., Vol.ii-Linear Algebra, and the corresponding
+   //  Fortran subroutine in EISPACK.
+
+      for (int i = 1; i < n; i++) {
+         e[i-1] = e[i];
+      }
+      e[n-1] = 0.0;
+
+      double f = 0.0;
+      double tst1 = 0.0;
+      double eps = Math.pow(2.0,-52.0);
+      for (int l = 0; l < n; l++) {
+
+         // Find small subdiagonal element
+
+         tst1 = Math.max(tst1,Math.abs(d[l]) + Math.abs(e[l]));
+         int m = l;
+         while (m < n) {
+            if (Math.abs(e[m]) <= eps*tst1) {
+               break;
+            }
+            m++;
+         }
+
+         // If m == l, d[l] is an eigenvalue,
+         // otherwise, iterate.
+
+         if (m > l) {
+            int iter = 0;
+            do {
+               iter = iter + 1;  // (Could check iteration count here.)
+
+               // Compute implicit shift
+
+               double g = d[l];
+               double p = (d[l+1] - g) / (2.0 * e[l]);
+               double r = Maths.hypot(p,1.0);
+               if (p < 0) {
+                  r = -r;
+               }
+               d[l] = e[l] / (p + r);
+               d[l+1] = e[l] * (p + r);
+               double dl1 = d[l+1];
+               double h = g - d[l];
+               for (int i = l+2; i < n; i++) {
+                  d[i] -= h;
+               }
+               f = f + h;
+
+               // Implicit QL transformation.
+
+               p = d[m];
+               double c = 1.0;
+               double c2 = c;
+               double c3 = c;
+               double el1 = e[l+1];
+               double s = 0.0;
+               double s2 = 0.0;
+               for (int i = m-1; i >= l; i--) {
+                  c3 = c2;
+                  c2 = c;
+                  s2 = s;
+                  g = c * e[i];
+                  h = c * p;
+                  r = Maths.hypot(p,e[i]);
+                  e[i+1] = s * r;
+                  s = e[i] / r;
+                  c = p / r;
+                  p = c * d[i] - s * g;
+                  d[i+1] = h + s * (c * g + s * d[i]);
+
+                  // Accumulate transformation.
+
+                  for (int k = 0; k < n; k++) {
+                     h = V[k][i+1];
+                     V[k][i+1] = s * V[k][i] + c * h;
+                     V[k][i] = c * V[k][i] - s * h;
+                  }
+               }
+               p = -s * s2 * c3 * el1 * e[l] / dl1;
+               e[l] = s * p;
+               d[l] = c * p;
+
+               // Check for convergence.
+
+            } while (Math.abs(e[l]) > eps*tst1);
+         }
+         d[l] = d[l] + f;
+         e[l] = 0.0;
+      }
+
+      // Sort eigenvalues and corresponding vectors.
+
+      for (int i = 0; i < n-1; i++) {
+         int k = i;
+         double p = d[i];
+         for (int j = i+1; j < n; j++) {
+            if (d[j] < p) {
+               k = j;
+               p = d[j];
+            }
+         }
+         if (k != i) {
+            d[k] = d[i];
+            d[i] = p;
+            for (int j = 0; j < n; j++) {
+               p = V[j][i];
+               V[j][i] = V[j][k];
+               V[j][k] = p;
+            }
+         }
+      }
+   }
+
+   // Nonsymmetric reduction to Hessenberg form.
+
+   private void orthes () {
+
+      //  This is derived from the Algol procedures orthes and ortran,
+      //  by Martin and Wilkinson, Handbook for Auto. Comp.,
+      //  Vol.ii-Linear Algebra, and the corresponding
+      //  Fortran subroutines in EISPACK.
+
+      int low = 0;
+      int high = n-1;
+
+      for (int m = low+1; m <= high-1; m++) {
+
+         // Scale column.
+
+         double scale = 0.0;
+         for (int i = m; i <= high; i++) {
+            scale = scale + Math.abs(H[i][m-1]);
+         }
+         if (scale != 0.0) {
+
+            // Compute Householder transformation.
+
+            double h = 0.0;
+            for (int i = high; i >= m; i--) {
+               ort[i] = H[i][m-1]/scale;
+               h += ort[i] * ort[i];
+            }
+            double g = Math.sqrt(h);
+            if (ort[m] > 0) {
+               g = -g;
+            }
+            h = h - ort[m] * g;
+            ort[m] = ort[m] - g;
+
+            // Apply Householder similarity transformation
+            // H = (I-u*u'/h)*H*(I-u*u')/h)
+
+            for (int j = m; j < n; j++) {
+               double f = 0.0;
+               for (int i = high; i >= m; i--) {
+                  f += ort[i]*H[i][j];
+               }
+               f = f/h;
+               for (int i = m; i <= high; i++) {
+                  H[i][j] -= f*ort[i];
+               }
+           }
+
+           for (int i = 0; i <= high; i++) {
+               double f = 0.0;
+               for (int j = high; j >= m; j--) {
+                  f += ort[j]*H[i][j];
+               }
+               f = f/h;
+               for (int j = m; j <= high; j++) {
+                  H[i][j] -= f*ort[j];
+               }
+            }
+            ort[m] = scale*ort[m];
+            H[m][m-1] = scale*g;
+         }
+      }
+
+      // Accumulate transformations (Algol's ortran).
+
+      for (int i = 0; i < n; i++) {
+         for (int j = 0; j < n; j++) {
+            V[i][j] = (i == j ? 1.0 : 0.0);
+         }
+      }
+
+      for (int m = high-1; m >= low+1; m--) {
+         if (H[m][m-1] != 0.0) {
+            for (int i = m+1; i <= high; i++) {
+               ort[i] = H[i][m-1];
+            }
+            for (int j = m; j <= high; j++) {
+               double g = 0.0;
+               for (int i = m; i <= high; i++) {
+                  g += ort[i] * V[i][j];
+               }
+               // Double division avoids possible underflow
+               g = (g / ort[m]) / H[m][m-1];
+               for (int i = m; i <= high; i++) {
+                  V[i][j] += g * ort[i];
+               }
+            }
+         }
+      }
+   }
+
+
+   // Complex scalar division.
+
+   private transient double cdivr, cdivi;
+   private void cdiv(double xr, double xi, double yr, double yi) {
+      double r,d;
+      if (Math.abs(yr) > Math.abs(yi)) {
+         r = yi/yr;
+         d = yr + r*yi;
+         cdivr = (xr + r*xi)/d;
+         cdivi = (xi - r*xr)/d;
+      } else {
+         r = yr/yi;
+         d = yi + r*yr;
+         cdivr = (r*xr + xi)/d;
+         cdivi = (r*xi - xr)/d;
+      }
+   }
+
+
+   // Nonsymmetric reduction from Hessenberg to real Schur form.
+
+   private void hqr2 () {
+
+      //  This is derived from the Algol procedure hqr2,
+      //  by Martin and Wilkinson, Handbook for Auto. Comp.,
+      //  Vol.ii-Linear Algebra, and the corresponding
+      //  Fortran subroutine in EISPACK.
+
+      // Initialize
+
+      int nn = this.n;
+      int n = nn-1;
+      int low = 0;
+      int high = nn-1;
+      double eps = Math.pow(2.0,-52.0);
+      double exshift = 0.0;
+      double p=0,q=0,r=0,s=0,z=0,t,w,x,y;
+
+      // Store roots isolated by balanc and compute matrix norm
+
+      double norm = 0.0;
+      for (int i = 0; i < nn; i++) {
+         if (i < low | i > high) {
+            d[i] = H[i][i];
+            e[i] = 0.0;
+         }
+         for (int j = Math.max(i-1,0); j < nn; j++) {
+            norm = norm + Math.abs(H[i][j]);
+         }
+      }
+
+      // Outer loop over eigenvalue index
+
+      int iter = 0;
+      while (n >= low) {
+
+         // Look for single small sub-diagonal element
+
+         int l = n;
+         while (l > low) {
+            s = Math.abs(H[l-1][l-1]) + Math.abs(H[l][l]);
+            if (s == 0.0) {
+               s = norm;
+            }
+            if (Math.abs(H[l][l-1]) < eps * s) {
+               break;
+            }
+            l--;
+         }
+
+         // Check for convergence
+         // One root found
+
+         if (l == n) {
+            H[n][n] = H[n][n] + exshift;
+            d[n] = H[n][n];
+            e[n] = 0.0;
+            n--;
+            iter = 0;
+
+         // Two roots found
+
+         } else if (l == n-1) {
+            w = H[n][n-1] * H[n-1][n];
+            p = (H[n-1][n-1] - H[n][n]) / 2.0;
+            q = p * p + w;
+            z = Math.sqrt(Math.abs(q));
+            H[n][n] = H[n][n] + exshift;
+            H[n-1][n-1] = H[n-1][n-1] + exshift;
+            x = H[n][n];
+
+            // Real pair
+
+            if (q >= 0) {
+               if (p >= 0) {
+                  z = p + z;
+               } else {
+                  z = p - z;
+               }
+               d[n-1] = x + z;
+               d[n] = d[n-1];
+               if (z != 0.0) {
+                  d[n] = x - w / z;
+               }
+               e[n-1] = 0.0;
+               e[n] = 0.0;
+               x = H[n][n-1];
+               s = Math.abs(x) + Math.abs(z);
+               p = x / s;
+               q = z / s;
+               r = Math.sqrt(p * p+q * q);
+               p = p / r;
+               q = q / r;
+
+               // Row modification
+
+               for (int j = n-1; j < nn; j++) {
+                  z = H[n-1][j];
+                  H[n-1][j] = q * z + p * H[n][j];
+                  H[n][j] = q * H[n][j] - p * z;
+               }
+
+               // Column modification
+
+               for (int i = 0; i <= n; i++) {
+                  z = H[i][n-1];
+                  H[i][n-1] = q * z + p * H[i][n];
+                  H[i][n] = q * H[i][n] - p * z;
+               }
+
+               // Accumulate transformations
+
+               for (int i = low; i <= high; i++) {
+                  z = V[i][n-1];
+                  V[i][n-1] = q * z + p * V[i][n];
+                  V[i][n] = q * V[i][n] - p * z;
+               }
+
+            // Complex pair
+
+            } else {
+               d[n-1] = x + p;
+               d[n] = x + p;
+               e[n-1] = z;
+               e[n] = -z;
+            }
+            n = n - 2;
+            iter = 0;
+
+         // No convergence yet
+
+         } else {
+
+            // Form shift
+
+            x = H[n][n];
+            y = 0.0;
+            w = 0.0;
+            if (l < n) {
+               y = H[n-1][n-1];
+               w = H[n][n-1] * H[n-1][n];
+            }
+
+            // Wilkinson's original ad hoc shift
+
+            if (iter == 10) {
+               exshift += x;
+               for (int i = low; i <= n; i++) {
+                  H[i][i] -= x;
+               }
+               s = Math.abs(H[n][n-1]) + Math.abs(H[n-1][n-2]);
+               x = y = 0.75 * s;
+               w = -0.4375 * s * s;
+            }
+
+            // MATLAB's new ad hoc shift
+
+            if (iter == 30) {
+                s = (y - x) / 2.0;
+                s = s * s + w;
+                if (s > 0) {
+                    s = Math.sqrt(s);
+                    if (y < x) {
+                       s = -s;
+                    }
+                    s = x - w / ((y - x) / 2.0 + s);
+                    for (int i = low; i <= n; i++) {
+                       H[i][i] -= s;
+                    }
+                    exshift += s;
+                    x = y = w = 0.964;
+                }
+            }
+
+            iter = iter + 1;   // (Could check iteration count here.)
+
+            // Look for two consecutive small sub-diagonal elements
+
+            int m = n-2;
+            while (m >= l) {
+               z = H[m][m];
+               r = x - z;
+               s = y - z;
+               p = (r * s - w) / H[m+1][m] + H[m][m+1];
+               q = H[m+1][m+1] - z - r - s;
+               r = H[m+2][m+1];
+               s = Math.abs(p) + Math.abs(q) + Math.abs(r);
+               p = p / s;
+               q = q / s;
+               r = r / s;
+               if (m == l) {
+                  break;
+               }
+               if (Math.abs(H[m][m-1]) * (Math.abs(q) + Math.abs(r)) <
+                  eps * (Math.abs(p) * (Math.abs(H[m-1][m-1]) + Math.abs(z) +
+                  Math.abs(H[m+1][m+1])))) {
+                     break;
+               }
+               m--;
+            }
+
+            for (int i = m+2; i <= n; i++) {
+               H[i][i-2] = 0.0;
+               if (i > m+2) {
+                  H[i][i-3] = 0.0;
+               }
+            }
+
+            // Double QR step involving rows l:n and columns m:n
+
+            for (int k = m; k <= n-1; k++) {
+               boolean notlast = (k != n-1);
+               if (k != m) {
+                  p = H[k][k-1];
+                  q = H[k+1][k-1];
+                  r = (notlast ? H[k+2][k-1] : 0.0);
+                  x = Math.abs(p) + Math.abs(q) + Math.abs(r);
+                  if (x != 0.0) {
+                     p = p / x;
+                     q = q / x;
+                     r = r / x;
+                  }
+               }
+               if (x == 0.0) {
+                  break;
+               }
+               s = Math.sqrt(p * p + q * q + r * r);
+               if (p < 0) {
+                  s = -s;
+               }
+               if (s != 0) {
+                  if (k != m) {
+                     H[k][k-1] = -s * x;
+                  } else if (l != m) {
+                     H[k][k-1] = -H[k][k-1];
+                  }
+                  p = p + s;
+                  x = p / s;
+                  y = q / s;
+                  z = r / s;
+                  q = q / p;
+                  r = r / p;
+
+                  // Row modification
+
+                  for (int j = k; j < nn; j++) {
+                     p = H[k][j] + q * H[k+1][j];
+                     if (notlast) {
+                        p = p + r * H[k+2][j];
+                        H[k+2][j] = H[k+2][j] - p * z;
+                     }
+                     H[k][j] = H[k][j] - p * x;
+                     H[k+1][j] = H[k+1][j] - p * y;
+                  }
+
+                  // Column modification
+
+                  for (int i = 0; i <= Math.min(n,k+3); i++) {
+                     p = x * H[i][k] + y * H[i][k+1];
+                     if (notlast) {
+                        p = p + z * H[i][k+2];
+                        H[i][k+2] = H[i][k+2] - p * r;
+                     }
+                     H[i][k] = H[i][k] - p;
+                     H[i][k+1] = H[i][k+1] - p * q;
+                  }
+
+                  // Accumulate transformations
+
+                  for (int i = low; i <= high; i++) {
+                     p = x * V[i][k] + y * V[i][k+1];
+                     if (notlast) {
+                        p = p + z * V[i][k+2];
+                        V[i][k+2] = V[i][k+2] - p * r;
+                     }
+                     V[i][k] = V[i][k] - p;
+                     V[i][k+1] = V[i][k+1] - p * q;
+                  }
+               }  // (s != 0)
+            }  // k loop
+         }  // check convergence
+      }  // while (n >= low)
+
+      // Backsubstitute to find vectors of upper triangular form
+
+      if (norm == 0.0) {
+         return;
+      }
+
+      for (n = nn-1; n >= 0; n--) {
+         p = d[n];
+         q = e[n];
+
+         // Real vector
+
+         if (q == 0) {
+            int l = n;
+            H[n][n] = 1.0;
+            for (int i = n-1; i >= 0; i--) {
+               w = H[i][i] - p;
+               r = 0.0;
+               for (int j = l; j <= n; j++) {
+                  r = r + H[i][j] * H[j][n];
+               }
+               if (e[i] < 0.0) {
+                  z = w;
+                  s = r;
+               } else {
+                  l = i;
+                  if (e[i] == 0.0) {
+                     if (w != 0.0) {
+                        H[i][n] = -r / w;
+                     } else {
+                        H[i][n] = -r / (eps * norm);
+                     }
+
+                  // Solve real equations
+
+                  } else {
+                     x = H[i][i+1];
+                     y = H[i+1][i];
+                     q = (d[i] - p) * (d[i] - p) + e[i] * e[i];
+                     t = (x * s - z * r) / q;
+                     H[i][n] = t;
+                     if (Math.abs(x) > Math.abs(z)) {
+                        H[i+1][n] = (-r - w * t) / x;
+                     } else {
+                        H[i+1][n] = (-s - y * t) / z;
+                     }
+                  }
+
+                  // Overflow control
+
+                  t = Math.abs(H[i][n]);
+                  if ((eps * t) * t > 1) {
+                     for (int j = i; j <= n; j++) {
+                        H[j][n] = H[j][n] / t;
+                     }
+                  }
+               }
+            }
+
+         // Complex vector
+
+         } else if (q < 0) {
+            int l = n-1;
+
+            // Last vector component imaginary so matrix is triangular
+
+            if (Math.abs(H[n][n-1]) > Math.abs(H[n-1][n])) {
+               H[n-1][n-1] = q / H[n][n-1];
+               H[n-1][n] = -(H[n][n] - p) / H[n][n-1];
+            } else {
+               cdiv(0.0,-H[n-1][n],H[n-1][n-1]-p,q);
+               H[n-1][n-1] = cdivr;
+               H[n-1][n] = cdivi;
+            }
+            H[n][n-1] = 0.0;
+            H[n][n] = 1.0;
+            for (int i = n-2; i >= 0; i--) {
+               double ra,sa,vr,vi;
+               ra = 0.0;
+               sa = 0.0;
+               for (int j = l; j <= n; j++) {
+                  ra = ra + H[i][j] * H[j][n-1];
+                  sa = sa + H[i][j] * H[j][n];
+               }
+               w = H[i][i] - p;
+
+               if (e[i] < 0.0) {
+                  z = w;
+                  r = ra;
+                  s = sa;
+               } else {
+                  l = i;
+                  if (e[i] == 0) {
+                     cdiv(-ra,-sa,w,q);
+                     H[i][n-1] = cdivr;
+                     H[i][n] = cdivi;
+                  } else {
+
+                     // Solve complex equations
+
+                     x = H[i][i+1];
+                     y = H[i+1][i];
+                     vr = (d[i] - p) * (d[i] - p) + e[i] * e[i] - q * q;
+                     vi = (d[i] - p) * 2.0 * q;
+                     if (vr == 0.0 & vi == 0.0) {
+                        vr = eps * norm * (Math.abs(w) + Math.abs(q) +
+                        Math.abs(x) + Math.abs(y) + Math.abs(z));
+                     }
+                     cdiv(x*r-z*ra+q*sa,x*s-z*sa-q*ra,vr,vi);
+                     H[i][n-1] = cdivr;
+                     H[i][n] = cdivi;
+                     if (Math.abs(x) > (Math.abs(z) + Math.abs(q))) {
+                        H[i+1][n-1] = (-ra - w * H[i][n-1] + q * H[i][n]) / x;
+                        H[i+1][n] = (-sa - w * H[i][n] - q * H[i][n-1]) / x;
+                     } else {
+                        cdiv(-r-y*H[i][n-1],-s-y*H[i][n],z,q);
+                        H[i+1][n-1] = cdivr;
+                        H[i+1][n] = cdivi;
+                     }
+                  }
+
+                  // Overflow control
+
+                  t = Math.max(Math.abs(H[i][n-1]),Math.abs(H[i][n]));
+                  if ((eps * t) * t > 1) {
+                     for (int j = i; j <= n; j++) {
+                        H[j][n-1] = H[j][n-1] / t;
+                        H[j][n] = H[j][n] / t;
+                     }
+                  }
+               }
+            }
+         }
+      }
+
+      // Vectors of isolated roots
+
+      for (int i = 0; i < nn; i++) {
+         if (i < low | i > high) {
+            for (int j = i; j < nn; j++) {
+               V[i][j] = H[i][j];
+            }
+         }
+      }
+
+      // Back transformation to get eigenvectors of original matrix
+
+      for (int j = nn-1; j >= low; j--) {
+         for (int i = low; i <= high; i++) {
+            z = 0.0;
+            for (int k = low; k <= Math.min(j,high); k++) {
+               z = z + V[i][k] * H[k][j];
+            }
+            V[i][j] = z;
+         }
+      }
+   }
+
+
+/* ------------------------
+   Constructor
+ * ------------------------ */
+
+   /** Check for symmetry, then construct the eigenvalue decomposition
+   @param A    Square matrix
+   @return     Structure to access D and V.
+   */
+
+   public EigenvalueDecomposition (Matrix Arg) {
+      double[][] A = Arg.getArray();
+      n = Arg.getColumnDimension();
+      V = new double[n][n];
+      d = new double[n];
+      e = new double[n];
+
+      issymmetric = true;
+      for (int j = 0; (j < n) & issymmetric; j++) {
+         for (int i = 0; (i < n) & issymmetric; i++) {
+            issymmetric = (A[i][j] == A[j][i]);
+         }
+      }
+
+      if (issymmetric) {
+         for (int i = 0; i < n; i++) {
+            for (int j = 0; j < n; j++) {
+               V[i][j] = A[i][j];
+            }
+         }
+
+         // Tridiagonalize.
+         tred2();
+
+         // Diagonalize.
+         tql2();
+
+      } else {
+         H = new double[n][n];
+         ort = new double[n];
+
+         for (int j = 0; j < n; j++) {
+            for (int i = 0; i < n; i++) {
+               H[i][j] = A[i][j];
+            }
+         }
+
+         // Reduce to Hessenberg form.
+         orthes();
+
+         // Reduce Hessenberg to real Schur form.
+         hqr2();
+      }
+   }
+
+/* ------------------------
+   Public Methods
+ * ------------------------ */
+
+   /** Return the eigenvector matrix
+   @return     V
+   */
+
+   public Matrix getV () {
+      return new Matrix(V,n,n);
+   }
+
+   /** Return the real parts of the eigenvalues
+   @return     real(diag(D))
+   */
+
+   public double[] getRealEigenvalues () {
+      return d;
+   }
+
+   /** Return the imaginary parts of the eigenvalues
+   @return     imag(diag(D))
+   */
+
+   public double[] getImagEigenvalues () {
+      return e;
+   }
+
+   /** Return the block diagonal eigenvalue matrix
+   @return     D
+   */
+
+   public Matrix getD () {
+      Matrix X = new Matrix(n,n);
+      double[][] D = X.getArray();
+      for (int i = 0; i < n; i++) {
+         for (int j = 0; j < n; j++) {
+            D[i][j] = 0.0;
+         }
+         D[i][i] = d[i];
+         if (e[i] > 0) {
+            D[i][i+1] = e[i];
+         } else if (e[i] < 0) {
+            D[i][i-1] = e[i];
+         }
+      }
+      return X;
+   }
+}

