diff --git a/pom.xml b/pom.xml index 4d7073e2..bc031a67 100644 --- a/pom.xml +++ b/pom.xml @@ -42,17 +42,17 @@ commons-cli 1.2 - - com.google.code.gson - gson - 2.2.4 - compile - - - org.reflections - reflections - 0.9.9-RC1 - + + com.google.code.gson + gson + 2.2.4 + compile + + + org.reflections + reflections + 0.9.9-RC1 + diff --git a/src/eva2/gui/PropertyPanel.java b/src/eva2/gui/PropertyPanel.java index 4fd12ce5..5354b93c 100644 --- a/src/eva2/gui/PropertyPanel.java +++ b/src/eva2/gui/PropertyPanel.java @@ -34,7 +34,7 @@ public class PropertyPanel extends JPanel { add(textLabel, gbConstraints); } - public void showDialog() { + public final void showDialog() { Window parent = (Window)this.getRootPane().getParent(); if (propertyDialog == null) { propertyDialog = new PropertyDialog(parent, propertyEditor, EVAHELP.cutClassName(propertyEditor.getClass().getName())); diff --git a/src/eva2/gui/plot/FunctionArea.java b/src/eva2/gui/plot/FunctionArea.java index 58dabf4c..2220ba96 100644 --- a/src/eva2/gui/plot/FunctionArea.java +++ b/src/eva2/gui/plot/FunctionArea.java @@ -33,7 +33,6 @@ public class FunctionArea extends DArea implements Serializable { private GraphPointSetLegend legendBox = null; private ScaledBorder scaledBorder; private DPointIcon currentPointIcon; - private JFileChooser fileChooser; private boolean legend = true; private boolean log = false; private ArrayList pointSetContainer; @@ -511,7 +510,7 @@ public class FunctionArea extends DArea implements Serializable { * */ protected void createFileChooser() { - fileChooser = new JFileChooser(new File("/resources")); + JFileChooser fileChooser = new JFileChooser(new File("/resources")); fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY); } diff --git a/src/eva2/gui/plot/Plot.java b/src/eva2/gui/plot/Plot.java index f1a947c8..77019f8d 100644 --- a/src/eva2/gui/plot/Plot.java +++ b/src/eva2/gui/plot/Plot.java @@ -183,7 +183,7 @@ public class Plot implements PlotInterface, Serializable { } /** - * + * ToDo: This is ugly as fuck. The plot shouldn't create internal frames. */ @Override public void init() { diff --git a/src/eva2/optimization/ModuleServer.java b/src/eva2/optimization/ModuleServer.java index 1ea98bcd..6facb160 100644 --- a/src/eva2/optimization/ModuleServer.java +++ b/src/eva2/optimization/ModuleServer.java @@ -17,7 +17,7 @@ import java.util.logging.Logger; /** * Collect available ModuleAdapter implementations and load them on request. */ -public class ModuleServer { +public final class ModuleServer { private static final Logger LOGGER = Logger.getLogger(ModuleServer.class.getName()); private static int instanceCounter = 0; diff --git a/src/eva2/optimization/modules/Processor.java b/src/eva2/optimization/modules/Processor.java index 34b00f53..b6e49c73 100644 --- a/src/eva2/optimization/modules/Processor.java +++ b/src/eva2/optimization/modules/Processor.java @@ -50,7 +50,7 @@ public class Processor extends Thread implements InterfaceProcessor, InterfacePo private InterfaceStatistics statistics; private InterfaceOptimizationParameters optimizationParameters; private boolean createInitialPopulations = true; - private boolean saveParams = true; + private boolean saveParams = false; private OptimizationStateListener optimizationStateListener; private boolean wasRestarted = false; private int runCounter = 0; @@ -170,6 +170,7 @@ public class Processor extends Thread implements InterfaceProcessor, InterfacePo EVAERROR.clearMsgCache(); while (isOptimizationRunning()) { setPriority(3); + // ToDo: Do we need this really? if (saveParams) { try { optimizationParameters.saveInstance(); diff --git a/src/eva2/optimization/population/Population.java b/src/eva2/optimization/population/Population.java index 3d13e158..c6ce08f6 100644 --- a/src/eva2/optimization/population/Population.java +++ b/src/eva2/optimization/population/Population.java @@ -123,9 +123,9 @@ public class Population extends ArrayList implements PopulationInterface, Clonea public Population(Population population) { LOGGER.log(Level.FINER, "New population has been created."); setSameParams(population); - for (int i = 0; i < population.size(); i++) { - if (population.get(i) != null) { - this.add((((AbstractEAIndividual) population.get(i))).clone()); + for (Object individual : population) { + if (individual != null) { + this.add((((AbstractEAIndividual) individual)).clone()); } } copyHistAndArchive(population); @@ -406,7 +406,6 @@ public class Population extends ArrayList implements PopulationInterface, Clonea createBinCardinality(this, true, seedCardinality.head(), seedCardinality.tail()); break; } - //System.out.println("After pop initialize: " + this.getStringRepresentation()); firePropertyChangedEvent(Population.POPULATION_INITIALIZED); } @@ -601,7 +600,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea return historyList; } - public void SetHistory(LinkedList theHist) { + public void setHistory(LinkedList theHist) { historyList = theHist; } @@ -715,8 +714,8 @@ public class Population extends ArrayList implements PopulationInterface, Clonea } this.historyList.add((AbstractEAIndividual) this.getBestEAIndividual().clone()); } - for (int i = 0; i < size(); i++) { - ((AbstractEAIndividual) get(i)).incrAge(); + for (Object individual : this) { + ((AbstractEAIndividual) individual).incrAge(); } this.generationCount++; firePropertyChangedEvent(NEXT_GENERATION_PERFORMED); @@ -1223,7 +1222,6 @@ public class Population extends ArrayList implements PopulationInterface, Clonea skip = super.size() - n; } -// hier getSorted aufrufen ArrayList sorted = getSorted(comp); res.clear(); for (int i = skip; i < skip + n; i++) { diff --git a/src/eva2/optimization/strategies/ClusterBasedNichingEA.java b/src/eva2/optimization/strategies/ClusterBasedNichingEA.java index 52ba789c..687699d1 100644 --- a/src/eva2/optimization/strategies/ClusterBasedNichingEA.java +++ b/src/eva2/optimization/strategies/ClusterBasedNichingEA.java @@ -736,7 +736,7 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis spec1.addPopulation(spec2); // keep longer history if (spec2.getHistoryLength() > spec1.getHistoryLength()) { - spec1.SetHistory(spec2.getHistory()); + spec1.setHistory(spec2.getHistory()); } if (spec2.getGeneration() > spec1.getGeneration()) { spec1.setGeneration(spec2.getGeneration()); @@ -760,10 +760,10 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis newSp.setUseHistory(true); if (startAtP1Gen) { // start explicitely as a child population of p1 newSp.setGeneration(parentSp.getGeneration()); - newSp.SetHistory((LinkedList) parentSp.getHistory().clone()); + newSp.setHistory((LinkedList) parentSp.getHistory().clone()); } else { // start anew (from undiff) newSp.setGeneration(0); - newSp.SetHistory(new LinkedList()); + newSp.setHistory(new LinkedList()); } if (optimizer instanceof InterfaceSpeciesAware) { diff --git a/src/eva2/optimization/strategies/EsDpiNiching.java b/src/eva2/optimization/strategies/EsDpiNiching.java index c70e8ba7..939d97ca 100644 --- a/src/eva2/optimization/strategies/EsDpiNiching.java +++ b/src/eva2/optimization/strategies/EsDpiNiching.java @@ -549,7 +549,7 @@ public class EsDpiNiching implements InterfaceOptimizer, Serializable, Interface if (origEsPop != null && (origEsPop >= 0)) { Population origPop = peakOpts[origEsPop].getPopulation(); clusteredPeakPops[i].copyHashData(origPop); - clusteredPeakPops[i].SetHistory(origPop.getHistory()); // copy the history for deactivation! + clusteredPeakPops[i].setHistory(origPop.getHistory()); // copy the history for deactivation! } else { // ok in the first iteration of if the indy was a random immigrant if (population.getGeneration() > 1 && (getNumRndImmigrants() == 0)) { System.err.println("Error, empty original es pop ID!"); diff --git a/src/eva2/tools/Serializer.java b/src/eva2/tools/Serializer.java index d50ecf9d..f483a3f6 100644 --- a/src/eva2/tools/Serializer.java +++ b/src/eva2/tools/Serializer.java @@ -37,13 +37,15 @@ public class Serializer { * @throws IOException */ private static void store(Serializable o, OutputStream outStream, boolean serializeInMem) throws IOException { - ObjectOutputStream out = new ObjectOutputStream(outStream); + ObjectOutputStream objectStream = new ObjectOutputStream(outStream); try { Object objToStore = o; if (serializeInMem) { objToStore = new SerializedObject(o); } - // I don't care! + objectStream.writeObject(objToStore); + objectStream.flush(); + objectStream.close(); } catch (java.io.NotSerializableException ex) { LOGGER.log(Level.SEVERE, "Object is not serializable!", ex); } @@ -142,7 +144,7 @@ public class Serializer { try { store(s, outStream, true); } catch (Exception ex) { - LOGGER.log(Level.SEVERE, "Could not write object to stream.", ex); + LOGGER.log(Level.FINER, "Could not write object to stream.", ex); } } diff --git a/src/eva2/tools/chart2d/ScaledBorder.java b/src/eva2/tools/chart2d/ScaledBorder.java index b109506e..ee07037b 100644 --- a/src/eva2/tools/chart2d/ScaledBorder.java +++ b/src/eva2/tools/chart2d/ScaledBorder.java @@ -15,22 +15,20 @@ import java.text.NumberFormat; * ( 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; + int markerLength = 2; /** * length in pixels of the arrows at the ends of the axes */ - int arrow_length = 10; + int arrowLength = 10; /** * a flag if the arrows should be visible */ - public boolean show_arrows = true; + public boolean showArrows = true; /** * distance between the x-values in digits @@ -212,12 +210,7 @@ public class ScaledBorder implements Border { @Override public void paintBorder(Component c, Graphics g, int x, int y, int width, int height) { - if (under_construction) { - System.out.println("ScaledBorder.paintBorder()"); - } - -// Here one might know how much of the graph is taken by the border only and possibly switch to exponential numbering? - + // Here one might know how much of the graph is taken by the border only and possibly switch to exponential numbering? if (foreground == null) { foreground = c.getForeground(); } @@ -255,35 +248,35 @@ public class ScaledBorder implements Border { g.drawLine(inner_insets.left, inner_insets.top + cd.height, inner_insets.left + cd.width, inner_insets.top + cd.height); - if (show_arrows) { + if (showArrows) { 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 - markerLength, inner_insets.top - y_values2arrow, + inner_insets.left, inner_insets.top - y_values2arrow - arrowLength); + g.drawLine(inner_insets.left + markerLength, inner_insets.top - y_values2arrow, + inner_insets.left, inner_insets.top - y_values2arrow - arrowLength); + g.drawLine(inner_insets.left - markerLength, inner_insets.top - y_values2arrow, + inner_insets.left + markerLength, 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 - markerLength, + inner_insets.left + cd.width + x_values2arrow + arrowLength, 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 + markerLength, + inner_insets.left + cd.width + x_values2arrow + arrowLength, inner_insets.top + cd.height); g.drawLine(inner_insets.left + cd.width + x_values2arrow, - inner_insets.top + cd.height - marker_length, + inner_insets.top + cd.height - markerLength, inner_insets.left + cd.width + x_values2arrow, - inner_insets.top + cd.height + marker_length); + inner_insets.top + cd.height + markerLength); } if (yLabel != null) { Dimension yld = new Dimension(fm.getAscent() + fm.getDescent(), fm.stringWidth(yLabel)); - AffineTransform T = new AffineTransform(0, -1, 1, 0, 0, 0); + AffineTransform T = new AffineTransform(0, 1, 1, 0, 0, 0); Font old = g.getFont(), f = old.deriveFont(T); g.setFont(f); g.drawString(yLabel, y_label2border + fm.getAscent(), inner_insets.top + (cd.height + yld.height) / 2); @@ -298,12 +291,12 @@ public class ScaledBorder implements Border { 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, + g.drawString("0", inner_insets.left - fm.stringWidth("0") - v2m - markerLength, 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.left - fm.stringWidth("0") - v2m - markerLength, inner_insets.top + cd.height); } @@ -320,20 +313,9 @@ public class ScaledBorder implements Border { * @param insets */ private void drawYValues(Graphics g, Insets insets) { - if (under_construction) { - System.out.println("ScaledBorder.drawYValues()"); - } - FontMetrics fm = g.getFontMetrics(); int fontAsc = fm.getAscent(), v2m = fm.stringWidth("0") / y_values2marker; -// double startVal,dn = (src_rect.y / src_dY ); -// startVal = Math.round(dn-0.5)*src_dY; -// -// if( startVal < src_rect.y || ( src_rect.x == 0 && src_rect.y == 0 ) ) { -// startVal+=src_dY; -// } - double startVal = Mathematics.firstMultipleAbove(src_rect.y, src_dY); double v, scaledV, minx = src_rect.x; @@ -355,9 +337,9 @@ public class ScaledBorder implements Border { Point p = m.getPoint(minx, scaledV); if (p != null) { g.drawString(text, - insets.left - fm.stringWidth(text) - v2m - marker_length, + insets.left - fm.stringWidth(text) - v2m - markerLength, p.y + fontAsc / 2); - g.drawLine(insets.left - marker_length, p.y, insets.left, p.y); + g.drawLine(insets.left - markerLength, p.y, insets.left, p.y); } if (v + src_dY <= v) { // System.err.println("Overflow error B in ScaledBorder! v,src_dY:" + v + ", " + src_dY); @@ -372,9 +354,6 @@ public class ScaledBorder implements Border { } public double getSrcdY(int fontMetricsHeight, int componentHeight) { - if (under_construction) { - System.out.println("ScaledBorder.getSrcdY()"); - } if ((!do_refresh && src_dY != -1) || !auto_scale_y) { return src_dY; } @@ -387,17 +366,10 @@ public class ScaledBorder implements Border { if (src_dY < minimal_increment) { src_dY = minimal_increment; } - if (under_construction) { - System.out.println("Setting src_dY to " + src_dY + " for " + src_rect); - } 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, @@ -422,16 +394,13 @@ public class ScaledBorder implements Border { } int strW = fm.stringWidth(text); g.drawString(text, labelX - strW / 2, xLineY + fontAsc); - g.drawLine(labelX, xLineY, labelX, xLineY + marker_length); + g.drawLine(labelX, xLineY, labelX, xLineY + markerLength); 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; } @@ -481,7 +450,7 @@ public class ScaledBorder implements Border { * 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 + * @param min the double value next to which the displayable value should be found * @return the displayable value */ public static double aBitBigger(double min) { @@ -525,7 +494,6 @@ public class ScaledBorder implements Border { * @param xOrY if true toggle for the x axis otherwise for the y axis */ public void toggleDecPattern(boolean xOrY) { -// System.out.println("Next pattern: " + nextYPattern); int current; if (xOrY) { current = nextXPattern; @@ -594,9 +562,6 @@ public class ScaledBorder implements Border { */ @Override public Insets getBorderInsets(Component c) { - if (under_construction) { - System.out.println("ScaledBorder.getBorderInsets()"); - } if (!do_refresh && old_insets != null) { return old_insets; } @@ -613,7 +578,6 @@ public class ScaledBorder implements Border { } FontMetrics fm = g.getFontMetrics(); -// int fontAsc = fm.getAscent(); int fontHeight = fm.getHeight(), digit_width = fm.stringWidth("0"); @@ -639,7 +603,6 @@ public class ScaledBorder implements Border { n += src_dY; } -// System.out.println("Steps approx: " + ((src_rect.y + src_rect.height)-start)/src_dY); if (((src_rect.y + src_rect.height) - start) / src_dY > 20) { inc = ((src_rect.y + src_rect.height) - start) / 20.; } else { @@ -649,7 +612,6 @@ public class ScaledBorder implements Border { System.err.println("Warning, too small increase step size!"); } for (; n <= src_rect.y + src_rect.height; n += inc) { -// System.out.println(n); // TODO here might be a bug for mean values double v = n; if (y_scale != null) { @@ -662,7 +624,7 @@ public class ScaledBorder implements Border { // avoid nearly endless loop for large src_rect.y value and small src_dY } - insets.left += 1 + y_label2border + maxWidth + digit_width / y_values2marker + marker_length; + insets.left += 1 + y_label2border + maxWidth + digit_width / y_values2marker + markerLength; // bottom: insets.bottom += 1 + fontHeight + x_label2border; @@ -671,14 +633,14 @@ public class ScaledBorder implements Border { } // top: - if (show_arrows) { - insets.top += y_values2arrow + arrow_length; + if (showArrows) { + insets.top += y_values2arrow + arrowLength; } insets.top += axis2border; // right: - if (show_arrows) { - insets.right += x_values2arrow + arrow_length; + if (showArrows) { + insets.right += x_values2arrow + arrowLength; } insets.right += axis2border; getSrcdX(fm, c.getSize());