src/wsi/ra/math/Jama/LUDecomposition.java

@@ -0,0 +1,318 @@
+package wsi.ra.math.Jama;
+
+
+   /** LU Decomposition.
+   <P>
+   For an m-by-n matrix A with m >= n, the LU decomposition is an m-by-n
+   unit lower triangular matrix L, an n-by-n upper triangular matrix U,
+   and a permutation vector piv of length m so that A(piv,:) = L*U.
+   If m < n, then L is m-by-m and U is m-by-n.
+   <P>
+   The LU decompostion with pivoting always exists, even if the matrix is
+   singular, so the constructor will never fail.  The primary use of the
+   LU decomposition is in the solution of square systems of simultaneous
+   linear equations.  This will fail if isNonsingular() returns false.
+   */
+
+public class LUDecomposition implements java.io.Serializable {
+
+/* ------------------------
+   Class variables
+ * ------------------------ */
+
+   /** Array for internal storage of decomposition.
+   @serial internal array storage.
+   */
+   private double[][] LU;
+
+   /** Row and column dimensions, and pivot sign.
+   @serial column dimension.
+   @serial row dimension.
+   @serial pivot sign.
+   */
+   private int m, n, pivsign;
+
+   /** Internal storage of pivot vector.
+   @serial pivot vector.
+   */
+   private int[] piv;
+
+/* ------------------------
+   Constructor
+ * ------------------------ */
+
+   /** LU Decomposition
+   @param  A   Rectangular matrix
+   @return     Structure to access L, U and piv.
+   */
+
+   public LUDecomposition (Matrix A) {
+
+   // Use a "left-looking", dot-product, Crout/Doolittle algorithm.
+//      System.out.println("A=");
+//      A.print(A.getRowDimension(),A.getColumnDimension());
+
+      LU = A.getArrayCopy();
+      m = A.getRowDimension();
+      n = A.getColumnDimension();
+      piv = new int[m];
+      for (int i = 0; i < m; i++) {
+         piv[i] = i;
+      }
+      pivsign = 1;
+      double[] LUrowi;
+      double[] LUcolj = new double[m];
+
+      // Outer loop.
+
+      for (int j = 0; j < n; j++) {
+
+         // Make a copy of the j-th column to localize references.
+
+         for (int i = 0; i < m; i++) {
+            LUcolj[i] = LU[i][j];
+         }
+
+         // Apply previous transformations.
+
+         for (int i = 0; i < m; i++) {
+            LUrowi = LU[i];
+
+            // Most of the time is spent in the following dot product.
+
+            int kmax = Math.min(i,j);
+            double s = 0.0;
+            for (int k = 0; k < kmax; k++) {
+               s += LUrowi[k]*LUcolj[k];
+            }
+
+            LUrowi[j] = LUcolj[i] -= s;
+         }
+
+         // Find pivot and exchange if necessary.
+
+         int p = j;
+         for (int i = j+1; i < m; i++) {
+            if (Math.abs(LUcolj[i]) > Math.abs(LUcolj[p])) {
+               p = i;
+            }
+         }
+         if (p != j) {
+            for (int k = 0; k < n; k++) {
+               double t = LU[p][k]; LU[p][k] = LU[j][k]; LU[j][k] = t;
+            }
+            int k = piv[p]; piv[p] = piv[j]; piv[j] = k;
+            pivsign = -pivsign;
+         }
+
+         // Compute multipliers.
+
+         if (j < m & LU[j][j] != 0.0) {
+            for (int i = j+1; i < m; i++) {
+               LU[i][j] /= LU[j][j];
+            }
+         }
+      }
+   }
+
+/* ------------------------
+   Temporary, experimental code.
+   ------------------------ *\
+
+   \** LU Decomposition, computed by Gaussian elimination.
+   <P>
+   This constructor computes L and U with the "daxpy"-based elimination
+   algorithm used in LINPACK and MATLAB.  In Java, we suspect the dot-product,
+   Crout algorithm will be faster.  We have temporarily included this
+   constructor until timing experiments confirm this suspicion.
+   <P>
+   @param  A             Rectangular matrix
+   @param  linpackflag   Use Gaussian elimination.  Actual value ignored.
+   @return               Structure to access L, U and piv.
+   *\
+
+   public LUDecomposition (Matrix A, int linpackflag) {
+      // Initialize.
+      LU = A.getArrayCopy();
+      m = A.getRowDimension();
+      n = A.getColumnDimension();
+      piv = new int[m];
+      for (int i = 0; i < m; i++) {
+         piv[i] = i;
+      }
+      pivsign = 1;
+      // Main loop.
+      for (int k = 0; k < n; k++) {
+         // Find pivot.
+         int p = k;
+         for (int i = k+1; i < m; i++) {
+            if (Math.abs(LU[i][k]) > Math.abs(LU[p][k])) {
+               p = i;
+            }
+         }
+         // Exchange if necessary.
+         if (p != k) {
+            for (int j = 0; j < n; j++) {
+               double t = LU[p][j]; LU[p][j] = LU[k][j]; LU[k][j] = t;
+            }
+            int t = piv[p]; piv[p] = piv[k]; piv[k] = t;
+            pivsign = -pivsign;
+         }
+         // Compute multipliers and eliminate k-th column.
+         if (LU[k][k] != 0.0) {
+            for (int i = k+1; i < m; i++) {
+               LU[i][k] /= LU[k][k];
+               for (int j = k+1; j < n; j++) {
+                  LU[i][j] -= LU[i][k]*LU[k][j];
+               }
+            }
+         }
+      }
+   }
+
+\* ------------------------
+   End of temporary code.
+ * ------------------------ */
+
+/* ------------------------
+   Public Methods
+ * ------------------------ */
+
+   /** Is the matrix nonsingular?
+   @return     true if U, and hence A, is nonsingular.
+   */
+
+   public boolean isNonsingular () {
+      for (int j = 0; j < n; j++) {
+	//System.out.println("LU[j][j]"+LU[j][j]);
+         if (LU[j][j] == 0)
+            return false;
+
+      }
+      return true;
+   }
+
+   /** Return lower triangular factor
+   @return     L
+   */
+
+   public Matrix getL () {
+      Matrix X = new Matrix(m,n);
+      double[][] L = X.getArray();
+      for (int i = 0; i < m; i++) {
+         for (int j = 0; j < n; j++) {
+            if (i > j) {
+               L[i][j] = LU[i][j];
+            } else if (i == j) {
+               L[i][j] = 1.0;
+            } else {
+               L[i][j] = 0.0;
+            }
+         }
+      }
+      return X;
+   }
+
+   /** Return upper triangular factor
+   @return     U
+   */
+
+   public Matrix getU () {
+      Matrix X = new Matrix(n,n);
+      double[][] U = X.getArray();
+      for (int i = 0; i < n; i++) {
+         for (int j = 0; j < n; j++) {
+            if (i <= j) {
+               U[i][j] = LU[i][j];
+            } else {
+               U[i][j] = 0.0;
+            }
+         }
+      }
+      return X;
+   }
+
+   /** Return pivot permutation vector
+   @return     piv
+   */
+
+   public int[] getPivot () {
+      int[] p = new int[m];
+      for (int i = 0; i < m; i++) {
+         p[i] = piv[i];
+      }
+      return p;
+   }
+
+   /** Return pivot permutation vector as a one-dimensional double array
+   @return     (double) piv
+   */
+
+   public double[] getDoublePivot () {
+      double[] vals = new double[m];
+      for (int i = 0; i < m; i++) {
+         vals[i] = (double) piv[i];
+      }
+      return vals;
+   }
+
+   /** Determinant
+   @return     det(A)
+   @exception  IllegalArgumentException  Matrix must be square
+   */
+
+   public double det () {
+      if (m != n) {
+         throw new IllegalArgumentException("Matrix must be square.");
+      }
+      double d = (double) pivsign;
+      for (int j = 0; j < n; j++) {
+         d *= LU[j][j];
+      }
+      return d;
+   }
+
+   /** Solve A*X = B
+   @param  B   A Matrix with as many rows as A and any number of columns.
+   @return     X so that L*U*X = B(piv,:)
+   @exception  IllegalArgumentException Matrix row dimensions must agree.
+   @exception  RuntimeException  Matrix is singular.
+   */
+
+   public Matrix solve (Matrix B) {
+      if (B.getRowDimension() != m) {
+         throw new IllegalArgumentException("Matrix row dimensions must agree.");
+      }
+      if (!this.isNonsingular()) {
+        //System.out.println("B=");
+        //B.print(B.getRowDimension(),B.getColumnDimension());
+        throw new RuntimeException("Matrix is singular.");
+      }
+
+      // Copy right hand side with pivoting
+      int nx = B.getColumnDimension();
+      Matrix Xmat = B.getMatrix(piv,0,nx-1);
+      double[][] X = Xmat.getArray();
+
+      // Solve L*Y = B(piv,:)
+      for (int k = 0; k < n; k++) {
+         for (int i = k+1; i < n; i++) {
+            for (int j = 0; j < nx; j++) {
+               X[i][j] -= X[k][j]*LU[i][k];
+            }
+         }
+      }
+      // Solve U*X = Y;
+      for (int k = n-1; k >= 0; k--) {
+         for (int j = 0; j < nx; j++) {
+            X[k][j] /= LU[k][k];
+         }
+         for (int i = 0; i < k; i++) {
+            for (int j = 0; j < nx; j++) {
+               X[i][j] -= X[k][j]*LU[i][k];
+            }
+         }
+      }
+      return Xmat;
+   }
+}

src/wsi/ra/math/Jama/QRDecomposition.java

@@ -0,0 +1,218 @@
+package wsi.ra.math.Jama;
+import wsi.ra.math.Jama.util.Maths;
+
+/** QR Decomposition.
+<P>
+   For an m-by-n matrix A with m >= n, the QR decomposition is an m-by-n
+   orthogonal matrix Q and an n-by-n upper triangular matrix R so that
+   A = Q*R.
+<P>
+   The QR decompostion always exists, even if the matrix does not have
+   full rank, so the constructor will never fail.  The primary use of the
+   QR decomposition is in the least squares solution of nonsquare systems
+   of simultaneous linear equations.  This will fail if isFullRank()
+   returns false.
+*/
+
+public class QRDecomposition implements java.io.Serializable {
+
+/* ------------------------
+   Class variables
+ * ------------------------ */
+
+   /** Array for internal storage of decomposition.
+   @serial internal array storage.
+   */
+   private double[][] QR;
+
+   /** Row and column dimensions.
+   @serial column dimension.
+   @serial row dimension.
+   */
+   private int m, n;
+
+   /** Array for internal storage of diagonal of R.
+   @serial diagonal of R.
+   */
+   private double[] Rdiag;
+
+/* ------------------------
+   Constructor
+ * ------------------------ */
+
+   /** QR Decomposition, computed by Householder reflections.
+   @param A    Rectangular matrix
+   @return     Structure to access R and the Householder vectors and compute Q.
+   */
+
+   public QRDecomposition (Matrix A) {
+      // Initialize.
+      QR = A.getArrayCopy();
+      m = A.getRowDimension();
+      n = A.getColumnDimension();
+      Rdiag = new double[n];
+
+      // Main loop.
+      for (int k = 0; k < n; k++) {
+         // Compute 2-norm of k-th column without under/overflow.
+         double nrm = 0;
+         for (int i = k; i < m; i++) {
+            nrm = Maths.hypot(nrm,QR[i][k]);
+         }
+
+         if (nrm != 0.0) {
+            // Form k-th Householder vector.
+            if (QR[k][k] < 0) {
+               nrm = -nrm;
+            }
+            for (int i = k; i < m; i++) {
+               QR[i][k] /= nrm;
+            }
+            QR[k][k] += 1.0;
+
+            // Apply transformation to remaining columns.
+            for (int j = k+1; j < n; j++) {
+               double s = 0.0;
+               for (int i = k; i < m; i++) {
+                  s += QR[i][k]*QR[i][j];
+               }
+               s = -s/QR[k][k];
+               for (int i = k; i < m; i++) {
+                  QR[i][j] += s*QR[i][k];
+               }
+            }
+         }
+         Rdiag[k] = -nrm;
+      }
+   }
+
+/* ------------------------
+   Public Methods
+ * ------------------------ */
+
+   /** Is the matrix full rank?
+   @return     true if R, and hence A, has full rank.
+   */
+
+   public boolean isFullRank () {
+      for (int j = 0; j < n; j++) {
+         if (Rdiag[j] == 0)
+            return false;
+      }
+      return true;
+   }
+
+   /** Return the Householder vectors
+   @return     Lower trapezoidal matrix whose columns define the reflections
+   */
+
+   public Matrix getH () {
+      Matrix X = new Matrix(m,n);
+      double[][] H = X.getArray();
+      for (int i = 0; i < m; i++) {
+         for (int j = 0; j < n; j++) {
+            if (i >= j) {
+               H[i][j] = QR[i][j];
+            } else {
+               H[i][j] = 0.0;
+            }
+         }
+      }
+      return X;
+   }
+
+   /** Return the upper triangular factor
+   @return     R
+   */
+
+   public Matrix getR () {
+      Matrix X = new Matrix(n,n);
+      double[][] R = X.getArray();
+      for (int i = 0; i < n; i++) {
+         for (int j = 0; j < n; j++) {
+            if (i < j) {
+               R[i][j] = QR[i][j];
+            } else if (i == j) {
+               R[i][j] = Rdiag[i];
+            } else {
+               R[i][j] = 0.0;
+            }
+         }
+      }
+      return X;
+   }
+
+   /** Generate and return the (economy-sized) orthogonal factor
+   @return     Q
+   */
+
+   public Matrix getQ () {
+      Matrix X = new Matrix(m,n);
+      double[][] Q = X.getArray();
+      for (int k = n-1; k >= 0; k--) {
+         for (int i = 0; i < m; i++) {
+            Q[i][k] = 0.0;
+         }
+         Q[k][k] = 1.0;
+         for (int j = k; j < n; j++) {
+            if (QR[k][k] != 0) {
+               double s = 0.0;
+               for (int i = k; i < m; i++) {
+                  s += QR[i][k]*Q[i][j];
+               }
+               s = -s/QR[k][k];
+               for (int i = k; i < m; i++) {
+                  Q[i][j] += s*QR[i][k];
+               }
+            }
+         }
+      }
+      return X;
+   }
+
+   /** Least squares solution of A*X = B
+   @param B    A Matrix with as many rows as A and any number of columns.
+   @return     X that minimizes the two norm of Q*R*X-B.
+   @exception  IllegalArgumentException  Matrix row dimensions must agree.
+   @exception  RuntimeException  Matrix is rank deficient.
+   */
+
+   public Matrix solve (Matrix B) {
+      if (B.getRowDimension() != m) {
+         throw new IllegalArgumentException("Matrix row dimensions must agree.");
+      }
+      if (!this.isFullRank()) {
+         throw new RuntimeException("Matrix is rank deficient.");
+      }
+
+      // Copy right hand side
+      int nx = B.getColumnDimension();
+      double[][] X = B.getArrayCopy();
+
+      // Compute Y = transpose(Q)*B
+      for (int k = 0; k < n; k++) {
+         for (int j = 0; j < nx; j++) {
+            double s = 0.0;
+            for (int i = k; i < m; i++) {
+               s += QR[i][k]*X[i][j];
+            }
+            s = -s/QR[k][k];
+            for (int i = k; i < m; i++) {
+               X[i][j] += s*QR[i][k];
+            }
+         }
+      }
+      // Solve R*X = Y;
+      for (int k = n-1; k >= 0; k--) {
+         for (int j = 0; j < nx; j++) {
+            X[k][j] /= Rdiag[k];
+         }
+         for (int i = 0; i < k; i++) {
+            for (int j = 0; j < nx; j++) {
+               X[i][j] -= X[k][j]*QR[i][k];
+            }
+         }
+      }
+      return (new Matrix(X,n,nx).getMatrix(0,n-1,0,nx-1));
+   }
+}

src/wsi/ra/math/Jama/SingularValueDecomposition.java

@@ -0,0 +1,540 @@
+package wsi.ra.math.Jama;
+import wsi.ra.math.Jama.util.*;
+
+
+   /** Singular Value Decomposition.
+   <P>
+   For an m-by-n matrix A with m >= n, the singular value decomposition is
+   an m-by-n orthogonal matrix U, an n-by-n diagonal matrix S, and
+   an n-by-n orthogonal matrix V so that A = U*S*V'.
+   <P>
+   The singular values, sigma[k] = S[k][k], are ordered so that
+   sigma[0] >= sigma[1] >= ... >= sigma[n-1].
+   <P>
+   The singular value decompostion always exists, so the constructor will
+   never fail.  The matrix condition number and the effective numerical
+   rank can be computed from this decomposition.
+   */
+
+public class SingularValueDecomposition implements java.io.Serializable {
+
+/* ------------------------
+   Class variables
+ * ------------------------ */
+
+   /** Arrays for internal storage of U and V.
+   @serial internal storage of U.
+   @serial internal storage of V.
+   */
+   private double[][] U, V;
+
+   /** Array for internal storage of singular values.
+   @serial internal storage of singular values.
+   */
+   private double[] s;
+
+   /** Row and column dimensions.
+   @serial row dimension.
+   @serial column dimension.
+   */
+   private int m, n;
+
+/* ------------------------
+   Constructor
+ * ------------------------ */
+
+   /** Construct the singular value decomposition
+   @param A    Rectangular matrix
+   @return     Structure to access U, S and V.
+   */
+
+   public SingularValueDecomposition (Matrix Arg) {
+
+      // Derived from LINPACK code.
+      // Initialize.
+      double[][] A = Arg.getArrayCopy();
+      m = Arg.getRowDimension();
+      n = Arg.getColumnDimension();
+      int nu = Math.min(m,n);
+      s = new double [Math.min(m+1,n)];
+      U = new double [m][nu];
+      V = new double [n][n];
+      double[] e = new double [n];
+      double[] work = new double [m];
+      boolean wantu = true;
+      boolean wantv = true;
+
+      // Reduce A to bidiagonal form, storing the diagonal elements
+      // in s and the super-diagonal elements in e.
+
+      int nct = Math.min(m-1,n);
+      int nrt = Math.max(0,Math.min(n-2,m));
+      for (int k = 0; k < Math.max(nct,nrt); k++) {
+         if (k < nct) {
+
+            // Compute the transformation for the k-th column and
+            // place the k-th diagonal in s[k].
+            // Compute 2-norm of k-th column without under/overflow.
+            s[k] = 0;
+            for (int i = k; i < m; i++) {
+               s[k] = Maths.hypot(s[k],A[i][k]);
+            }
+            if (s[k] != 0.0) {
+               if (A[k][k] < 0.0) {
+                  s[k] = -s[k];
+               }
+               for (int i = k; i < m; i++) {
+                  A[i][k] /= s[k];
+               }
+               A[k][k] += 1.0;
+            }
+            s[k] = -s[k];
+         }
+         for (int j = k+1; j < n; j++) {
+            if ((k < nct) & (s[k] != 0.0))  {
+
+            // Apply the transformation.
+
+               double t = 0;
+               for (int i = k; i < m; i++) {
+                  t += A[i][k]*A[i][j];
+               }
+               t = -t/A[k][k];
+               for (int i = k; i < m; i++) {
+                  A[i][j] += t*A[i][k];
+               }
+            }
+
+            // Place the k-th row of A into e for the
+            // subsequent calculation of the row transformation.
+
+            e[j] = A[k][j];
+         }
+         if (wantu & (k < nct)) {
+
+            // Place the transformation in U for subsequent back
+            // multiplication.
+
+            for (int i = k; i < m; i++) {
+               U[i][k] = A[i][k];
+            }
+         }
+         if (k < nrt) {
+
+            // Compute the k-th row transformation and place the
+            // k-th super-diagonal in e[k].
+            // Compute 2-norm without under/overflow.
+            e[k] = 0;
+            for (int i = k+1; i < n; i++) {
+               e[k] = Maths.hypot(e[k],e[i]);
+            }
+            if (e[k] != 0.0) {
+               if (e[k+1] < 0.0) {
+                  e[k] = -e[k];
+               }
+               for (int i = k+1; i < n; i++) {
+                  e[i] /= e[k];
+               }
+               e[k+1] += 1.0;
+            }
+            e[k] = -e[k];
+            if ((k+1 < m) & (e[k] != 0.0)) {
+
+            // Apply the transformation.
+
+               for (int i = k+1; i < m; i++) {
+                  work[i] = 0.0;
+               }
+               for (int j = k+1; j < n; j++) {
+                  for (int i = k+1; i < m; i++) {
+                     work[i] += e[j]*A[i][j];
+                  }
+               }
+               for (int j = k+1; j < n; j++) {
+                  double t = -e[j]/e[k+1];
+                  for (int i = k+1; i < m; i++) {
+                     A[i][j] += t*work[i];
+                  }
+               }
+            }
+            if (wantv) {
+
+            // Place the transformation in V for subsequent
+            // back multiplication.
+
+               for (int i = k+1; i < n; i++) {
+                  V[i][k] = e[i];
+               }
+            }
+         }
+      }
+
+      // Set up the final bidiagonal matrix or order p.
+
+      int p = Math.min(n,m+1);
+      if (nct < n) {
+         s[nct] = A[nct][nct];
+      }
+      if (m < p) {
+         s[p-1] = 0.0;
+      }
+      if (nrt+1 < p) {
+         e[nrt] = A[nrt][p-1];
+      }
+      e[p-1] = 0.0;
+
+      // If required, generate U.
+
+      if (wantu) {
+         for (int j = nct; j < nu; j++) {
+            for (int i = 0; i < m; i++) {
+               U[i][j] = 0.0;
+            }
+            U[j][j] = 1.0;
+         }
+         for (int k = nct-1; k >= 0; k--) {
+            if (s[k] != 0.0) {
+               for (int j = k+1; j < nu; j++) {
+                  double t = 0;
+                  for (int i = k; i < m; i++) {
+                     t += U[i][k]*U[i][j];
+                  }
+                  t = -t/U[k][k];
+                  for (int i = k; i < m; i++) {
+                     U[i][j] += t*U[i][k];
+                  }
+               }
+               for (int i = k; i < m; i++ ) {
+                  U[i][k] = -U[i][k];
+               }
+               U[k][k] = 1.0 + U[k][k];
+               for (int i = 0; i < k-1; i++) {
+                  U[i][k] = 0.0;
+               }
+            } else {
+               for (int i = 0; i < m; i++) {
+                  U[i][k] = 0.0;
+               }
+               U[k][k] = 1.0;
+            }
+         }
+      }
+
+      // If required, generate V.
+
+      if (wantv) {
+         for (int k = n-1; k >= 0; k--) {
+            if ((k < nrt) & (e[k] != 0.0)) {
+               for (int j = k+1; j < nu; j++) {
+                  double t = 0;
+                  for (int i = k+1; i < n; i++) {
+                     t += V[i][k]*V[i][j];
+                  }
+                  t = -t/V[k+1][k];
+                  for (int i = k+1; i < n; i++) {
+                     V[i][j] += t*V[i][k];
+                  }
+               }
+            }
+            for (int i = 0; i < n; i++) {
+               V[i][k] = 0.0;
+            }
+            V[k][k] = 1.0;
+         }
+      }
+
+      // Main iteration loop for the singular values.
+
+      int pp = p-1;
+      int iter = 0;
+      double eps = Math.pow(2.0,-52.0);
+      while (p > 0) {
+         int k,kase;
+
+         // Here is where a test for too many iterations would go.
+
+         // This section of the program inspects for
+         // negligible elements in the s and e arrays.  On
+         // completion the variables kase and k are set as follows.
+
+         // kase = 1     if s(p) and e[k-1] are negligible and k<p
+         // kase = 2     if s(k) is negligible and k<p
+         // kase = 3     if e[k-1] is negligible, k<p, and
+         //              s(k), ..., s(p) are not negligible (qr step).
+         // kase = 4     if e(p-1) is negligible (convergence).
+
+         for (k = p-2; k >= -1; k--) {
+            if (k == -1) {
+               break;
+            }
+            if (Math.abs(e[k]) <= eps*(Math.abs(s[k]) + Math.abs(s[k+1]))) {
+               e[k] = 0.0;
+               break;
+            }
+         }
+         if (k == p-2) {
+            kase = 4;
+         } else {
+            int ks;
+            for (ks = p-1; ks >= k; ks--) {
+               if (ks == k) {
+                  break;
+               }
+               double t = (ks != p ? Math.abs(e[ks]) : 0.) +
+                          (ks != k+1 ? Math.abs(e[ks-1]) : 0.);
+               if (Math.abs(s[ks]) <= eps*t)  {
+                  s[ks] = 0.0;
+                  break;
+               }
+            }
+            if (ks == k) {
+               kase = 3;
+            } else if (ks == p-1) {
+               kase = 1;
+            } else {
+               kase = 2;
+               k = ks;
+            }
+         }
+         k++;
+
+         // Perform the task indicated by kase.
+
+         switch (kase) {
+
+            // Deflate negligible s(p).
+
+            case 1: {
+               double f = e[p-2];
+               e[p-2] = 0.0;
+               for (int j = p-2; j >= k; j--) {
+                  double t = Maths.hypot(s[j],f);
+                  double cs = s[j]/t;
+                  double sn = f/t;
+                  s[j] = t;
+                  if (j != k) {
+                     f = -sn*e[j-1];
+                     e[j-1] = cs*e[j-1];
+                  }
+                  if (wantv) {
+                     for (int i = 0; i < n; i++) {
+                        t = cs*V[i][j] + sn*V[i][p-1];
+                        V[i][p-1] = -sn*V[i][j] + cs*V[i][p-1];
+                        V[i][j] = t;
+                     }
+                  }
+               }
+            }
+            break;
+
+            // Split at negligible s(k).
+
+            case 2: {
+               double f = e[k-1];
+               e[k-1] = 0.0;
+               for (int j = k; j < p; j++) {
+                  double t = Maths.hypot(s[j],f);
+                  double cs = s[j]/t;
+                  double sn = f/t;
+                  s[j] = t;
+                  f = -sn*e[j];
+                  e[j] = cs*e[j];
+                  if (wantu) {
+                     for (int i = 0; i < m; i++) {
+                        t = cs*U[i][j] + sn*U[i][k-1];
+                        U[i][k-1] = -sn*U[i][j] + cs*U[i][k-1];
+                        U[i][j] = t;
+                     }
+                  }
+               }
+            }
+            break;
+
+            // Perform one qr step.
+
+            case 3: {
+
+               // Calculate the shift.
+
+               double scale = Math.max(Math.max(Math.max(Math.max(
+                       Math.abs(s[p-1]),Math.abs(s[p-2])),Math.abs(e[p-2])),
+                       Math.abs(s[k])),Math.abs(e[k]));
+               double sp = s[p-1]/scale;
+               double spm1 = s[p-2]/scale;
+               double epm1 = e[p-2]/scale;
+               double sk = s[k]/scale;
+               double ek = e[k]/scale;
+               double b = ((spm1 + sp)*(spm1 - sp) + epm1*epm1)/2.0;
+               double c = (sp*epm1)*(sp*epm1);
+               double shift = 0.0;
+               if ((b != 0.0) | (c != 0.0)) {
+                  shift = Math.sqrt(b*b + c);
+                  if (b < 0.0) {
+                     shift = -shift;
+                  }
+                  shift = c/(b + shift);
+               }
+               double f = (sk + sp)*(sk - sp) + shift;
+               double g = sk*ek;
+
+               // Chase zeros.
+
+               for (int j = k; j < p-1; j++) {
+                  double t = Maths.hypot(f,g);
+                  double cs = f/t;
+                  double sn = g/t;
+                  if (j != k) {
+                     e[j-1] = t;
+                  }
+                  f = cs*s[j] + sn*e[j];
+                  e[j] = cs*e[j] - sn*s[j];
+                  g = sn*s[j+1];
+                  s[j+1] = cs*s[j+1];
+                  if (wantv) {
+                     for (int i = 0; i < n; i++) {
+                        t = cs*V[i][j] + sn*V[i][j+1];
+                        V[i][j+1] = -sn*V[i][j] + cs*V[i][j+1];
+                        V[i][j] = t;
+                     }
+                  }
+                  t = Maths.hypot(f,g);
+                  cs = f/t;
+                  sn = g/t;
+                  s[j] = t;
+                  f = cs*e[j] + sn*s[j+1];
+                  s[j+1] = -sn*e[j] + cs*s[j+1];
+                  g = sn*e[j+1];
+                  e[j+1] = cs*e[j+1];
+                  if (wantu && (j < m-1)) {
+                     for (int i = 0; i < m; i++) {
+                        t = cs*U[i][j] + sn*U[i][j+1];
+                        U[i][j+1] = -sn*U[i][j] + cs*U[i][j+1];
+                        U[i][j] = t;
+                     }
+                  }
+               }
+               e[p-2] = f;
+               iter = iter + 1;
+            }
+            break;
+
+            // Convergence.
+
+            case 4: {
+
+               // Make the singular values positive.
+
+               if (s[k] <= 0.0) {
+                  s[k] = (s[k] < 0.0 ? -s[k] : 0.0);
+                  if (wantv) {
+                     for (int i = 0; i <= pp; i++) {
+                        V[i][k] = -V[i][k];
+                     }
+                  }
+               }
+
+               // Order the singular values.
+
+               while (k < pp) {
+                  if (s[k] >= s[k+1]) {
+                     break;
+                  }
+                  double t = s[k];
+                  s[k] = s[k+1];
+                  s[k+1] = t;
+                  if (wantv && (k < n-1)) {
+                     for (int i = 0; i < n; i++) {
+                        t = V[i][k+1]; V[i][k+1] = V[i][k]; V[i][k] = t;
+                     }
+                  }
+                  if (wantu && (k < m-1)) {
+                     for (int i = 0; i < m; i++) {
+                        t = U[i][k+1]; U[i][k+1] = U[i][k]; U[i][k] = t;
+                     }
+                  }
+                  k++;
+               }
+               iter = 0;
+               p--;
+            }
+            break;
+         }
+      }
+   }
+
+/* ------------------------
+   Public Methods
+ * ------------------------ */
+
+   /** Return the left singular vectors
+   @return     U
+   */
+
+   public Matrix getU () {
+      return new Matrix(U,m,Math.min(m+1,n));
+   }
+
+   /** Return the right singular vectors
+   @return     V
+   */
+
+   public Matrix getV () {
+      return new Matrix(V,n,n);
+   }
+
+   /** Return the one-dimensional array of singular values
+   @return     diagonal of S.
+   */
+
+   public double[] getSingularValues () {
+      return s;
+   }
+
+   /** Return the diagonal matrix of singular values
+   @return     S
+   */
+
+   public Matrix getS () {
+      Matrix X = new Matrix(n,n);
+      double[][] S = X.getArray();
+      for (int i = 0; i < n; i++) {
+         for (int j = 0; j < n; j++) {
+            S[i][j] = 0.0;
+         }
+         S[i][i] = this.s[i];
+      }
+      return X;
+   }
+
+   /** Two norm
+   @return     max(S)
+   */
+
+   public double norm2 () {
+      return s[0];
+   }
+
+   /** Two norm condition number
+   @return     max(S)/min(S)
+   */
+
+   public double cond () {
+      return s[0]/s[Math.min(m,n)-1];
+   }
+
+   /** Effective numerical matrix rank
+   @return     Number of nonnegligible singular values.
+   */
+
+   public int rank () {
+      double eps = Math.pow(2.0,-52.0);
+      double tol = Math.max(m,n)*s[0]*eps;
+      int r = 0;
+      for (int i = 0; i < s.length; i++) {
+         if (s[i] > tol) {
+            r++;
+         }
+      }
+      return r;
+   }
+}

src/wsi/ra/math/Jama/util/Maths.java

@@ -0,0 +1,21 @@
+package wsi.ra.math.Jama.util;
+
+public class Maths {
+
+   /** sqrt(a^2 + b^2) without under/overflow. **/
+
+   public static double hypot(double a, double b) {
+      double r;
+      double aa = Math.abs(a);
+      double bb = Math.abs(b);
+      if (aa > bb) {
+         r = b/a;
+         r = aa*Math.sqrt(1+r*r);
+      } else if (b != 0) {
+         r = a/b;
+         r = bb*Math.sqrt(1+r*r);
+      } else
+         r = 0.0;
+      return r;
+   }
+}

src/wsi/ra/math/RNG.java

@@ -0,0 +1,184 @@
+package wsi.ra.math;
+/**
+ * Title:        JavaEvA
+ * Description:
+ * Copyright:    Copyright (c) 2003
+ * Company:      University of Tuebingen, Computer Architecture
+ * @author Holger Ulmer, Felix Streichert, Hannes Planatscher
+ * @version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:40 $
+ *            $Author: ulmerh $
+ */
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+import java.util.Random;
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+/**
+ *
+ */
+public class RNG extends Random {
+  private static Random random;
+  private static long randomSeed;
+  /**
+   *
+   */
+  static {
+    randomSeed=System.currentTimeMillis();
+    random=new Random(randomSeed);
+  }
+  /**
+   *
+   */
+  public static void setseed(long x) {
+    randomSeed=x;
+    if (x==0)
+      randomSeed=System.currentTimeMillis();
+    if (x==999)
+      return;
+    random=new Random(randomSeed);
+  }
+  /**
+   *
+   */
+  public static void setRandomseed() {
+    randomSeed=System.currentTimeMillis();
+    random=new Random(randomSeed);
+  }
+  /**
+   *
+   */
+  public static void setRandom(Random base_random) {
+    random=base_random;
+  }
+  /**
+   *
+   */
+  public static void setRandomSeed(long new_seed){
+    randomSeed=new_seed;
+    random.setSeed(randomSeed);
+  }
+  /**
+   *
+   */
+  public static long getRandomSeed() {
+    return randomSeed;
+  }
+  /**
+   *
+   */
+  public static int randomInt() {
+    return randomInt(0,1);
+  }
+  public static int randomInt(int lo,int hi) {
+    return (Math.abs(random.nextInt())%(hi-lo+1))+lo;
+  }
+  /**
+   *
+   */
+  public static long randomLong() {
+    return randomLong(0,1);
+  }
+  /**
+   *
+   */
+  public static long randomLong(long lo,long hi) {
+    return (Math.abs(random.nextLong())%(hi-lo+1))+lo;
+  }
+  /**
+   *
+   */
+  public static float randomFloat() {
+    return random.nextFloat();
+  }
+  /**
+   *
+   */
+  public static float randomFloat(float lo,float hi) {
+    return (hi-lo)*random.nextFloat()+lo;
+  }
+  /**
+   *
+   */
+  public static double randomDouble() {
+    return random.nextDouble();
+  }
+  /**
+   *
+   */
+  public static double randomDouble(double lo,double hi) {
+    return (hi-lo)*random.nextDouble()+lo;
+  }
+  /**
+   *
+   */
+  public static double[] randomDoubleArray(double[] lo,double[] hi) {
+    double[] xin = new double[lo.length];
+    for (int i=0;i<lo.length;i++)
+      xin[i] = (hi[i]-lo[i])*random.nextDouble()+lo[i];
+    return xin;
+  }
+  /**
+   *
+   */
+  public static double[] randomDoubleArray(double lo,double hi,int size) {
+    double[] xin = new double[size];
+    for (int i=0;i<size;i++)
+      xin[i] = (hi-lo)*random.nextDouble()+lo;
+    return xin;
+  }
+
+  /**
+   *
+   */
+  public static double[] randomDoubleArray(double[] lo,double[] hi,double[] xin) {
+     for (int i=0;i<lo.length;i++)
+      xin[i] = (hi[i]-lo[i])*random.nextDouble()+lo[i];
+    return xin;
+  }
+  /**
+   *
+   */
+  public static boolean randomBoolean() {
+     return (randomInt()==1);
+  }
+  /**
+   *
+   */
+  public static int randomBit() {
+     return randomInt();
+  }
+  /**
+   *
+   */
+  public static boolean flipCoin(double p) {
+     return (randomDouble()<p ? true : false);
+  }
+  /**
+   *
+   */
+  public static float gaussianFloat(float dev) {
+     return (float)random.nextGaussian()*dev;
+  }
+  /**
+   *
+   */
+  public static double gaussianDouble(double dev) {
+     return random.nextGaussian()*dev;
+  }
+  /**
+   *
+   */
+  public static float exponentialFloat(float mean) {
+     return (float)(-mean*Math.log(randomDouble()));
+  }
+  /**
+   *
+   */
+  public static double exponentialDouble(double mean) {
+     return -mean*Math.log(randomDouble());
+  }
+}
+

src/wsi/ra/math/interpolation/AbstractDataModifier.java

@@ -0,0 +1,52 @@
+///////////////////////////////////////////////////////////////////////////////
+//  Filename: $RCSfile: AbstractDataModifier.java,v $
+//  Purpose:  Some interpolation stuff.
+//  Language: Java
+//  Compiler: JDK 1.4
+//  Authors:  Joerg K. Wegner
+//  Version:  $Revision: 1.1 $
+//            $Date: 2003/07/22 19:24:58 $
+//            $Author: wegnerj $
+//
+//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+//
+///////////////////////////////////////////////////////////////////////////////
+
+package wsi.ra.math.interpolation;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+/*==========================================================================*
+* CLASS DECLARATION
+*==========================================================================*/
+
+/**
+ * The minimal set of functions which should implemented in a data modifier for
+ * <code>AbstractDataSet</code>.
+ */
+public abstract class AbstractDataModifier
+{
+
+	/*-------------------------------------------------------------------------*
+	 * abstract methods
+	 *-------------------------------------------------------------------------*/
+
+	/**
+	* Modifies the X data.
+	*/
+	public abstract void modifyX(double[] setX);
+	/**
+	* Modifies the Y data.
+	*/
+	public abstract void modifyY(double[] setY);
+	/**
+	* Modifies the data.
+	*/
+	public abstract void modify(double[] setX, double[] setY);
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/math/interpolation/AbstractDataSet.java

@@ -0,0 +1,116 @@
+///////////////////////////////////////////////////////////////////////////////
+//  Filename: $RCSfile: AbstractDataSet.java,v $
+//  Purpose:  Some interpolation stuff.
+//  Language: Java
+//  Compiler: JDK 1.4
+//  Authors:  Joerg K. Wegner
+//  Version:  $Revision: 1.1 $
+//            $Date: 2003/07/22 19:25:04 $
+//            $Author: wegnerj $
+//
+//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+//
+///////////////////////////////////////////////////////////////////////////////
+
+package wsi.ra.math.interpolation;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+/*==========================================================================*
+* CLASS DECLARATION
+*==========================================================================*/
+
+public abstract class AbstractDataSet
+{
+	/*-------------------------------------------------------------------------*
+	 * public member variables
+	 *-------------------------------------------------------------------------*/
+
+	/*--------------------------------------------------------------o-----------*
+	 * protected member variables
+	 *-------------------------------------------------------------------------*/
+	/**
+	* double array of X data.
+	*
+	* @see #yDoubleData
+	*/
+	protected double[] xDoubleData = { -1, 1 };
+	/**
+	* double array of Y data.
+	*
+	* @see #xDoubleData
+	*/
+	protected double[] yDoubleData = { 1, 1 };
+
+	/*-------------------------------------------------------------------------*
+	 * abstract methods
+	 *-------------------------------------------------------------------------*/
+
+	/**
+	* Returns the length of the data set
+	* @return   the length of the data set
+	*/
+	public int getLength()
+	{
+		return xDoubleData.length;
+	}
+	/**
+	* Returns an array of the X data
+	* @return   the array of the X data
+	*/
+	public double[] getXData()
+	{
+		return xDoubleData;
+	}
+	/**
+	* Returns an array of the Y data
+	* @return   the array of the Y data
+	*/
+	public double[] getYData()
+	{
+		return yDoubleData;
+	}
+	/**
+	* Returns the X label of the data set
+	* @return   the X label of the data set
+	*/
+	public abstract String getXLabel();
+	/**
+	* Returns the Y label of the data set
+	* @return   the Y label of the data set
+	*/
+	public abstract String getYLabel();
+
+	/**
+	* Modifies the X data.
+	*
+	* @param the data modifier
+	*/
+	public void modifyXData(AbstractDataModifier modifier)
+	{
+		modifier.modifyX(xDoubleData);
+	}
+	/**
+	* Modifies the Y data.
+	*
+	* @param the data modifier
+	*/
+	public void modifyYData(AbstractDataModifier modifier)
+	{
+		modifier.modifyY(yDoubleData);
+	}
+	/**
+	* Modifies the data.
+	*
+	* @param the data modifier
+	*/
+	public void modifyData(AbstractDataModifier modifier)
+	{
+		modifier.modify(xDoubleData, yDoubleData);
+	}
+}
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/math/interpolation/BasicDataSet.java

@@ -0,0 +1,100 @@
+///////////////////////////////////////////////////////////////////////////////
+//  Filename: $RCSfile: BasicDataSet.java,v $
+//  Purpose:  Some interpolation stuff.
+//  Language: Java
+//  Compiler: JDK 1.4
+//  Authors:  Joerg K. Wegner
+//  Version:  $Revision: 1.1 $
+//            $Date: 2003/07/22 19:25:11 $
+//            $Author: wegnerj $
+//
+//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+//
+///////////////////////////////////////////////////////////////////////////////
+
+package wsi.ra.math.interpolation;
+
+import wsi.ra.sort.XYDoubleArray;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+/**
+ * The minimum wrapper class for an <code>AbstractDataSet</code>.
+ */
+public class BasicDataSet extends AbstractDataSet
+{
+	/*-------------------------------------------------------------------------*
+	 * protected member variables
+	 *-------------------------------------------------------------------------*/
+	protected int dataType = -1;
+	protected String xLabel = null;
+	protected String yLabel = null;
+
+	/*------------------------------------------------------------------------*
+	 * constructor
+	 *------------------------------------------------------------------------*/
+	public BasicDataSet()
+	{
+		this(null, null, null, null);
+	}
+
+	public BasicDataSet(XYDoubleArray data)
+	{
+		this(data.x, data.y, null, null);
+	}
+
+	public BasicDataSet(XYDoubleArray data, String xLabel, String yLabel)
+	{
+		this(data.x, data.y, xLabel, yLabel);
+	}
+
+	public BasicDataSet(
+		double[] xDoubleData,
+		double[] yDoubleData,
+		int dataType)
+	{
+		this(xDoubleData, yDoubleData, null, null);
+	}
+
+	public BasicDataSet(
+		double[] xDoubleData,
+		double[] yDoubleData,
+		String xLabel,
+		String yLabel)
+	{
+		this.xDoubleData = xDoubleData;
+		this.yDoubleData = yDoubleData;
+		this.xLabel = xLabel;
+		this.yLabel = yLabel;
+	}
+
+	/*-------------------------------------------------------------------------*
+	* public methods
+	*-------------------------------------------------------------------------*/
+
+	public int getDataType()
+	{
+		return dataType;
+	}
+
+	public String getXLabel()
+	{
+		return xLabel;
+	}
+
+	public String getYLabel()
+	{
+		return yLabel;
+	}
+
+	public String getAdditionalInformation(String parm1)
+	{
+		return new String();
+	}
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/math/interpolation/InterpolationException.java

@@ -0,0 +1,44 @@
+///////////////////////////////////////////////////////////////////////////////
+//  Filename: $RCSfile: InterpolationException.java,v $
+//  Purpose:  Some interpolation stuff.
+//  Language: Java
+//  Compiler: JDK 1.4
+//  Authors:  Joerg K. Wegner
+//  Version:  $Revision: 1.1 $
+//            $Date: 2003/07/22 19:25:17 $
+//            $Author: wegnerj $
+//
+//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+//
+///////////////////////////////////////////////////////////////////////////////
+
+package wsi.ra.math.interpolation;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+/**
+ * Exception for interpolation error.
+ */
+public class InterpolationException extends Exception
+{
+
+	public InterpolationException()
+	{
+		super();
+	}
+	public InterpolationException(String s)
+	{
+		super(s);
+	}
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/math/interpolation/LinearInterpolation.java

@@ -0,0 +1,573 @@
+///////////////////////////////////////////////////////////////////////////////
+//  Filename: $RCSfile: LinearInterpolation.java,v $
+//  Purpose:  Some interpolation stuff.
+//  Language: Java
+//  Compiler: JDK 1.4
+//  Authors:  Joerg K. Wegner
+//  Original author: Charles S. Stanton
+//  Version:  $Revision: 1.1 $
+//            $Date: 2003/07/22 19:25:23 $
+//            $Author: wegnerj $
+//
+//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+//
+///////////////////////////////////////////////////////////////////////////////
+
+package wsi.ra.math.interpolation;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+//import cern.jet.stat.*;
+
+/**
+ * Defines the routines for the spline interpolation of data.
+ */
+public class LinearInterpolation
+{
+	AbstractDataSet abstractDataSet = null;
+	private double[] x, y;
+	//vectors of x,y
+	private double sumX = 0;
+	private double sumY = 0;
+	private double sumXY = 0;
+	private double sumXsquared = 0;
+	private double sumYsquared = 0;
+	private double Sxx, Sxy, Syy, n;
+	private double a = 0, b = 0;
+	//coefficients of regression
+	private int dataLength;
+	private double[][] residual;
+	// residual[0][i] = x[i], residual[1][i]= residual
+	private double maxAbsoluteResidual = 0.0;
+	private double SSR = 0.0;
+	//regression sum of squares
+	private double SSE = 0.0;
+	//error sum of squares
+	private double minX = Double.POSITIVE_INFINITY;
+	private double maxX = Double.NEGATIVE_INFINITY;
+	private double minY = Double.POSITIVE_INFINITY;
+	private double maxY = Double.NEGATIVE_INFINITY;
+
+	//MISC
+	String xName, yName;
+	double aCILower, aCIUpper, bCILower, bCIUpper; //confidence interval
+	double t, bSE, aSE;
+	double MSE, F;
+	static double[] t025 =
+		{
+			Double.NaN,
+			12.706,
+			4.303,
+			3.182,
+			2.776,
+			2.571,
+			2.447,
+			2.365,
+			2.306,
+			2.262,
+			2.228,
+			2.201,
+			2.179,
+			2.160,
+			2.145,
+			2.131,
+			2.120,
+			2.110,
+			2.101,
+			2.093,
+			2.086,
+			2.080,
+			2.075,
+			2.069,
+			2.064,
+			2.060,
+			2.056,
+			2.052,
+			2.048,
+			2.045,
+			1.960 };
+
+	/*------------------------------------------------------------------------*
+	 * constructor
+	 *------------------------------------------------------------------------*/
+	/**
+	 * Initializes this class.
+	 */
+	public LinearInterpolation() throws InterpolationException
+	{
+		this.abstractDataSet = null;
+	}
+
+	/**
+	 * Constructor for regression calculator.
+	 *
+	 * @param  x  is the array of x data
+	 * @param  y  is the array of y data
+	 */
+	public LinearInterpolation(double[] x, double[] y)
+	{
+		this.x = x;
+		this.y = y;
+		if (x.length != y.length)
+		{
+			System.out.println("x, y vectors must be of same length");
+		}
+		else
+		{
+			dataLength = x.length;
+			doStatistics();
+		}
+
+	}
+
+	/**
+	 * Initializes this class and calculates the second derivative of the spline.
+	 *
+	 * @param abstractDataSet the <code>AbstractDataSet</code>
+	 */
+	public LinearInterpolation(AbstractDataSet abstractDataSet)
+		throws InterpolationException
+	{
+		this.setAbstractDataSet(abstractDataSet);
+	}
+
+	public void setAbstractDataSet(AbstractDataSet abstractDataSet)
+		throws InterpolationException
+	{
+		this.abstractDataSet = abstractDataSet;
+		x = abstractDataSet.getXData();
+		y = abstractDataSet.getYData();
+		if (x.length != y.length)
+		{
+			System.out.println("x, y vectors must be of same length");
+		}
+		else
+		{
+			dataLength = x.length;
+			doStatistics();
+		}
+	}
+
+	/**
+	 * Find the p value for a given value of F.
+	 * Requires the COLT high performance library:
+	 * http://hoschek.home.cern.ch/hoschek/colt/
+	 *
+	 * @param  fValue  the value for the CDF
+	 * @return         The P value
+	 */
+	//	public double getP(double fValue) {
+	//		double answer;
+	//		double y1;
+	//		double y2;
+	//		//nu1 = 1;
+	//		//x2 =1
+	//		double nu2 = n - 2;
+	//		y1 = nu2 / (nu2 + fValue);
+	//		y2 = 0.0;
+	//		answer = Gamma.incompleteBeta(nu2 / 2.0, 1 / 2.0, y1)
+	//				 - Gamma.incompleteBeta(nu2 / 2.0, 1 / 2.0, y2);
+	//		return answer;
+	//	}
+
+	/*
+	 *  Here are the accessor methods
+	 *
+	 */
+	/**
+	 *  Gets the intercept of the regression line.
+	 *
+	 * @return    The intercept.
+	 */
+	public double getIntercept()
+	{
+		return a;
+	}
+
+	/**
+	 *  Gets the Slope of the regression line.
+	 *
+	 * @return    The slope.
+	 */
+	public double getSlope()
+	{
+		return b;
+	}
+
+	/**
+	 *  Gets the residuals of the regression.
+	 *
+	 * @return    The residuals.
+	 */
+	public double[][] getResiduals()
+	{
+		return residual;
+	}
+
+	/**
+	 *  Gets the x data for the regression.
+	 *
+	 * @return    The array of x values.
+	 */
+	public double[] getDataX()
+	{
+		return x;
+	}
+
+	/**
+	 *  Gets the y data for the regression.
+	 *
+	 * @return    The array of y values.
+	 */
+	public double[] getDataY()
+	{
+		return y;
+	}
+
+	/**
+	 *  Gets the minimum of the x values.
+	 *
+	 * @return    The minimum.
+	 */
+	public double getMinX()
+	{
+		return minX;
+	}
+
+	/**
+	 *  Gets the maximum of the x values.
+	 *
+	 * @return    The maximum.
+	 */
+	public double getMaxX()
+	{
+		return maxX;
+	}
+
+	/**
+	 *  Gets the minimum of the y values.
+	 *
+	 * @return    The minumum.
+	 */
+	public double getMinY()
+	{
+		return minY;
+	}
+
+	/**
+	 *  Gets the maximum of the y values.
+	 *
+	 * @return    The maximum.
+	 */
+	public double getMaxY()
+	{
+		return maxY;
+	}
+
+	/**
+	 *  Gets the maximum absolute residual.
+	 *
+	 * @return    The maximum.
+	 */
+	public double getMaxAbsoluteResidual()
+	{
+		return maxAbsoluteResidual;
+	}
+
+	/**
+	 *  Gets the sum of the square x deviations from mean of x.
+	 *
+	 * @return    The Sxx value
+	 */
+	public double getSxx()
+	{
+		return Sxx;
+	}
+
+	/**
+	 *  Gets the sum of the square y deviations from mean of y.
+	 *
+	 * @return    The Syy value
+	 */
+	public double getSyy()
+	{
+		return Syy;
+	}
+
+	/**
+	 *  Gets  SSR = Sxy * Sxy / Sxx;
+	 *
+	 * @return    The SSR value
+	 */
+	public double getSSR()
+	{
+		return SSR;
+	}
+
+	/**
+	 *  Gets SSE = Syy - SSR.
+	 *
+	 * @return    The SSE value
+	 */
+	public double getSSE()
+	{
+		return SSE;
+	}
+
+	/**
+	 *  Gets the mean square error MSE.
+	 *
+	 * @return    The MSE value
+	 */
+	public double getMSE()
+	{
+		return SSE / (n - 2);
+	}
+
+	/**
+	 *  Gets the mean XBar of x.
+	 *
+	 * @return    The XBar value
+	 */
+	public double getXBar()
+	{
+		return sumX / n;
+	}
+
+	/**
+	 *  Gets the mean YBar of y.
+	 *
+	 * @return    The YBar value
+	 */
+	public double getYBar()
+	{
+		return sumY / n;
+	}
+
+	/**
+	 *  Gets the sample size.
+	 *
+	 * @return    The sample size.
+	 */
+	public int getDataLength()
+	{
+		return x.length;
+	}
+
+	/**
+	 *  Gets the Pearson R statistic of the regression.
+	 *
+	 * @return    The PearsonR value
+	 */
+	public double getPearsonR()
+	{
+		return Sxy / Math.sqrt(Sxx * Syy);
+	}
+
+	/**
+	 *  Gets the sum of the x squared values.
+	 *
+	 * @return    The sum of the x squared values.
+	 */
+	public double getSumXSquared()
+	{
+		return sumXsquared;
+	}
+
+	/**
+	 * reset data to 0
+	 */
+	public void reset()
+	{
+		x = new double[0];
+		y = new double[0];
+		dataLength = 0;
+		n = 0.0;
+		residual = new double[0][0];
+
+		sumX = 0;
+		sumXsquared = 0;
+		sumY = 0;
+		sumYsquared = 0;
+		sumXY = 0;
+
+	}
+
+	/**
+	 *  Adds a new point to the regression (for interactive use).
+	 *
+	 * @param  xValue  The new x value
+	 * @param  yValue  The new y value
+	 */
+	public void addPoint(double xValue, double yValue)
+	{
+		dataLength++;
+		double[] xNew = new double[dataLength];
+		double[] yNew = new double[dataLength];
+		System.arraycopy(x, 0, xNew, 0, dataLength - 1);
+		System.arraycopy(y, 0, yNew, 0, dataLength - 1);
+		xNew[dataLength - 1] = xValue;
+		yNew[dataLength - 1] = yValue;
+		x = xNew;
+		y = yNew;
+		updateStatistics(xValue, yValue);
+	}
+
+	private void doStatistics()
+	{
+		//Find sum of squares for x,y and sum of xy
+		for (int i = 0; i < dataLength; i++)
+		{
+			minX = Math.min(minX, x[i]);
+			maxX = Math.max(maxX, x[i]);
+			minY = Math.min(minY, y[i]);
+			maxY = Math.max(maxY, y[i]);
+			sumX += x[i];
+			sumY += y[i];
+			sumXsquared += x[i] * x[i];
+			sumYsquared += y[i] * y[i];
+			sumXY += x[i] * y[i];
+		}
+		//Caculate regression coefficients
+		n = (double) dataLength;
+		Sxx = sumXsquared - sumX * sumX / n;
+		Syy = sumYsquared - sumY * sumY / n;
+		Sxy = sumXY - sumX * sumY / n;
+		b = Sxy / Sxx;
+		a = (sumY - b * sumX) / n;
+		SSR = Sxy * Sxy / Sxx;
+		SSE = Syy - SSR;
+		calculateResiduals();
+	}
+
+	private void calculateResiduals()
+	{
+		residual = new double[2][dataLength];
+		maxAbsoluteResidual = 0.0;
+		for (int i = 0; i < dataLength; i++)
+		{
+			residual[0][i] = x[i];
+			residual[1][i] = y[i] - (a + b * x[i]);
+			maxAbsoluteResidual =
+				Math.max(maxAbsoluteResidual, Math.abs(y[i] - (a + b * x[i])));
+		}
+	}
+
+	//update statistics for a single additional data point
+	private void updateStatistics(double xValue, double yValue)
+	{
+		//Find sum of squares for x,y and sum of xy
+		n++;
+		sumX += xValue;
+		sumY += yValue;
+		sumXsquared += xValue * xValue;
+		sumYsquared += yValue * yValue;
+		sumXY += xValue * yValue;
+		//Caculate regression coefficients
+		n = (double) dataLength;
+		Sxx = sumXsquared - sumX * sumX / n;
+		Syy = sumYsquared - sumY * sumY / n;
+		Sxy = sumXY - sumX * sumY / n;
+		b = Sxy / Sxx;
+		a = (sumY - b * sumX) / n;
+		SSR = Sxy * Sxy / Sxx;
+		SSE = Syy - SSR;
+		calculateResiduals();
+	}
+
+	/**
+	 * regression line y = a + bx.
+	 * 
+	 * @param x
+	 * @return double
+	 * @throws InterpolationException
+	 */
+	public double getY(double x) throws InterpolationException
+	{
+		return a + b * x;
+	}
+
+	public String toString()
+	{
+		StringBuffer sb = new StringBuffer(1000);
+
+		sb.append("Regression Statistics for " + yName + " = a + b*" + xName);
+		sb.append("");
+		sb.append("Sample Statistics");
+		int n = this.getDataLength();
+		sb.append("Sample size     n = " + n);
+		sb.append("Mean of " + yName + "   Y bar = " + this.getYBar());
+		sb.append("s_Y");
+		sb.append("= " + Math.sqrt(this.getSyy() / ((float) (n - 1))));
+		sb.append("Pearson correlation R = " + this.getPearsonR());
+		sb.append("");
+		sb.append("Coefficient Estimates");
+		a = this.getIntercept();
+		b = this.getSlope();
+		sb.append("a = " + a);
+		sb.append("b = " + b);
+		sb.append("");
+
+		sb.append("95%  Confidence Intervals");
+
+		if (n > 32)
+		{
+			t = t025[30];
+		}
+		else if (n > 2)
+		{
+			t = t025[n - 2];
+		}
+		else
+		{
+			t = Double.NaN;
+		}
+		MSE = this.getMSE();
+		if (n > 2)
+		{
+			bSE = Math.sqrt(MSE / this.getSxx());
+		}
+		else
+		{
+			bSE = Double.NaN;
+		}
+		aSE = bSE * Math.sqrt(this.getSumXSquared() / n);
+		aCILower = a - t * aSE;
+		aCIUpper = a + t * aSE;
+		sb.append("a   :    (" + aCILower + ", " + aCIUpper + ")");
+		bCILower = b - t * bSE;
+		bCIUpper = b + t * bSE;
+		sb.append("b    :    (" + bCILower + ", " + bCIUpper + ")");
+		sb.append("");
+		sb.append("Analysis of Variance");
+		sb.append("Source      Degrees Freedom   Sum of Squares");
+		sb.append("");
+		SSR = this.getSSR();
+		//allow one degree of freedom for mean
+		sb.append(
+			"model                            1                                 "
+				+ SSR);
+		sb.append(
+			"error                         "
+				+ (n - 2)
+				+ "                         "
+				+ this.getSSE());
+		sb.append(
+			"total(corrected)              "
+				+ (n - 1)
+				+ "                            "
+				+ this.getSyy());
+		sb.append("");
+		sb.append("MSE =" + MSE);
+		F = SSR / MSE;
+		sb.append("F = " + F + "    ");
+		//sb.append("p = " + this.getP(F));
+
+		return sb.toString();
+	}
+}
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/math/interpolation/PolyInterpolation.java

@@ -0,0 +1,453 @@
+///////////////////////////////////////////////////////////////////////////////
+//  Filename: $RCSfile: PolyInterpolation.java,v $
+//  Purpose:  Some interpolation stuff.
+//  Language: Java
+//  Compiler: JDK 1.4
+//  Authors:  Joerg K. Wegner
+//  Version:  $Revision: 1.1 $
+//            $Date: 2003/07/22 19:25:30 $
+//            $Author: wegnerj $
+//
+//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+//
+///////////////////////////////////////////////////////////////////////////////
+
+package wsi.ra.math.interpolation;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+/**
+ * Defines the routines for the interpolation of data.
+ */
+public class PolyInterpolation
+{
+	AbstractDataSet abstractDataSet = null;
+	boolean sloppy = true;
+	double[] polynomialCoefficients = null;
+
+	/*------------------------------------------------------------------------*
+	 * constructor
+	 *------------------------------------------------------------------------*/
+	/**
+	 * Initializes this class.
+	 */
+	public PolyInterpolation() throws InterpolationException
+	{
+		this.abstractDataSet = null;
+		sloppy = true;
+		polynomialCoefficients = null;
+	}
+
+	/**
+	 * Initializes this class and calculates the coefficients of the polynom.
+	 *
+	 * @param abstractDataSet the <code>AbstractDataSet</code>
+	 */
+	public PolyInterpolation(AbstractDataSet abstractDataSet)
+		throws InterpolationException
+	{
+		this.abstractDataSet = abstractDataSet;
+		sloppy = true;
+		this.polynomialCoefficients = calculatePolynomialCoefficients();
+	}
+
+	/**
+	 * Initializes this class and calculates the coefficients of the polynom.
+	 *
+	 * @param abstractDataSet the <code>AbstractDataSet</code>
+	 * @param sloppy if <code>true</code> Neville's algorithm which is used in the
+	 *     <code>polynomialInterpolation</code>-routines does only print a
+	 *    warning message on the screen and does not throw an
+	 *    <code>Exception</code> if two x values are identical.
+	 */
+	public PolyInterpolation(AbstractDataSet abstractDataSet, boolean sloppy)
+		throws InterpolationException
+	{
+		this.abstractDataSet = abstractDataSet;
+		this.sloppy = sloppy;
+		this.polynomialCoefficients = calculatePolynomialCoefficients();
+	}
+
+	/**
+	 * Sets the new <code>AbstractDataSet</code> and calculates the coefficients
+	 * of the polynom.
+	 *
+	 * @param abstractDataSet the <code>AbstractDataSet</code>
+	 */
+	public void setAbstractDataSet(AbstractDataSet abstractDataSet)
+		throws InterpolationException
+	{
+		this.abstractDataSet = abstractDataSet;
+		this.polynomialCoefficients = calculatePolynomialCoefficients();
+	}
+
+	/**
+	 * Uses the polynom with the calculated coefficients to calculate the
+	 * <code>y</code> value. This algorithm was taken from:<br>
+	 * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
+	 * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
+	 * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
+	 * Cambridge University Press,
+	 * ISBN 0-521-43108-5,
+	 * chapter 5, pages 173-176.</a><br>
+	 * The Neville's algorithm which is used in the <code>polynomialInterpolation</code>-
+	 * routines returns also the error of this interpolated point.
+	 *
+	 * @param x the x value
+	 * @return the interpolated y value
+	 * @see #polynomialInterpolation(double)
+	 * @see #polynomialInterpolation(AbstractDataSet, double)
+	 * @see #polynomialInterpolation(double[], double[], double)
+	 * @see #getYandDerivatives(double, int)
+	 * @see #calculatePolynomialCoefficients()
+	 * @see #calculatePolynomialCoefficients(AbstractDataSet)
+	 * @see #calculatePolynomialCoefficients(double[], double[])
+	 */
+
+	public double getY(double x)
+	{
+		int n = polynomialCoefficients.length - 1;
+		double y = polynomialCoefficients[n];
+		for (int j = n - 1; j >= 0; j--)
+			y = y * x + polynomialCoefficients[j];
+
+		return y;
+	}
+
+	/**
+	 * Uses the polynom with the calculated coefficients to calculate the
+	 * <code>y</code> value and the derivatives at the point <code>x</code>,
+	 * <code>y</code>. This algorithm was taken from:<br>
+	 * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
+	 * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
+	 * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
+	 * Cambridge University Press,
+	 * ISBN 0-521-43108-5,
+	 * chapter 5, pages 173-176.</a><br>
+	 * The Neville's algorithm which is used in the <code>polynomialInterpolation</code>-
+	 * routines returns also the error of this interpolated point.
+	 *
+	 * @param x the x value
+	 * @param ndDerivateNumber the number of the calculated derivatives
+	 * @return the interpolated y value at ...[0], the 1st derivativ value at
+	 *         ...[1], the 2nd derivativ at ...[2] and so on ...
+	 * @see #getY(double)
+	 * @see #polynomialInterpolation(double)
+	 * @see #polynomialInterpolation(AbstractDataSet, double)
+	 * @see #polynomialInterpolation(double[], double[], double)
+	 * @see #calculatePolynomialCoefficients()
+	 * @see #calculatePolynomialCoefficients(AbstractDataSet)
+	 * @see #calculatePolynomialCoefficients(double[], double[])
+	 */
+	public double[] getYandDerivatives(double x, int ndDerivateNumber)
+		throws InterpolationException
+	{
+		if (ndDerivateNumber < 0)
+			throw new InterpolationException("Negative derivative numbers make no sense.");
+		else if (ndDerivateNumber == 0)
+		{
+			double[] pd = new double[1];
+			pd[0] = getY(x);
+			return pd;
+		}
+
+		int nnd, j, i;
+		int nc = polynomialCoefficients.length - 1;
+		double[] pd = new double[ndDerivateNumber + 1];
+		double cnst = 1.0;
+
+		pd[0] = polynomialCoefficients[nc];
+		for (j = 1; j <= ndDerivateNumber; j++)
+			pd[j] = 0.0;
+		for (i = nc - 1; i >= 0; i--)
+		{
+			nnd = (ndDerivateNumber < (nc - i) ? ndDerivateNumber : nc - i);
+			for (j = nnd; j >= 1; j--)
+				pd[j] = pd[j] * x + pd[j - 1];
+			pd[0] = pd[0] * x + polynomialCoefficients[i];
+		}
+		for (i = 2; i <= ndDerivateNumber; i++)
+		{
+			cnst *= i;
+			pd[i] *= cnst;
+		}
+
+		return pd;
+	}
+
+	/**
+	 * Neville's interpolation algorithm. This algorithm was taken from:<br>
+	 * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
+	 * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
+	 * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
+	 * Cambridge University Press,
+	 * ISBN 0-521-43108-5,
+	 * chapter 3, pages 108-122.</a><br>
+	 *
+	 * @param x the x value
+	 * @return the interpolated y value and the interpolation error
+	 * @see #polynomialInterpolation(AbstractDataSet, double)
+	 * @see #polynomialInterpolation(double[], double[], double)
+	 * @see #getY(double)
+	 * @see #getYandDerivatives(double, int)
+	 * @see #calculatePolynomialCoefficients()
+	 * @see #calculatePolynomialCoefficients(AbstractDataSet)
+	 * @see #calculatePolynomialCoefficients(double[], double[])
+	 */
+	public PolynomialInterpolationResult polynomialInterpolation(double x)
+		throws InterpolationException
+	{
+		if (abstractDataSet == null)
+			throw new InterpolationException(
+				"No data." + " The AbstractDataSet was not defined.");
+		return polynomialInterpolation(
+			abstractDataSet.getXData(),
+			abstractDataSet.getYData(),
+			x);
+	}
+
+	/**
+	 * Neville's interpolation algorithm. This algorithm was taken from:<br>
+	 * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
+	 * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
+	 * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
+	 * Cambridge University Press,
+	 * ISBN 0-521-43108-5,
+	 * chapter 3, pages 108-122.</a><br>
+	 *
+	 * @param abstractDataSet the <code>AbstractDataSet</code>
+	 * @param x the x value
+	 * @return the interpolated y value and the interpolation error
+	 * @see #polynomialInterpolation(double)
+	 * @see #polynomialInterpolation(double[], double[], double)
+	 * @see #getY(double)
+	 * @see #getYandDerivatives(double, int)
+	 * @see #calculatePolynomialCoefficients()
+	 * @see #calculatePolynomialCoefficients(AbstractDataSet)
+	 * @see #calculatePolynomialCoefficients(double[], double[])
+	 */
+	public PolynomialInterpolationResult polynomialInterpolation(
+		AbstractDataSet abstractDataSet,
+		double x)
+		throws InterpolationException
+	{
+		if (abstractDataSet == null)
+			throw new InterpolationException(
+				"No data." + " The AbstractDataSet was not defined.");
+		return polynomialInterpolation(
+			abstractDataSet.getXData(),
+			abstractDataSet.getYData(),
+			x);
+	}
+
+	/**
+	 * Neville's interpolation algorithm. This algorithm was taken from:<br>
+	 * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
+	 * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
+	 * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
+	 * Cambridge University Press,
+	 * ISBN 0-521-43108-5,
+	 * chapter 3, pages 108-122.</a><br>
+	 *
+	 * @param xa the array of x values
+	 * @param ya the array of y values
+	 * @param x the x value
+	 * @return the interpolated y value and the interpolation error
+	 * @see #polynomialInterpolation(double)
+	 * @see #polynomialInterpolation(AbstractDataSet, double)
+	 * @see #getY(double)
+	 * @see #getYandDerivatives(double, int)
+	 * @see #calculatePolynomialCoefficients()
+	 * @see #calculatePolynomialCoefficients(AbstractDataSet)
+	 * @see #calculatePolynomialCoefficients(double[], double[])
+	 */
+	public PolynomialInterpolationResult polynomialInterpolation(
+		double[] xa,
+		double[] ya,
+		double x)
+		throws InterpolationException
+	{
+		if (xa == null || ya == null)
+			throw new InterpolationException("No data.");
+		int i, m, ns = 1;
+		double den, dif, dift, ho, hp, w;
+		double[] c = new double[xa.length + 1];
+		double[] d = new double[xa.length + 1];
+		PolynomialInterpolationResult result =
+			new PolynomialInterpolationResult();
+
+		dif = Math.abs(x - xa[1 - 1]);
+		for (i = 1; i <= xa.length; i++)
+		{
+			if ((dift = Math.abs(x - xa[i - 1])) < dif)
+			{
+				ns = i;
+				dif = dift;
+			}
+			c[i] = ya[i - 1];
+			d[i] = ya[i - 1];
+			//System.out.println("x"+xa[i-1]+" y"+ya[i-1]);
+		}
+		result.y = ya[ns - 1];
+		//System.out.println("y="+result.y+" ns="+ns);
+		ns--;
+		for (m = 1; m < xa.length; m++)
+		{
+			for (i = 1; i <= xa.length - m; i++)
+			{
+				ho = xa[i - 1] - x;
+				hp = xa[i + m - 1] - x;
+				w = c[i + 1] - d[i];
+				if ((den = ho - hp) == 0.0)
+				{
+					if (sloppy)
+					{
+						System.out.println(
+							"Two identical x values. The values must be distinct.");
+						den = 1.0;
+					}
+					else
+						throw new InterpolationException("Two identical x values.");
+				}
+				den = w / den;
+				d[i] = hp * den;
+				c[i] = ho * den;
+			}
+			result.y
+				+= (result.yError =
+					(2 * ns < (xa.length - m) ? c[ns + 1] : d[ns--]));
+		}
+		return result;
+	}
+
+	/**
+	 * Calculates the coefficients of a polynom of the grade <code>N-1</code>. This
+	 * interpolation algorithm was taken from:<br>
+	 * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
+	 * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
+	 * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
+	 * Cambridge University Press,
+	 * ISBN 0-521-43108-5,
+	 * chapter 3, pages 108-122.</a><br>
+	 *
+	 * @return the array with the polynomial coefficients y = ...[0] +
+	 *         ...[1]*x<SUP>2</SUP> + ...[2]*x<SUP>3</SUP> + ...
+	 * @see #calculatePolynomialCoefficients(AbstractDataSet)
+	 * @see #calculatePolynomialCoefficients(double[], double[])
+	 * @see #polynomialInterpolation(double)
+	 * @see #polynomialInterpolation(AbstractDataSet, double)
+	 * @see #polynomialInterpolation(double[], double[], double)
+	 * @see #getY(double)
+	 * @see #getYandDerivatives(double, int)
+	 */
+	public double[] calculatePolynomialCoefficients()
+		throws InterpolationException
+	{
+		if (abstractDataSet == null)
+			throw new InterpolationException(
+				"No data." + " The AbstractDataSet was not defined.");
+		return calculatePolynomialCoefficients(
+			abstractDataSet.getXData(),
+			abstractDataSet.getYData());
+	}
+
+	/**
+	 * Calculates the coefficients of a polynom of the grade <code>N-1</code>. This
+	 * interpolation algorithm was taken from:<br>
+	 * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
+	 * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
+	 * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
+	 * Cambridge University Press,
+	 * ISBN 0-521-43108-5,
+	 * chapter 3, pages 108-122.</a><br>
+	 *
+	 * @param abstractDataSet the <code>AbstractDataSet</code>
+	 * @return the array with the polynomial coefficients y = ...[0] +
+	 *         ...[1]*x<SUP>2</SUP> + ...[2]*x<SUP>3</SUP> + ...
+	 * @see #calculatePolynomialCoefficients()
+	 * @see #calculatePolynomialCoefficients(double[], double[])
+	 * @see #polynomialInterpolation(double)
+	 * @see #polynomialInterpolation(AbstractDataSet, double)
+	 * @see #polynomialInterpolation(double[], double[], double)
+	 * @see #getY(double)
+	 * @see #getYandDerivatives(double, int)
+	 */
+	public double[] calculatePolynomialCoefficients(AbstractDataSet abstractDataSet)
+		throws InterpolationException
+	{
+		if (abstractDataSet == null)
+			throw new InterpolationException(
+				"No data." + " The AbstractDataSet was not defined.");
+		return calculatePolynomialCoefficients(
+			abstractDataSet.getXData(),
+			abstractDataSet.getYData());
+	}
+
+	/**
+	 * Calculates the coefficients of a polynom of the grade <code>N-1</code>. This
+	 * interpolation algorithm was taken from:<br>
+	 * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
+	 * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
+	 * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
+	 * Cambridge University Press,
+	 * ISBN 0-521-43108-5,
+	 * chapter 3, pages 108-122.</a><br>
+	 *
+	 * @param x the array of x values
+	 * @param y the array of y values
+	 * @return the array with the polynomial coefficients y = ...[0] +
+	 *         ...[1]*x<SUP>2</SUP> + ...[2]*x<SUP>3</SUP> + ...
+	 * @see #calculatePolynomialCoefficients()
+	 * @see #calculatePolynomialCoefficients(AbstractDataSet)
+	 * @see #polynomialInterpolation(double)
+	 * @see #polynomialInterpolation(AbstractDataSet, double)
+	 * @see #polynomialInterpolation(double[], double[], double)
+	 * @see #getY(double)
+	 * @see #getYandDerivatives(double, int)
+	 */
+	public double[] calculatePolynomialCoefficients(double x[], double y[])
+	{
+		int k, j, i, n = x.length - 1;
+		double phi, ff, b;
+		double[] s = new double[n + 1];
+		double[] cof = new double[n + 1];
+
+		for (i = 0; i <= n; i++)
+		{
+			s[i] = cof[i] = 0.0;
+		}
+		s[n] = -x[0];
+
+		for (i = 1; i <= n; i++)
+		{
+			for (j = n - i; j <= n - 1; j++)
+			{
+				s[j] -= x[i] * s[j + 1];
+			}
+			s[n] -= x[i];
+		}
+
+		for (j = 0; j < n; j++)
+		{
+			phi = n + 1;
+			for (k = n; k >= 1; k--)
+			{
+				phi = k * s[k] + x[j] * phi;
+			}
+			ff = y[j] / phi;
+			b = 1.0;
+			for (k = n; k >= 0; k--)
+			{
+				cof[k] += b * ff;
+				b = s[k] + x[j] * b;
+			}
+		}
+		return cof;
+	}
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/math/interpolation/PolynomialInterpolationResult.java

@@ -0,0 +1,56 @@
+///////////////////////////////////////////////////////////////////////////////
+//  Filename: $RCSfile: PolynomialInterpolationResult.java,v $
+//  Purpose:  Some interpolation stuff.
+//  Language: Java
+//  Compiler: JDK 1.4
+//  Authors:  Joerg K. Wegner
+//  Version:  $Revision: 1.1 $
+//            $Date: 2003/07/22 19:25:36 $
+//            $Author: wegnerj $
+//
+//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+//
+///////////////////////////////////////////////////////////////////////////////
+
+package wsi.ra.math.interpolation;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+/**
+ * The result data for a polynomial interpolation.
+ */
+public class PolynomialInterpolationResult
+{
+	/*-------------------------------------------------------------------------*
+	 * public member variables
+	 *-------------------------------------------------------------------------*/
+
+	public double y = Double.NaN;
+	public double yError = Double.NaN;
+
+	/*------------------------------------------------------------------------*
+	 * constructor
+	 *------------------------------------------------------------------------*/
+
+	public PolynomialInterpolationResult()
+	{
+		y = Double.NaN;
+		yError = Double.NaN;
+	}
+
+	public PolynomialInterpolationResult(double y, double yError)
+	{
+		this.y = y;
+		this.yError = yError;
+	}
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/math/interpolation/SplineInterpolation.java

@@ -0,0 +1,299 @@
+///////////////////////////////////////////////////////////////////////////////
+//  Filename: $RCSfile: SplineInterpolation.java,v $
+//  Purpose:  Some interpolation stuff.
+//  Language: Java
+//  Compiler: JDK 1.4
+//  Authors:  Joerg K. Wegner
+//  Version:  $Revision: 1.1 $
+//            $Date: 2003/07/22 19:25:42 $
+//            $Author: wegnerj $
+//
+//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+//
+///////////////////////////////////////////////////////////////////////////////
+
+package wsi.ra.math.interpolation;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+/**
+ * Defines the routines for the spline interpolation of data.
+ */
+public class SplineInterpolation
+{
+	AbstractDataSet abstractDataSet = null;
+	double[] secondDerivative = null;
+	double[] xArray = null;
+	double[] yArray = null;
+	boolean ascendingData = true;
+
+	/*------------------------------------------------------------------------*
+	 * constructor
+	 *------------------------------------------------------------------------*/
+	/**
+	 * Initializes this class.
+	 */
+	public SplineInterpolation() throws InterpolationException
+	{
+		this.abstractDataSet = null;
+		this.secondDerivative = null;
+	}
+
+	/**
+	 * Initializes this class and calculates the second derivative of the spline.
+	 *
+	 * @param abstractDataSet the <code>AbstractDataSet</code>
+	 */
+	public SplineInterpolation(AbstractDataSet abstractDataSet)
+		throws InterpolationException
+	{
+		this.setAbstractDataSet(abstractDataSet);
+	}
+
+	/**
+	 * Sets the new <code>AbstractDataSet</code> and calculates the second
+	 * derivative of the spline.
+	 *
+	 * @param abstractDataSet the <code>AbstractDataSet</code>
+	 */
+	public void setAbstractDataSet(AbstractDataSet abstractDataSet)
+		throws InterpolationException
+	{
+		this.abstractDataSet = abstractDataSet;
+		double[] x = abstractDataSet.getXData();
+		double[] y = abstractDataSet.getYData();
+		boolean ascending = false;
+		boolean descending = false;
+		int n = x.length;
+
+		xArray = new double[n];
+		yArray = new double[n];
+		xArray[n - 1] = x[0];
+		yArray[n - 1] = y[0];
+		for (int i = 0; i < n - 1; i++)
+		{
+			xArray[i] = x[n - i - 1];
+			yArray[i] = y[n - i - 1];
+			if (x[i] < x[i + 1])
+			{
+				//if(descending)throw new InterpolationException("The x values must be"+
+				//          " in continous ascending/descending order.");
+				ascending = true;
+			}
+			else
+			{
+				//if(ascending)throw new InterpolationException("The x values must be"+
+				//          " in continous ascending/descending order.");
+				descending = true;
+			}
+		}
+		ascendingData = ascending;
+
+		if (ascendingData)
+		{
+			xArray = null;
+			yArray = null;
+			xArray = abstractDataSet.getXData();
+			yArray = abstractDataSet.getYData();
+		}
+		this.secondDerivative =
+			spline(
+				xArray,
+				yArray,
+				(yArray[1] - yArray[0]) / (xArray[1] - xArray[0]),
+				(yArray[n - 1] - yArray[n - 2]) / (xArray[1] - xArray[n - 2]));
+	}
+
+	/**
+	 * Uses the spline with the calculated second derivative values to calculate
+	 * the <code>y</code> value. This algorithm was taken from:<br>
+	 * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
+	 * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
+	 * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
+	 * Cambridge University Press,
+	 * ISBN 0-521-43108-5,
+	 * chapter 5, pages 173-176.</a><br>
+	 */
+	public double getY(double x) throws InterpolationException
+	{
+		return splineInterpolation(xArray, yArray, secondDerivative, x);
+	}
+
+	public double getDerivative(double x) throws InterpolationException
+	{
+		return splineInterpolatedDerivative(
+			xArray,
+			yArray,
+			secondDerivative,
+			x);
+	}
+
+	/**
+	 * Calculates the second derivative of the data. It's important that the
+	 * x<sub>i</sub> values of the function y<sub>i</sub>=f(x<sub>i</sub>) are
+	 * in ascending order, as x<sub>0</sub>&lt;x<sub>1</sub>&lt;x<sub>2</sub>&lt;... .
+	 * This algorithm was taken from:<br>
+	 * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
+	 * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
+	 * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
+	 * Cambridge University Press,
+	 * ISBN 0-521-43108-5,
+	 * chapter 3, pages 113-116.</a><br>
+	 */
+	public double[] spline(double[] x, double[] y, double yp0, double ypn)
+		throws InterpolationException
+	{
+		if (x[0] > x[1])
+			throw new InterpolationException(
+				"The x values must be" + " in ascending order.");
+		int n = x.length;
+		double[] y2 = new double[n];
+		double[] u = new double[n - 1];
+		int i, k;
+		double p, qn, sig, un;
+
+		if (yp0 > 0.99e30)
+			y2[0] = u[0] = 0.0;
+		else
+		{
+			y2[0] = -0.5;
+			u[0] =
+				(3.0 / (x[1] - x[0])) * ((y[1] - y[0]) / (x[1] - x[0]) - yp0);
+		}
+		for (i = 2; i <= n - 1; i++)
+		{
+			sig = (x[i - 1] - x[i - 2]) / (x[i] - x[i - 2]);
+			p = sig * y2[i - 2] + 2.0;
+			y2[i - 1] = (sig - 1.0) / p;
+			u[i - 1] =
+				(y[i] - y[i - 1]) / (x[i] - x[i - 1])
+					- (y[i - 1] - y[i - 2]) / (x[i - 1] - x[i - 2]);
+			u[i - 1] =
+				(6.0 * u[i - 1] / (x[i] - x[i - 2]) - sig * u[i - 2]) / p;
+		}
+		if (ypn > 0.99e30)
+		{
+			qn = un = 0.0;
+		}
+		else
+		{
+			qn = 0.5;
+			un =
+				(3.0 / (x[n - 1] - x[n - 2]))
+					* (ypn - (y[n - 1] - y[n - 2]) / (x[n - 1] - x[n - 2]));
+		}
+		y2[n - 1] = (un - qn * u[n - 2]) / (qn * y2[n - 2] + 1.0);
+		for (k = n - 1; k >= 1; k--)
+		{
+			y2[k - 1] = y2[k - 1] * y2[k] + u[k - 1];
+		}
+
+		return y2;
+	}
+
+	/**
+	 * Calculates the second derivative of the data. This algorithm
+	 * was taken from:<br>
+	 * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
+	 * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
+	 * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
+	 * Cambridge University Press,
+	 * ISBN 0-521-43108-5,
+	 * chapter 3, pages 113-116.</a><br>
+	 */
+	public double splineInterpolation(
+		double[] xa,
+		double[] ya,
+		double[] y2a,
+		double x)
+		throws InterpolationException
+	{
+		int n = xa.length;
+		if (n != ya.length || n != y2a.length)
+		{
+			throw new InterpolationException("Arrays have different lengths.");
+		}
+		double y;
+		int klo, khi, k;
+		double h, b, a;
+
+		klo = 0;
+		khi = n - 1;
+		while (khi - klo > 1)
+		{
+			k = (khi + klo) >> 1;
+			if (xa[k] > x)
+				khi = k;
+			else
+				klo = k;
+		}
+		h = xa[khi] - xa[klo];
+		//System.out.println(""+x+" between "+xa[khi]+" "+xa[klo]);
+		if (h == 0.0)
+			throw new InterpolationException("Two identical x values. The values must be distinct.");
+		a = (xa[khi] - x) / h;
+		b = (x - xa[klo]) / h;
+		y =
+			a * ya[klo]
+				+ b * ya[khi]
+				+ ((a * a * a - a) * y2a[klo] + (b * b * b - b) * y2a[khi])
+					* (h * h)
+					/ 6.0;
+		return y;
+	}
+
+	/**
+	 * Calculates the second derivative of the data. This algorithm
+	 * was taken from:<br>
+	 * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
+	 * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
+	 * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
+	 * Cambridge University Press,
+	 * ISBN 0-521-43108-5,
+	 * chapter 3, pages 113-116.</a><br>
+	 */
+	public double splineInterpolatedDerivative(
+		double[] xa,
+		double[] ya,
+		double[] y2a,
+		double x)
+		throws InterpolationException
+	{
+		int n = xa.length;
+		if (n != ya.length || n != y2a.length)
+		{
+			throw new InterpolationException("Arrays have different lengths.");
+		}
+		double dydx;
+		int klo, khi, k;
+		double h, b, a;
+
+		klo = 0;
+		khi = n - 1;
+		while (khi - klo > 1)
+		{
+			k = (khi + klo) >> 1;
+			if (xa[k] > x)
+				khi = k;
+			else
+				klo = k;
+		}
+		h = xa[khi] - xa[klo];
+		//System.out.println(""+x+" between "+xa[khi]+" "+xa[klo]);
+		if (h == 0.0)
+			throw new InterpolationException("Two identical x values. The values must be distinct.");
+		a = (xa[khi] - x) / h;
+		b = (x - xa[klo]) / h;
+		dydx =
+			(ya[khi] - ya[klo]) / h
+				- ((3 * (a * a) - 1) * h * y2a[klo]) / 6.0
+				+ ((3 * (b * b) - 1) * h * y2a[khi]) / 6.0;
+		return dydx;
+	}
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/print/PagePrinter.java

@@ -0,0 +1,156 @@
+/**
+ *  Filename: $RCSfile: PagePrinter.java,v $
+ *  Purpose:
+ *  Language: Java
+ *  Compiler: JDK 1.3
+ *  Authors:  Fabian Hennecke
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:40 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.print;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+import java.awt.* ;
+import java.awt.print.* ;
+import java.awt.image.BufferedImage ;
+import javax.swing.* ;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+public class PagePrinter
+{
+  Component c;
+  Graphics g;
+  PageFormat pf;
+  public boolean fit_in_possible = true;
+
+  public PagePrinter( Component c, Graphics g, PageFormat pf ) {
+    this.c = c;
+    this.g = g;
+    this.pf = pf;
+  }
+
+  public int print(){
+    Dimension old = c.getSize();
+
+    int x = (int)pf.getImageableX(),
+        y = (int)pf.getImageableY();
+
+    g.translate( x, y );
+
+    double w = (int)pf.getImageableWidth(),
+           h = (int)pf.getImageableHeight();
+
+    if( old.width > w || old.height > h ){
+      boolean rec_turn = false, rec_fit_in = false;
+      if( ( old.width > old.height && h > w ) ||
+          ( old.width < old.height && h < w ) ) {
+        rec_turn = true;
+        if( old.width > h || old.height > w ) rec_fit_in = true;
+      }
+      else rec_fit_in = true;
+
+      JLabel[] text = new JLabel[4];
+      text[0] = new JLabel("The component which should be printed");
+      text[1] = new JLabel("is too large.");
+      text[2] = new JLabel("You can choose if the component should be");
+      JCheckBox cbFitIn = new JCheckBox("fitted-in", rec_fit_in),
+                cbTurn = new JCheckBox("turned", rec_turn );
+      text[3] = new JLabel("(Recommended choice is pre-selected)");
+
+      if( !fit_in_possible ){
+        cbFitIn.setEnabled( false );
+        cbFitIn.setSelected( false );
+      }
+
+      GridBagLayout gbl = new GridBagLayout();
+      JPanel panel = new JPanel( gbl );
+      GridBagConstraints gbc = new GridBagConstraints();
+      gbc.gridx = gbc.gridy = 0;
+      gbc.weightx = gbc.weighty = .5;
+
+      gbc.gridwidth = 2;
+      gbl.setConstraints( text[0], gbc );
+      panel.add( text[0] );
+
+      gbc.gridy++;
+      gbl.setConstraints( text[1], gbc );
+      panel.add( text[1] );
+
+      gbc.gridy++;
+      gbl.setConstraints( text[2], gbc );
+      panel.add( text[2] );
+
+      gbc.gridy++;
+      gbc.gridwidth = 1;
+      gbl.setConstraints( cbFitIn, gbc );
+      panel.add( cbFitIn );
+
+      gbc.gridx++;
+      gbl.setConstraints( cbTurn, gbc );
+      panel.add( cbTurn );
+      gbc.gridx = 0;
+      gbc.gridwidth = 2;
+      gbc.gridy++;
+      gbl.setConstraints( text[3], gbc);
+      panel.add( text[3] );
+
+      int choice = JOptionPane.showOptionDialog( c, panel, "Fit-in",
+                                    JOptionPane.OK_CANCEL_OPTION,
+                                    JOptionPane.QUESTION_MESSAGE,
+                                    null, null, null );
+
+      if( choice == JOptionPane.CANCEL_OPTION || choice == JOptionPane.CLOSED_OPTION )
+        return Printable.NO_SUCH_PAGE;
+
+      else if( choice == JOptionPane.OK_OPTION ){
+
+        if( cbTurn.isSelected() ){
+          BufferedImage img;
+          if( cbFitIn.isSelected() ){
+            double m = Math.min( h / (double)old.width, w / (double)old.height );
+            img = (BufferedImage)c.createImage( (int)( old.height * m ), (int)( old.width * m ) );
+            Graphics2D g2 = img.createGraphics();
+            g2.rotate( Math.toRadians( 90 ) );
+            g2.translate( 0, - old.height * m );
+            c.setSize( (int)( old.width * m ), (int)( old.height * m ) );
+            c.paint( g2 );
+            c.setSize( old );
+          }
+          else{
+            img = (BufferedImage)c.createImage( old.height, old.width );
+            Graphics2D g2 = img.createGraphics();
+            g2.rotate( Math.toRadians( 90 ) );
+            g2.translate( 0, - old.height );
+            c.paint( g2 );
+          }
+          g.drawImage( img, 0, 0, c.getBackground(), c );
+        }
+
+        else{
+          if( cbFitIn.isSelected() ){
+            double m = Math.min( w / (double)old.width, h / (double)old.height );
+            c.setSize( (int)( old.width * m ), (int)( old.height * m ) );
+            c.paint( g );
+            c.setSize( old );
+          }
+          else c.paint( g );
+        }
+      }
+    }
+    else  c.paint( g );
+    return Printable.PAGE_EXISTS;
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/sort/XYDoubleArray.java

@@ -0,0 +1,114 @@
+/**
+ *  Filename: $RCSfile: XYDoubleArray.java,v $
+ *  Purpose:  A description of the contents of this file.
+ *  Language: Java
+ *  Compiler: JDK 1.4
+ *  Authors:  Joerg K. Wegner
+ *  Version:  $Revision: 1.6 $
+ *            $Date: 2001/10/17 11:37:42 $
+ *            $Author: wegnerj $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+/*==========================================================================*
+ * PACKAGE
+ *==========================================================================*/
+
+package wsi.ra.sort;
+
+/*==========================================================================*
+ * IMPORTS
+ *==========================================================================*/
+
+//import wsi.ra.jchart2d.*;
+import java.util.*;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+/**
+ * Defines two <code>double[]</code> arrays.
+ *
+ * @version         $Revision: 1.6 $, $Date: 2001/10/17 11:37:42 $
+ *
+ */
+public class XYDoubleArray implements Cloneable{
+  /*-------------------------------------------------------------------------*
+   * public member variables
+   *-------------------------------------------------------------------------*/
+  //public static final int TABLE_OUTPUT=JChart2DUtils.TABLE_OUTPUT;
+  //public static final int VECTOR_OUTPUT=JChart2DUtils.VECTOR_OUTPUT;
+  public double[] x=null;
+  public double[] y=null;
+
+  /*-------------------------------------------------------------------------*
+   * constructor
+   *-------------------------------------------------------------------------*/
+  public XYDoubleArray(int length)
+  {
+    this.x=new double[length];
+    this.y=new double[length];
+  }
+
+  public XYDoubleArray(double[] x, double[] y)
+  {
+    this.x=x;
+    this.y=y;
+  }
+
+  /*-------------------------------------------------------------------------*
+   * public methods
+   *-------------------------------------------------------------------------*/
+
+  public final void swap(int a, int b)
+  {
+    double xx = x[a]; x[a] = x[b]; x[b] = xx;
+    double yy = y[a]; y[a] = y[b]; y[b] = yy;
+  }
+
+  /*public final void sortX(){
+    QuickInsertSort quickInsertSort = new QuickInsertSort();
+    quickInsertSort.sortX(this);
+  }
+
+  public final void sortY(){
+    QuickInsertSort quickInsertSort = new QuickInsertSort();
+    quickInsertSort.sortY(this);
+  }*/
+
+  //
+  // uses jchart2d methods !;-(
+  //
+  /*public String toString(){
+    return toString(TABLE_OUTPUT);
+  }
+
+  private String toString(int output){
+    if(x==null || y==null)return null;
+    BasicDataSet data=new BasicDataSet(x, y,
+                                       AbstractDataSet.CONTINUOUS_DATA,
+                                       "x",
+                                       "y");
+    String s=JChart2DUtils.writeDataSetToString(data, output);
+    return s;
+  }*/
+
+  public Object clone()
+  {
+    double[] newX=new double[x.length];
+    double[] newY=new double[y.length];
+    XYDoubleArray newArray=new XYDoubleArray(newX, newY);
+
+    for(int i=0;i<x.length;i++){
+      newArray.x[i]=x[i];
+      newArray.y[i]=y[i];
+    }
+
+    return newArray;
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/tool/BasicResourceLoader.java

@@ -0,0 +1,589 @@
+///////////////////////////////////////////////////////////////////////////////
+//  Filename: $RCSfile: BasicResourceLoader.java,v $
+//  Purpose:  Atom representation.
+//  Language: Java
+//  Compiler: JDK 1.4
+//  Authors:  Joerg Kurt Wegner, Gerd Mueller
+//  Version:  $Revision: 1.3 $
+//            $Date: 2005/02/17 16:48:44 $
+//            $Author: wegner $
+//
+// Copyright OELIB:          OpenEye Scientific Software, Santa Fe,
+//                           U.S.A., 1999,2000,2001
+// Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of
+//                           Tuebingen, Germany, 2001,2002,2003,2004,2005
+// Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany,
+//                           2003,2004,2005
+//
+//  This program is free software; you can redistribute it and/or modify
+//  it under the terms of the GNU General Public License as published by
+//  the Free Software Foundation version 2 of the License.
+//
+//  This program is distributed in the hope that it will be useful,
+//  but WITHOUT ANY WARRANTY; without even the implied warranty of
+//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//  GNU General Public License for more details.
+///////////////////////////////////////////////////////////////////////////////
+package wsi.ra.tool;
+
+import java.io.BufferedInputStream;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.LineNumberReader;
+
+import java.net.URL;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Properties;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+import java.util.zip.ZipInputStream;
+
+import wsi.ra.tool.DummyCategory;
+
+
+/**
+ *  Loads resource file from directory OR jar file. Now it is easier possible to
+ *  access resource files in a directory structure or a .jar/.zip file.
+ *
+ * @.author		Marcel Kronfeld
+ * @.author     wegnerj
+ * @.author     Robin Friedman, rfriedman@TriadTherapeutics.com
+ * @.author     Gerd Mueller
+ * @.license GPL
+ * @.cvsversion    $Revision: 1.3 $, $Date: 2005/02/17 16:48:44 $
+ */
+public class BasicResourceLoader implements ResourceLoader
+{
+    //~ Static fields/initializers /////////////////////////////////////////////
+
+    /**
+     *  Obtain a suitable logger.
+     */
+    private static DummyCategory logger = DummyCategory.getInstance(
+            BasicResourceLoader.class.getName());
+    private static BasicResourceLoader resourceLoader;
+
+    //~ Constructors ///////////////////////////////////////////////////////////
+
+    /**
+     *  Constructor for the ResourceLoader object
+     */
+    private BasicResourceLoader()
+    {
+    }
+
+    //~ Methods ////////////////////////////////////////////////////////////////
+
+    /**
+     *  Description of the Method
+     *
+     * @return    Description of the Return Value
+     */
+    public static synchronized BasicResourceLoader instance()
+    {
+        if (resourceLoader == null)
+        {
+            resourceLoader = new BasicResourceLoader();
+        }
+
+        return resourceLoader;
+    }
+
+    /**
+     *  Description of the Method
+     *
+     * @param  resourceFile  Description of the Parameter
+     * @return               Description of the Return Value
+     */
+    public static List readLines(String resourceFile)
+    {
+        return readLines(resourceFile, false);
+    }
+
+    /**
+     *  Description of the Method
+     *
+     * @param  resourceFile    Description of the Parameter
+     * @param  ignoreComments  Description of the Parameter
+     * @return                 Description of the Return Value
+     */
+    public static List readLines(String resourceFile,
+        boolean ignoreCommentedLines)
+    {
+    	return readLines(resourceFile, new String[] {"#"}, 0, -1);
+    }
+    
+    /**
+     *  Description of the Method
+     *
+     * @param  resourceFile    Description of the Parameter
+     * @param  ignorePrefix		array of prefixes which mark a line to be ignored 
+     * @param lOffset		offset of the first line to read
+     * @param lCnt			number of lines to read, if <= 0, all lines are read
+     * @return                 Description of the Return Value
+     */
+    public static List readLines(String resourceFile,
+        String[] ignorePrefix, int lOffset, int lCnt)
+    {
+        if (resourceFile == null)
+        {
+            return null;
+        }
+
+        byte[] bytes = BasicResourceLoader.instance()
+                                          .getBytesFromResourceLocation(
+                resourceFile);
+
+        if (bytes == null)
+        {
+            return null;
+        }
+
+        ByteArrayInputStream sReader = new ByteArrayInputStream(bytes);
+        LineNumberReader lnr = new LineNumberReader(new InputStreamReader(
+                    sReader));
+
+        String line;
+        ArrayList<String> lineData = new ArrayList<String>(100);
+
+        int lineCnt = 0;
+        try
+        {
+            while ((line = lnr.readLine()) != null)
+            {
+				line = line.trim();
+				if (strStartsWithPrefix(line, ignorePrefix) < 0) {
+					if (lineCnt >= lOffset) lineData.add(line);
+					lineCnt++;
+					if ((lCnt > 0) && (lineData.size() == lCnt)) break; 
+				}
+//                if (line.trim().length() > 0) {
+//	            	if ((ignorePrefix == null) || (strStartsWithPrefix(line, ignorePrefix) < 0)) {
+//	            		// if there are no prefixes given or none of them fits, add the line
+//                        lineData.add(line);
+//	                }
+//                }
+            }
+        }
+        catch (IOException ex)
+        {
+            logger.error(ex.getMessage());
+        }
+
+        return lineData;
+    }
+
+    /**
+	 * Parse columns of a data array containing double data. Columns may be selected by giving their
+	 * indices in an int array. If selectedCols is null, all columns are selected. All selected columns
+	 * are expected to contain double data and to be of same length. If rawData is null, null is returned.
+	 * 
+	 * @param rawData 	Strings containing an array with double data columns 
+	 * @param colSplit	String regexp for the splitting of a line
+	 * @param selectedCols		indices of the columns to retrieve, null for all.
+	 * @return
+	 */
+	public static double[][] parseDoubleArray(ArrayList<String> rawData, String colSplit, int[] selectedCols) {
+		String[] entries;
+		double dat[][] = null;
+		if (rawData != null) {
+			try {
+				for (int i=0; i<rawData.size(); i++) {
+					entries = rawData.get(i).split(colSplit);
+					if (i == 0) {	// at the first pass
+						dat = new double[rawData.size()][(selectedCols == null) ? entries.length : selectedCols.length];
+					}
+					fillLine(dat, i, entries, selectedCols);
+				}
+			} catch (Exception e) {
+				e.printStackTrace();
+				System.err.println(e.getMessage());
+			}
+		}
+		return dat;
+	}
+	
+	/**
+	 * Walk through a 2-d-array and retrieve the first bunch of lines for which the given column data lies
+	 * within start and end limits, both inclusively. The original array is not altered.
+	 * 
+	 * @param data		data array to search
+	 * @param col		column to inspect
+	 * @param start		first value to start retrieving from
+	 * @param end		last value to retrieve
+	 * @return
+	 */
+	public static double[][] getLinesByCol(double[][] data, int col, double start, double end) {
+		int cnt = 0;
+		int startIndex = 0;
+		for (int i=0; i<data.length; i++) { 
+			if ((data[i][col] >= start) && (data[i][col] <= end)) {
+				if (cnt == 0) startIndex = i;
+				cnt++;
+			} else if (cnt > 0) break;
+		}
+		
+		double[][] selData = new double[cnt][data[0].length];
+		System.arraycopy(data, startIndex, selData, 0, cnt);
+		return selData;
+	}
+	
+    /**
+	 * Load double data from a text file. An ignore list of prefixes may be specified. The start line and number of lines
+	 * to read may be specified, if lCnt is -1, as many lines as possible are read. The cols array may contain an integer
+	 * list of columns to be read. If null, as many columns as possible are read.
+	 * The data file is expected to be uniform, meaning that all lines which are not ignored, contain double data values
+	 * in all columns.
+	 * 
+	 * @param fname		file name to read
+	 * @param ignorePrefix	lines starting with any of these Strings will be ignored 
+	 * @param colSplit	String regexp for the splitting of a line
+	 * @param lOffset	start at a certain line (0 for top)
+	 * @param lCnt		read as many lines, -1 or 0 for all (from offset). Ignored lines are not counted!
+	 * @param selectedCols		indices of the columns to retrieve, null for all.
+	 * @return
+	 */
+	public static double[][] loadDoubleData(String fname, String[] ignorePrefix, String colSplit, int lOffset, int lCnt, int[] selectedCols) {
+		return parseDoubleArray((ArrayList<String>)readLines(fname, ignorePrefix, lOffset, lCnt), colSplit, selectedCols);
+	}
+    
+	/**
+	 * Fill a line of an array with double values parsed from a String array. A subset of 
+	 * Columns may be selected by giving their indeces in an integer array cols. If cols
+	 * is null, all are converted.
+	 *  
+	 * @param dest
+	 * @param lineCnt
+	 * @param entries
+	 * @param cols
+	 */
+	public static void fillLine(double[][] dest, int lineCnt, String[] entries, int[] cols) {
+		if (((cols == null) && (dest[lineCnt].length != entries.length)) || (cols != null && (dest[lineCnt].length != cols.length))) {
+			System.err.println("error, array dimensions dont match! (SIFTComparisonMatrix");
+		}
+		if (cols == null) {
+			for (int i=0; i<entries.length; i++) {
+				dest[lineCnt][i] = Double.valueOf(entries[i]);
+			}
+		} else {
+			for (int i=0; i<cols.length; i++) {
+				dest[lineCnt][i] = Double.valueOf(entries[cols[i]]);
+			}
+		}
+	}
+	
+	/**
+	 * Test a string for prefixes. If a prefix matches, return its index, else return -1.
+	 * @param str
+	 * @param pref
+	 * @return
+	 */
+	public static int strStartsWithPrefix(String str, String[] pref) {
+		int i=0;
+		if (pref != null) { 
+			for (String prefix : pref) {
+				if (str.startsWith(prefix)) return i;
+				i++;
+			}
+		}
+		return -1;
+	}
+
+    /**
+     *  Gets the byte data from a file at the given resource location.
+     *
+     * @param  rawResrcLoc  Description of the Parameter
+     * @return                   the byte array of file.
+     */
+    public byte[] getBytesFromResourceLocation(String rawResrcLoc)
+    {
+        String resourceLocation = rawResrcLoc.replace('\\', '/');
+
+        //System.out.println("Try to get: "+resourceLocation);
+        if (resourceLocation == null)
+        {
+            return null;
+        }
+
+        // to avoid hours of debugging non-found-files under linux with
+        // some f... special characters at the end which will not be shown
+        // at the console output !!!
+        resourceLocation = resourceLocation.trim();
+
+        // is a relative path defined ?
+        // this can only be possible, if this is a file resource loacation
+        if (resourceLocation.startsWith("..") ||
+                resourceLocation.startsWith("/") ||
+                resourceLocation.startsWith("\\") ||
+                ((resourceLocation.length() > 1) &&
+                    (resourceLocation.charAt(1) == ':')))
+        {
+            return getBytesFromFile(resourceLocation);
+        }
+
+        InputStream in = ClassLoader.getSystemResourceAsStream(resourceLocation);
+
+        if (in == null)
+        {
+            // try again for web start applications
+            in = this.getClass().getClassLoader().getResourceAsStream(
+                    resourceLocation);
+        }
+
+        if (in == null)
+        {
+            return null;
+        }
+
+        if (logger.isDebugEnabled())
+        {
+            logger.debug("Stream opened for " + resourceLocation);
+        }
+
+        byte[] bytes = getBytesFromStream(in);
+
+        return bytes;
+    }
+
+    /**
+     *  Gets the byte data from a file contained in a JAR or ZIP file.
+     *
+     * @param  urlToZipArchive      Description of the Parameter
+     * @param  internalArchivePath  Description of the Parameter
+     * @return                      the byte array of the file.
+     */
+    private byte[] getBytesFromArchive(String urlToZipArchive,
+        String internalArchivePath)
+    {
+        URL url = null;
+        int size = -1;
+        byte[] b = null;
+
+        try
+        {
+            url = new URL(urlToZipArchive);
+
+            // extracts just sizes only.
+            ZipFile zf = new ZipFile(url.getFile());
+            Enumeration e = zf.entries();
+
+            while (e.hasMoreElements())
+            {
+                ZipEntry ze = (ZipEntry) e.nextElement();
+
+                if (ze.getName().equals(internalArchivePath))
+                {
+                    if (ze.isDirectory())
+                    {
+                        return null;
+                    }
+
+                    // only files with <65536 bytes are allowed
+                    if (ze.getSize() > 65536)
+                    {
+                        System.out.println(
+                            "Resource files should be smaller than 65536 bytes...");
+                    }
+
+                    size = (int) ze.getSize();
+                }
+            }
+
+            zf.close();
+
+            FileInputStream fis = new FileInputStream(url.getFile());
+            BufferedInputStream bis = new BufferedInputStream(fis);
+            ZipInputStream zis = new ZipInputStream(bis);
+            ZipEntry ze = null;
+
+            while ((ze = zis.getNextEntry()) != null)
+            {
+                if (ze.getName().equals(internalArchivePath))
+                {
+                    b = new byte[(int) size];
+
+                    int rb = 0;
+                    int chunk = 0;
+
+                    while (((int) size - rb) > 0)
+                    {
+                        chunk = zis.read(b, rb, (int) size - rb);
+
+                        if (chunk == -1)
+                        {
+                            break;
+                        }
+
+                        rb += chunk;
+                    }
+                }
+            }
+        }
+        catch (Exception e)
+        {
+            logger.error(e.getMessage());
+
+            return null;
+        }
+
+        return b;
+    }
+
+    /**
+     *  Gets the byte data from a file.
+     *
+     * @param  fileName  Description of the Parameter
+     * @return           the byte array of the file.
+     */
+    private byte[] getBytesFromFile(String fileName)
+    {
+        if (fileName.startsWith("/cygdrive/"))
+        {
+            int length = "/cygdrive/".length();
+            fileName = fileName.substring(length, length + 1) + ":" +
+                fileName.substring(length + 1);
+        }
+
+        if (logger.isDebugEnabled())
+        {
+            logger.debug("Trying to get file from " + fileName);
+        }
+
+        File file = new File(fileName);
+        FileInputStream fis = null;
+
+        try
+        {
+            fis = new FileInputStream(file);
+        }
+        catch (Exception e)
+        {
+            logger.error(e.getMessage());
+
+            return null;
+        }
+
+        BufferedInputStream bis = new BufferedInputStream(fis);
+
+        // only files with <65536 bytes are allowed
+        //if( file.length() > 65536 ) System.out.println("Resource files should be smaller than 65536 bytes...");
+        int size = (int) file.length();
+        byte[] b = new byte[size];
+        int rb = 0;
+        int chunk = 0;
+
+        try
+        {
+            while (((int) size - rb) > 0)
+            {
+                chunk = bis.read(b, rb, (int) size - rb);
+
+                if (chunk == -1)
+                {
+                    break;
+                }
+
+                rb += chunk;
+            }
+        }
+        catch (Exception e)
+        {
+            logger.error(e.getMessage());
+
+            return null;
+        }
+
+        return b;
+    }
+
+    /**
+     *  Gets the byte data from a file.
+     *
+     * @param  fileName  Description of the Parameter
+     * @return           the byte array of the file.
+     */
+    private byte[] getBytesFromStream(InputStream stream)
+    {
+        if (stream == null)
+        {
+            return null;
+        }
+
+        if (logger.isDebugEnabled())
+        {
+            logger.debug("Trying to get file from stream.");
+        }
+
+        BufferedInputStream bis = new BufferedInputStream(stream);
+
+        try
+        {
+            int size = (int) bis.available();
+            byte[] b = new byte[size];
+            int rb = 0;
+            int chunk = 0;
+
+            while (((int) size - rb) > 0)
+            {
+                chunk = bis.read(b, rb, (int) size - rb);
+
+                if (chunk == -1)
+                {
+                    break;
+                }
+
+                rb += chunk;
+            }
+
+            return b;
+        }
+        catch (Exception e)
+        {
+            logger.error(e.getMessage());
+
+            return null;
+        }
+    }
+    
+	/**
+	 *
+	 */
+	public static Properties readProperties(String resourceName) throws Exception {
+//		if (TRACE)
+//			System.out.println("EvAClient.readProperties of " + resourceName);
+		Properties prop = new Properties();
+		BasicResourceLoader loader = BasicResourceLoader.instance();
+
+		byte bytes[] = loader.getBytesFromResourceLocation(resourceName);
+		if (bytes != null) {
+			ByteArrayInputStream bais = new ByteArrayInputStream(bytes);
+			prop.load(bais);
+		}
+		if (prop != null)
+			return prop;
+		/////////////
+
+		int slInd = resourceName.lastIndexOf('/');
+		if (slInd != -1)
+			resourceName = resourceName.substring(slInd + 1);
+		Properties userProps = new Properties();
+		File propFile = new File(File.separatorChar + "resources" + File.separatorChar + resourceName);
+		if (propFile.exists()) {
+			try {
+				userProps.load(new FileInputStream(propFile));
+			} catch (Exception ex) {
+				System.out.println("Problem reading user properties: " + propFile);
+			}
+		}
+		return userProps;
+	}
+	
+	
+}

src/wsi/ra/tool/DummyCategory.java

@@ -0,0 +1,41 @@
+package wsi.ra.tool;
+
+/**
+ * Dummy class replacing the log4j Category because log4j couldnt be included in a clean
+ * way and seemingly wasnt used in the main classes anyways.
+ * 
+ * @author mkron, mpaly
+ *
+ */
+public class DummyCategory {
+	static DummyCategory dummy = new DummyCategory();
+	static boolean bDebugEnabled = false;
+	
+	public void error() {
+		System.err.println("Error");
+	}
+	
+	public void error(String msg) {
+		System.err.println(msg);
+	}
+
+	public static DummyCategory getInstance(String str) {
+		return dummy;
+	}
+	
+    public boolean isDebugEnabled() {
+    	return bDebugEnabled;
+    }
+    
+    public void debug(String str) {
+    	System.err.println(str);
+    }
+    
+    public void info(String str) {
+    	System.err.println(str);
+    }
+    
+    public void warn(String str) {
+    	System.err.println(str);
+    }
+}

src/wsi/ra/tool/IntegerArrayList.java

@@ -0,0 +1,161 @@
+/**
+ *  Filename: $RCSfile: IntegerArrayList.java,v $
+ *  Purpose:  This class is similar to 'java.util.ArrayList', except that it can
+ *            only hold and manage integer values.
+ *  Language: Java
+ *  Compiler: JDK 1.2
+ *  Authors:  Fred Rapp
+ *  Version:  $Revision: 1.1.1.1 $
+ *            $Date: 2003/07/03 14:59:40 $
+ *            $Author: ulmerh $
+ *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+ */
+
+package wsi.ra.tool;
+
+/*==========================================================================*
+ * CLASS DECLARATION
+ *==========================================================================*/
+
+/**
+ * This class is similar to 'java.util.ArrayList', except that it can
+ * only hold and manage integer values.
+ */
+public class IntegerArrayList
+{
+  /*-------------------------------------------------------------------------*
+   * private member variables
+   *-------------------------------------------------------------------------*/
+
+  private int[] integerArray = null;
+  private int   integerCount = 0;
+
+  private int initialSize;
+  private int incrementFactor;
+
+  /*------------------------------------------------------------------------*
+   * constructor
+   *------------------------------------------------------------------------*/
+
+  public IntegerArrayList()
+  {
+    // call other constructor with default values
+    this(100, 3);
+  }
+
+  public IntegerArrayList(int initialSize, int incrementFactor)
+  {
+    this.initialSize     = initialSize;
+    this.incrementFactor = incrementFactor;
+
+    // create new integer array of initial size
+    integerArray = new int[initialSize];
+  }
+
+  public void destroy() { integerArray = null; integerCount = 0; }
+
+  /*-------------------------------------------------------------------------*
+   * public methods
+   *-------------------------------------------------------------------------*/
+
+  /**
+   * Clears the contents of this integer list and sets it back to it's initial state.
+   */
+  public void clear() { integerArray = new int[initialSize]; integerCount = 0; }
+
+  /**
+   * Returns the number of components in this list.
+   */
+  public int size() { return integerCount; }
+
+  /**
+   * Parses given string to integer and adds it to the integer list.
+   * @return true if parsing was successful, false if an error occured.
+   */
+  public boolean add(String stringValue)
+  {
+    boolean success = false;
+    try {
+      int value = Integer.parseInt(stringValue);
+      add(value);
+      success = true;
+    }
+    catch (Exception e) {}
+    return success;
+  }
+
+  /**
+   * Adds a new integer value to the integer list.
+   */
+  public void add(int value)
+  {
+    // check integer array size
+    if (integerCount == integerArray.length)
+    {
+      // increase size of int array
+      int old_length = integerArray.length;
+      int new_length = incrementFactor * old_length;
+      int[] new_array = new int[new_length];
+      for (int i=0; i<old_length; i++) {
+        new_array[i] = integerArray[i];
+      }
+      integerArray = new_array;
+    }
+    // add given value to array
+    integerArray[integerCount++] = value;
+  }
+
+  /**
+   * Returns the integer value at the given position or 'min-value' if out of array bounds.
+   */
+  public int get(int index)
+  {
+    if ((index < 0) || (index >= integerCount)) { return Integer.MIN_VALUE; }
+
+    return integerArray[index];
+  }
+
+  /**
+   * Returns the contents of this list as an array of integer values.
+   * @param exactLength  determines if the returned array should have the exactly right length, or if longer arrays are allowed
+   */
+  public int[] getIntegerArray(boolean exactLength)
+  {
+    // check if we can simply return our internal integer array
+    if (!exactLength || (integerArray.length == integerCount)) { return integerArray; }
+
+    // make a copy of the array with the exactly right length
+    int size = integerCount;
+    int[] new_array = new int[ size];
+    for (int i=0; i< size; i++) { new_array[i] = integerArray[i]; }
+    return new_array;
+  }
+
+  /**
+   * Returns the contents of this list as an array of double values.
+   */
+  public double[] getDoubleArray()
+  {
+    // make a copy of the array
+    int size = integerCount;
+    double[] new_array = new double[ size];
+    for (int i=0; i< size; i++) { new_array[i] = integerArray[i]; }
+    return new_array;
+  }
+
+  /**
+   * Returns the contents of this list as an array of strings.
+   */
+  public String[] getStringArray()
+  {
+    // make a copy of the array
+    int size = integerCount;
+    String[] new_array = new String[ size];
+    for (int i=0; i<size; i++) { new_array[i] = "" + integerArray[i]; }
+    return new_array;
+  }
+}
+
+/****************************************************************************
+ * END OF FILE
+ ****************************************************************************/

src/wsi/ra/tool/ResourceLoader.java

@@ -0,0 +1,52 @@
+///////////////////////////////////////////////////////////////////////////////
+//Filename: $RCSfile: ResourceLoader.java,v $
+//Purpose:  TODO description.
+//Language: Java
+//Compiler: JDK 1.5
+//Created:  Jan 16, 2005
+//Authors:  Joerg Kurt Wegner
+//Version:  $Revision: 1.8 $
+//          $Date: 2005/02/17 16:48:44 $
+//          $Author: wegner $
+//
+// Copyright OELIB:          OpenEye Scientific Software, Santa Fe,
+//                           U.S.A., 1999,2000,2001
+// Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of
+//                           Tuebingen, Germany, 2001,2002,2003,2004,2005
+// Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany,
+//                           2003,2004,2005
+//
+//This program is free software; you can redistribute it and/or modify
+//it under the terms of the GNU General Public License as published by
+//the Free Software Foundation version 2 of the License.
+//
+//This program is distributed in the hope that it will be useful,
+//but WITHOUT ANY WARRANTY; without even the implied warranty of
+//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//GNU General Public License for more details.
+///////////////////////////////////////////////////////////////////////////////
+package wsi.ra.tool;
+
+/**
+ * TODO description.
+ *
+ * @.author     wegnerj
+ * @.license    GPL
+ * @.cvsversion $Revision: 1.8 $, $Date: 2005/02/17 16:48:44 $
+ */
+public interface ResourceLoader
+{
+    //~ Methods ////////////////////////////////////////////////////////////////
+
+    /**
+     *  Gets the byte data from a file at the given resource location.
+     *
+     * @param  rawResrcLoc  Description of the Parameter
+     * @return                   the byte array of file.
+     */
+    byte[] getBytesFromResourceLocation(String rawResrcLoc);
+}
+
+///////////////////////////////////////////////////////////////////////////////
+//END OF FILE.
+///////////////////////////////////////////////////////////////////////////////

src/wsi/ra/tool/StatisticUtils.java

@@ -0,0 +1,534 @@
+///////////////////////////////////////////////////////////////////////////////
+//  Filename: $RCSfile: StatisticUtils.java,v $
+//  Purpose:  Interface definition for calling external programs from JOELib.
+//  Language: Java
+//  Compiler: JDK 1.4
+//  Authors:  Joerg K. Wegner
+//  Version:  $Revision: 1.1 $
+//            $Date: 2004/02/28 17:19:28 $
+//            $Author: ulmerh $
+//
+//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
+//
+///////////////////////////////////////////////////////////////////////////////
+
+package wsi.ra.tool;
+
+/**
+ * Statistic utils.
+ */
+public class StatisticUtils
+{
+  /** The natural logarithm of 2. */
+  public static double log2 = Math.log(2);
+
+  /** The small deviation allowed in double comparisons */
+  public static double SMALL = 1e-6;
+
+  /**
+   * Returns the correlation coefficient of two double vectors.
+   *
+   * @param y1 double vector 1
+   * @param y2 double vector 2
+   * @param n the length of two double vectors
+   * @return the correlation coefficient
+   */
+  public final static double correlation(double y1[],double y2[],int n) {
+
+    int i;
+    double av1 = 0.0, av2 = 0.0, y11 = 0.0, y22 = 0.0, y12 = 0.0, c;
+
+    if (n <= 1) {
+      return 1.0;
+    }
+    for (i = 0; i < n; i++) {
+      av1 += y1[i];
+      av2 += y2[i];
+    }
+    av1 /= (double) n;
+    av2 /= (double) n;
+    for (i = 0; i < n; i++) {
+      y11 += (y1[i] - av1) * (y1[i] - av1);
+      y22 += (y2[i] - av2) * (y2[i] - av2);
+      y12 += (y1[i] - av1) * (y2[i] - av2);
+    }
+    if (y11 * y22 == 0.0) {
+      c=1.0;
+    } else {
+      c = y12 / Math.sqrt(Math.abs(y11 * y22));
+    }
+
+    return c;
+  }
+
+  /**
+   * Computes differential shannon entropy
+   *
+   * @return DSE=SE(AB)-0.5*[SE(A)+SE(B)]
+   */
+  public static double differentialShannon(int counts1[],int counts2[], int n, int countsSum1, int countsSum2)
+  {
+    double seA=0.0;
+    double seB=0.0;
+    double seAB=0.0;
+    double c=0.0;
+    int AB;
+    int allSum = countsSum1+countsSum2;
+    for(int i=0;i<n;i++)
+    {
+      AB = counts1[i] + counts2[i];
+      seA -= xlogx(((double)counts1[i])/((double)countsSum1));
+      seB -= xlogx(((double)counts2[i])/((double)countsSum2));
+      seAB -= xlogx(((double)AB)/((double)allSum));
+    }
+
+    c= seAB - 0.5*(seA+seB);
+
+    return c;
+  }
+
+  /**
+   * Computes entropy for an array of integers.
+   *
+   * @param counts array of counts
+   * @return - a log2 a - b log2 b - c log2 c + (a+b+c) log2 (a+b+c)
+   * when given array [a b c]
+   */
+  public static double info(int counts[]) {
+
+    int total = 0;
+    int c;
+    double x = 0;
+    for (int j = 0; j < counts.length; j++) {
+      x -= xlogx(counts[j]);
+      total += counts[j];
+    }
+    return x + xlogx(total);
+  }
+
+  /**
+   * Computes shannon entropy for an array of integers.
+   *
+   * @param counts array of counts
+   * @return - a log2 a - b log2 b - c log2 c
+   * when given array [a b c]
+   */
+  public static double shannon(int counts[], int countsSum) {
+
+    double x = 0;
+    for (int j = 0; j < counts.length; j++) {
+      x -= xlogx( ((double)counts[j])/ ((double)countsSum));
+    }
+    return x;
+  }
+
+
+  /**
+   * Returns the logarithm of a for base 2.
+   *
+   * @param a a double
+   */
+  public static final double log2(double a) {
+
+    return Math.log(a) / log2;
+  }
+
+  /**
+   * Returns index of maximum element in a given
+   * array of doubles. First maximum is returned.
+   *
+   * @param doubles the array of doubles
+   * @return the index of the maximum element
+   */
+  public static int maxIndex(double [] doubles) {
+
+    double maximum = 0;
+    int maxIndex = 0;
+
+    for (int i = 0; i < doubles.length; i++) {
+      if ((i == 0) || (doubles[i] > maximum)) {
+	maxIndex = i;
+	maximum = doubles[i];
+      }
+    }
+
+    return maxIndex;
+  }
+
+  /**
+   * Returns index of maximum element in a given
+   * array of integers. First maximum is returned.
+   *
+   * @param ints the array of integers
+   * @return the index of the maximum element
+   */
+  public static int maxIndex(int [] ints) {
+
+    int maximum = 0;
+    int maxIndex = 0;
+
+    for (int i = 0; i < ints.length; i++) {
+      if ((i == 0) || (ints[i] > maximum)) {
+	maxIndex = i;
+	maximum = ints[i];
+      }
+    }
+
+    return maxIndex;
+  }
+
+  /**
+   * Computes the mean for an array of doubles.
+   *
+   * @param vector the array
+   * @return the mean
+   */
+  public static double mean(double[] vector) {
+
+    double sum = 0;
+
+    if (vector.length == 0) {
+      return 0;
+    }
+    for (int i = 0; i < vector.length; i++) {
+      sum += vector[i];
+    }
+    return sum / (double) vector.length;
+  }
+
+  /**
+   * Returns index of minimum element in a given
+   * array of integers. First minimum is returned.
+   *
+   * @param ints the array of integers
+   * @return the index of the minimum element
+   */
+  public static int minIndex(int [] ints) {
+
+    int minimum = 0;
+    int minIndex = 0;
+
+    for (int i = 0; i < ints.length; i++) {
+      if ((i == 0) || (ints[i] < minimum)) {
+	minIndex = i;
+	minimum = ints[i];
+      }
+    }
+
+    return minIndex;
+  }
+
+  /**
+   * Returns index of minimum element in a given
+   * array of doubles. First minimum is returned.
+   *
+   * @param doubles the array of doubles
+   * @return the index of the minimum element
+   */
+  public static int minIndex(double [] doubles) {
+
+    double minimum = 0;
+    int minIndex = 0;
+
+    for (int i = 0; i < doubles.length; i++) {
+      if ((i == 0) || (doubles[i] < minimum)) {
+	minIndex = i;
+	minimum = doubles[i];
+      }
+    }
+
+    return minIndex;
+  }
+
+  /**
+   * Normalizes the doubles in the array by their sum.
+   *
+   * @param doubles the array of double
+   * @exception IllegalArgumentException if sum is Zero or NaN
+   */
+  public static void normalize(double[] doubles) {
+
+    double sum = 0;
+    for (int i = 0; i < doubles.length; i++) {
+      sum += doubles[i];
+    }
+    normalize(doubles, sum);
+  }
+
+  /**
+   * Normalizes the doubles in the array using the given value.
+   *
+   * @param doubles the array of double
+   * @param sum the value by which the doubles are to be normalized
+   * @exception IllegalArgumentException if sum is zero or NaN
+   */
+  public static void normalize(double[] doubles, double sum) {
+
+    if (Double.isNaN(sum)) {
+      throw new IllegalArgumentException("Can't normalize array. Sum is NaN.");
+    }
+    if (sum == 0) {
+      // Maybe this should just be a return.
+      throw new IllegalArgumentException("Can't normalize array. Sum is zero.");
+    }
+    for (int i = 0; i < doubles.length; i++) {
+      doubles[i] /= sum;
+    }
+  }
+
+
+  /**
+   * Computes the variance for an array of doubles.
+   *
+   * @param vector the array
+   * @return the variance
+   */
+  public static double variance(double[] vector) {
+
+    double sum = 0, sumSquared = 0;
+
+    if (vector.length <= 1) {
+      return 0;
+    }
+    for (int i = 0; i < vector.length; i++) {
+      sum += vector[i];
+      sumSquared += (vector[i] * vector[i]);
+    }
+    double result = (sumSquared - (sum * sum / (double) vector.length)) /
+      (double) (vector.length - 1);
+
+    // We don't like negative variance
+    if (result < 0) {
+      return 0;
+    } else {
+      return result;
+    }
+  }
+
+  /**
+   * Computes the sum of the elements of an array of doubles.
+   *
+   * @param doubles the array of double
+   * @return the sum of the elements
+   */
+  public static double sum(double[] doubles) {
+
+    double sum = 0;
+
+    for (int i = 0; i < doubles.length; i++) {
+      sum += doubles[i];
+    }
+    return sum;
+  }
+
+  /**
+   * Computes the sum of the elements of an array of integers.
+   *
+   * @param ints the array of integers
+   * @return the sum of the elements
+   */
+  public static int sum(int[] ints) {
+
+    int sum = 0;
+
+    for (int i = 0; i < ints.length; i++) {
+      sum += ints[i];
+    }
+    return sum;
+  }
+
+  /**
+   * Returns c*log2(c) for a given integer value c.
+   *
+   * @param c an integer value
+   * @return c*log2(c) (but is careful to return 0 if c is 0)
+   */
+  public static final double xlogx(int c) {
+
+    if (c == 0) {
+      return 0.0;
+    }
+    return c * StatisticUtils.log2((double) c);
+  }
+
+  /**
+   * Returns c*log2(c) for a given value c.
+   *
+   * @param c an integer value
+   * @return c*log2(c) (but is careful to return 0 if c is 0)
+   */
+  public static final double xlogx(double c) {
+
+    if (c == 0) {
+      return 0.0;
+    }
+    return c * StatisticUtils.log2( c);
+  }
+
+  /**
+   * Tests if a is equal to b.
+   *
+   * @param a a double
+   * @param b a double
+   */
+  public static final boolean eq(double a, double b){
+
+    return (a - b < SMALL) && (b - a < SMALL);
+  }
+
+  /**
+   * Tests if a is smaller or equal to b.
+   *
+   * @param a a double
+   * @param b a double
+   */
+  public static final boolean smOrEq(double a,double b) {
+
+    return (a-b < SMALL);
+  }
+
+  /**
+   * Tests if a is greater or equal to b.
+   *
+   * @param a a double
+   * @param b a double
+   */
+  public static final boolean grOrEq(double a,double b) {
+
+    return (b-a < SMALL);
+  }
+
+  /**
+   * Tests if a is smaller than b.
+   *
+   * @param a a double
+   * @param b a double
+   */
+  public static final boolean sm(double a,double b) {
+
+    return (b-a > SMALL);
+  }
+
+  /**
+   * Tests if a is greater than b.
+   *
+   * @param a a double
+   * @param b a double
+   */
+  public static final boolean gr(double a,double b) {
+
+    return (a-b > SMALL);
+  }
+
+  /**
+   * returns root mean square error.
+   */
+  public static final double rmsError(double array1[], double array2[])
+  {
+    if ((array1 == null) || (array2 == null)) { return -1.0; }
+
+    double errorValueRMS = 0;
+    for (int i=0; i<array1.length; i++)
+    {
+      // add squared error value
+      errorValueRMS += (array1[i] - array2[i]) * (array1[i] - array2[i]);
+    }
+    // calculate mean and root of the sum of the squared error values
+    errorValueRMS = Math.sqrt(errorValueRMS / (double) array1.length);
+
+    return errorValueRMS;
+  }
+
+  /**
+   * Returns the correlation coefficient r^2.
+   *
+   * Correlation ("Statistik", 7 Aufl., Hartung, 1989, Kapitel 9 und 10, S.546-608):
+   * a=yMess[i];
+   * b=yWahr[i];
+   * aa=a*a;
+   * bb=b*b;
+   * ab=a*b;
+   * numerator=sumAB-(sumA*sumB/n);
+   * denominator=sqrt[(sumAA-(sumA*sumA/n))*(sumBB-(sumB*sumB/n))];
+   * R=correlationcoefficient=numerator/denominator;
+   *
+   * @author Joerg K. Wegner
+   */
+  public static double getCorrelationCoefficient(double array1[], double array2[])
+  {
+    if ((array1 == null) || (array2 == null)) { return -2.0; }
+
+    double sumA  = 0;
+    double sumB  = 0;
+    double sumAB = 0;
+    double sumAA = 0;
+    double sumBB = 0;
+
+    for (int i=0; i<array1.length; i++)
+    {
+      double a = array1[i];
+      double b = array2[i];
+
+      sumA  += a;
+      sumB  += b;
+      sumAA += a*a;
+      sumBB += b*b;
+      sumAB += a*b;
+    }
+
+    double n = (double) array1.length;
+    double numerator   = sumAB - (sumA*sumB/n);
+    double denominator = Math.sqrt((sumAA - (sumA*sumA/n)) * (sumBB - (sumB*sumB/n)));
+    double corrCoefficient = numerator / denominator;
+    corrCoefficient *= corrCoefficient;
+
+    return corrCoefficient;
+  }
+
+  /**
+   * Main method for testing this class.
+   */
+  public static void main(String[] ops) {
+
+//    System.out.println("test (0.5, 100): " +
+//		       StatisticUtils.test(100));
+  }
+
+// The following methods got mysteriously lost maybe during cvs-svn refactoring.
+// For the time being I add method thunks which give a warning when called. (mkron)
+  public static double quadratic_entropy(double[] ds) {
+	  // TODO Auto-generated method stub
+	  System.err.println("warning, not implemented!");
+	  return 0;
+  }
+
+  public static double mutual_information(double[] ds, double[] ds2, int nbins) {
+	  // TODO Auto-generated method stub
+	  System.err.println("warning, not implemented!");
+	  return 0;
+  }
+
+	public static double quadratic_mutinf(double[] feature, double[] labels) {
+		// TODO Auto-generated method stub
+		System.err.println("warning, not implemented!");
+		return 0;
+	}
+	
+	public static double quadratic_mutinf(double[] feature, double[] labels, int[] classes) {
+		// TODO Auto-generated method stub
+		System.err.println("warning, not implemented!");
+		return 0;
+	}
+
+	public static double SUquadratic(double[] feature, double[] labels) {
+		// TODO Auto-generated method stub
+		System.err.println("warning, not implemented!");
+		return 0;
+	}
+
+	public static double SUquadratic(double[] feature, double[] labels, int[] classes) {
+		// TODO Auto-generated method stub
+		System.err.println("warning, not implemented!");
+		return 0;
+	}
+}

src/wsi/ra/tool/matlab/JMatLink.c

@@ -0,0 +1,481 @@
+/*****************************************************************************
+
+*                           JMatLink                                         *
+
+******************************************************************************
+
+* (c) 1999-2001 Stefan Mueller  (email: stefan@held-mueller.de)              *
+
+******************************************************************************
+
+* 19.01.1999  beginning (reuse of HelloWorld example, Java Tutorial)  (0.01) *
+
+* 06.02.1999  separation from gui                                     (0.02) *
+
+* 27.03.1999  engGetScalar, engGetVector, engGetArray                 (0.03) *
+
+*             engGetScalar already working                                   *
+
+* 01.04.1999  engGetArray: hints from bwymans@home.com                       *
+
+* 02.05.1999  engGetArray is working now                              (0.04) *
+
+* 20.05.1999  begin of engPutArray                                           *
+
+* 13.08.1999  renamed all native methods to ...NATIVE                 (0.05) *
+
+* 30.08.1999  beginning to include some failure checks                (0.06) *
+
+* 31.08.1999  increased BUFSIZE to account for larger outputs         (0.07) *
+
+* 11.09.1999  get char arrays from workspace                          (0.08) *
+
+* 10.10.1999  engPutArray[][] completed                               (0.10) *
+
+* 04/07/2001  restart work on JMatLink                                (0.11) *
+
+* 05/24/2001  engOpenSingleUse                                        (0.11) *
+
+*             Introduce pool of engine pointers                              *
+
+*             Removed engPutArray, engPutArray[], always use engPutArray[][] *
+
+* 07/31/01    Code Cleanup                                                   *
+
+* 08/11/01    Moved to new version numer                              (1.00) *
+
+******************************************************************************/
+
+
+
+
+
+/* **** ToDo ****
+
+*  complex number support
+
+*
+
+*/
+
+
+
+
+
+#include <jni.h>
+
+#include "JMatLink.h"
+
+#include <stdio.h>
+
+
+
+
+
+#include <stdlib.h>
+
+#include <string.h>
+
+#include "engine.h"
+
+
+
+#define V5_COMPAT
+
+#define  BUFSIZE 2560
+
+
+
+    mxArray *T      = NULL;
+
+    mxArray *result = NULL;
+
+    char buffer[BUFSIZE];
+
+    double *TP;
+
+    mxArray  *arrayP;
+
+    jdouble  scalar;
+
+    int      engOpenMarkerI = 0;    // Remember the engine that was opened with
+
+                                   //   engOpen-command 
+
+
+
+    #define enginePMax 10          // Maximum number of engines opened at the 
+
+                                   //   same time.
+
+    Engine *engineP[ enginePMax ]; // Array of pointers to engines
+
+                                   // Element 0 is reserved
+
+
+
+    jboolean debugB = JNI_FALSE;       // No debug messages from start
+
+   
+
+
+
+/******************************************************************************/
+
+int getUnusedEnginePointer()
+
+{
+
+    /* Find unsed entry in array of pointers to engine */
+
+    /* j=0 is reserved!!                               */
+
+
+
+    int j;
+
+
+
+    for (j=1; j<enginePMax; j++) 
+
+    {
+
+        if ( engineP[j] == NULL )
+
+        {
+
+            if (debugB) printf("engOpen %i", j);
+
+            return j;                // Unused entry in array
+
+        }
+
+        else
+
+        {
+
+
+
+        }
+
+    }
+
+
+
+    if (debugB) printf("engOpen: getUnusedEnginePointer no more pointers available");
+
+
+
+    return 0; // all entries in use
+
+}
+
+
+
+void delEnginePointer(int p)
+
+{
+
+
+
+    if (    ( p < 1           )
+
+         || ( p >= enginePMax )
+
+       )
+
+    {
+
+        return; // pointer out of allowed region
+
+    }
+
+
+
+    // free entry in array
+
+    engineP[p] = 0;
+
+
+
+}
+
+
+
+
+
+JNIEXPORT void JNICALL Java_wsi_ra_tool_matlab_JMatLink_setDebugNATIVE
+
+            (JNIEnv *env, jobject obj, jboolean d)
+
+{
+
+    if (d) debugB = JNI_TRUE;
+
+    else   debugB = JNI_FALSE;
+
+     
+
+}
+
+
+
+
+
+/********************************************************************************/
+
+ 
+
+/********************************************************************************/
+
+/********************    int   engOpenNATIVE( startcmd )    *********************/
+
+/********************************************************************************/
+
+
+
+JNIEXPORT jint JNICALL Java_wsi_ra_tool_matlab_JMatLink_engOpenNATIVE__Ljava_lang_String_2
+
+                                 (JNIEnv *env, jobject obj, jstring startCmdS_JNI)
+
+{
+
+    int         engineI;   
+
+    const char *openS; 
+
+
+
+    if (engOpenMarkerI != 0) return engOpenMarkerI; // engOpen already used before
+
+                                        // return handle valid connection
+
+
+
+    openS = (*env)->GetStringUTFChars(env, startCmdS_JNI, 0);
+
+
+
+    /* find unused entry in engine array */
+
+    engineI = getUnusedEnginePointer();
+
+
+
+    if (engineI==0) return 0;  // no more pointers available
+
+
+
+    if (!(engineP[engineI] = engOpen(openS)) )
+
+    {
+
+        if (debugB) fprintf(stderr, "\nCan't start MATLAB engine\n");
+
+        (*env)->ReleaseStringUTFChars(env, startCmdS_JNI, openS); // free memory
+
+        delEnginePointer(engineI);
+
+        return 0;
+
+    }
+
+
+
+    engOpenMarkerI = engineI; // Remember engine that was opened with engOpen()    
+
+
+
+    (*env)->ReleaseStringUTFChars(env, startCmdS_JNI, openS); // free memory
+
+
+
+    return engineI;
+
+}
+
+
+
+/********************************************************************************/
+
+/****************    int   engOpenSingleUseNATIVE( startcmd )    ****************/
+
+/********************************************************************************/
+
+JNIEXPORT jint JNICALL Java_wsi_ra_tool_matlab_JMatLink_engOpenSingleUseNATIVE 
+
+                               (JNIEnv *env, jobject obj, jstring startCmdS_JNI)
+
+{
+
+    const char *openS     = (*env)->GetStringUTFChars(env, startCmdS_JNI, 0);
+
+    int         retStatus = 0;
+
+    int         engineI;   
+
+
+
+    /* find unused entry in engine array */
+
+    engineI = getUnusedEnginePointer();
+
+
+
+    if (engineI==0) return 0;  // no more pointers avaiblable
+
+
+
+    if (!(engineP[engineI] = engOpenSingleUse(openS, NULL, &retStatus)))
+
+    {
+
+        if (debugB) fprintf(stderr, "\nCan't start MATLAB engine\n");
+
+        (*env)->ReleaseStringUTFChars(env, startCmdS_JNI, openS); // free memory
+
+
+
+        delEnginePointer(engineI);
+
+        return 0;
+
+    }
+
+
+
+    (*env)->ReleaseStringUTFChars(env, startCmdS_JNI, openS); // free memory
+
+
+
+    return engineI;
+
+}
+
+
+
+
+
+/********************************************************************************/
+
+/****************        int  engCloseNATIVE( int epI )          ****************/
+
+/********************************************************************************/
+
+JNIEXPORT jint JNICALL Java_wsi_ra_tool_matlab_JMatLink_engCloseNATIVE__I  
+
+                                           (JNIEnv *env, jobject obj, jint engine)
+
+{
+
+    int retValI;
+
+
+
+    // Check if engine pointer is within allowed region
+
+    if (( engine < 1 ) || ( engine >= enginePMax ))
+
+    {
+
+        return 0; // Pointer is out of allowed region
+
+    }
+
+
+
+
+
+    if ( engineP[ engine ] != NULL )
+
+    {
+
+        retValI = engClose(engineP[ engine ]);
+
+        delEnginePointer( engine );
+
+        if (engine == engOpenMarkerI)
+
+        {
+
+            // This engine was opened with engOpen() before
+
+            engOpenMarkerI = 0;
+
+        }
+
+        if (debugB) printf("\n engClose \n");
+
+    }
+
+    else
+
+    {
+
+        return 0;
+
+    }
+
+}
+
+
+
+
+
+
+
+/********************************************************************************/
+
+/***********   int  engEvalStringNATIVE( int epI, String evalS )    *************/
+
+/********************************************************************************/
+
+JNIEXPORT jint JNICALL Java_wsi_ra_tool_matlab_JMatLink_engEvalStringNATIVE__ILjava_lang_String_2
+
+                        (JNIEnv *env, jobject obj, jint engine, jstring evalS_JNI)
+
+{
+
+    int  retValI = 0;
+
+    const char *evalS = (*env)->GetStringUTFChars(env, evalS_JNI, 0);
+
+
+
+
+
+    // Check if engine pointer is within allowed region
+
+    if (( engine < 1 ) || ( engine >= enginePMax ))
+
+    {
+
+        return 0; // Pointer is out of allowed region
+
+    }
+
+  
+
+    retValI = engEvalString(engineP[ engine ], evalS);
+
+
+
+    //printf("evalString %i",OpenB);
+
+
+
+    (*env)->ReleaseStringUTFChars(env, evalS_JNI, evalS); // free memory
+
+
+
+    return retValI;
+
+}
+
+
+
+
+
+
+
+/********************************************************************************/

src/wsi/ra/tool/matlab/JMatLink.h

@@ -0,0 +1,149 @@
+/* DO NOT EDIT THIS FILE - it is machine generated */
+#include <jni.h>
+
+/* Header for class wsi_ra_tool_matlab_JMatLink */
+
+#ifndef _Included_wsi_ra_tool_matlab_JMatLink
+#define _Included_wsi_ra_tool_matlab_JMatLink
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* Inaccessible static: threadInitNumber */
+
+/* Inaccessible static: stopThreadPermission */
+
+#undef wsi_ra_tool_matlab_JMatLink_MIN_PRIORITY
+#define wsi_ra_tool_matlab_JMatLink_MIN_PRIORITY 1L
+
+#undef wsi_ra_tool_matlab_JMatLink_NORM_PRIORITY
+#define wsi_ra_tool_matlab_JMatLink_NORM_PRIORITY 5L
+
+#undef wsi_ra_tool_matlab_JMatLink_MAX_PRIORITY
+#define wsi_ra_tool_matlab_JMatLink_MAX_PRIORITY 10L
+
+#undef wsi_ra_tool_matlab_JMatLink_idleI
+#define wsi_ra_tool_matlab_JMatLink_idleI 0L
+
+#undef wsi_ra_tool_matlab_JMatLink_engOpenI
+#define wsi_ra_tool_matlab_JMatLink_engOpenI 1L
+
+#undef wsi_ra_tool_matlab_JMatLink_engCloseI
+#define wsi_ra_tool_matlab_JMatLink_engCloseI 2L
+
+#undef wsi_ra_tool_matlab_JMatLink_engEvalStringI
+#define wsi_ra_tool_matlab_JMatLink_engEvalStringI 3L
+
+#undef wsi_ra_tool_matlab_JMatLink_engGetScalarI
+#define wsi_ra_tool_matlab_JMatLink_engGetScalarI 4L
+
+#undef wsi_ra_tool_matlab_JMatLink_engGetVectorI
+#define wsi_ra_tool_matlab_JMatLink_engGetVectorI 5L
+
+#undef wsi_ra_tool_matlab_JMatLink_engGetArrayI
+#define wsi_ra_tool_matlab_JMatLink_engGetArrayI 6L
+
+#undef wsi_ra_tool_matlab_JMatLink_engPutArray2dI
+#define wsi_ra_tool_matlab_JMatLink_engPutArray2dI 9L
+
+#undef wsi_ra_tool_matlab_JMatLink_engOutputBufferI
+#define wsi_ra_tool_matlab_JMatLink_engOutputBufferI 10L
+
+#undef wsi_ra_tool_matlab_JMatLink_engGetCharArrayI
+#define wsi_ra_tool_matlab_JMatLink_engGetCharArrayI 11L
+
+#undef wsi_ra_tool_matlab_JMatLink_destroyJMatLinkI
+#define wsi_ra_tool_matlab_JMatLink_destroyJMatLinkI 12L
+
+#undef wsi_ra_tool_matlab_JMatLink_engOpenSingleUseI
+#define wsi_ra_tool_matlab_JMatLink_engOpenSingleUseI 13L
+
+/*
+
+ * Class:     wsi_ra_tool_matlab_JMatLink
+
+ * Method:    displayHelloWorld
+
+ * Signature: ()V
+
+ */
+
+JNIEXPORT void JNICALL Java_wsi_ra_tool_matlab_JMatLink_displayHelloWorld
+
+  (JNIEnv *, jobject);
+
+
+/*
+
+ * Class:     wsi_ra_tool_matlab_JMatLink
+
+ * Method:    engTestNATIVE
+
+ * Signature: ()V
+
+ */
+
+JNIEXPORT void JNICALL Java_wsi_ra_tool_matlab_JMatLink_engTestNATIVE
+
+  (JNIEnv *, jobject);
+
+
+/*
+
+ * Class:     wsi_ra_tool_matlab_JMatLink
+
+ * Method:    engOpenNATIVE
+
+ * Signature: (Ljava/lang/String;)I
+
+ */
+
+JNIEXPORT jint JNICALL Java_wsi_ra_tool_matlab_JMatLink_engOpenNATIVE
+
+  (JNIEnv *, jobject, jstring);
+
+
+/*
+
+ * Class:     wsi_ra_tool_matlab_JMatLink
+
+ * Method:    engOpenSingleUseNATIVE
+
+ * Signature: (Ljava/lang/String;)I
+
+ */
+
+JNIEXPORT jint JNICALL Java_wsi_ra_tool_matlab_JMatLink_engOpenSingleUseNATIVE
+
+  (JNIEnv *, jobject, jstring);
+
+
+/*
+
+ * Class:     wsi_ra_tool_matlab_JMatLink
+
+ * Method:    engCloseNATIVE
+
+ * Signature: (I)I
+
+ */
+
+JNIEXPORT jint JNICALL Java_wsi_ra_tool_matlab_JMatLink_engCloseNATIVE
+
+  (JNIEnv *, jobject, jint);
+
+
+/*
+
+ * Class:     wsi_ra_tool_matlab_JMatLink
+
+ * Method:    engEvalStringNATIVE
+
+ * Signature: (ILjava/lang/String;)I
+
+ */
+
+JNIEXPORT jint JNICALL Java_wsi_ra_tool_matlab_JMatLink_engEvalStringNATIVE
+
+  (JNIEnv *, jobject, jint, jstring);

src/wsi/ra/tool/matlab/Makefile

@@ -0,0 +1,27 @@
+# This makefile builds JMatLink library on RH7.3.
+
+# Joerg K. Wegner 27/09/02
+
+#
+
+# for using this feature
+
+# setenv MATLAB /afs/informatik.uni-tuebingen.de/i386_rh62/ra/Matlab-6.1
+
+# setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:$MATLAB/extern/lib/glnx86/
+
+
+
+CC = gcc
+
+LD = ld
+
+
+
+# MATLAB
+
+MATLAB = /afs/informatik.uni-tuebingen.de/i386_rh62/ra/Matlab-6.1
+
+MLIB = -L$(MATLAB)/extern/lib/glnx86
+
+MINCLUDE = -I$(MATLAB)/extern/include