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Removed TimeSeries class. Not used inside EvA2 and therefore obsolete.
This commit is contained in:
Fabian Becker 2013-01-29 14:06:36 +00:00
parent bcf7a9a8a2
commit 0d339aba22
1 changed files with 0 additions and 270 deletions
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src/eva2/server/go/problems/inference/metabolic/TimeSeries.java
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@ -1,270 +0,0 @@
package eva2.server.go.problems.inference.metabolic;
import java.io.Serializable;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import java.util.StringTokenizer;
/**
* This class is able to parse and store the contents of a time series data
* file. These files are supposed to be a matrix, whose columns are separated by
* spaces or tabs. Every row is supposed to contain a time value in the first
* column. Every other column contains the concentration of the appropriate
* metabolite. Because the concentrations of different metabolites are not
* measured at the same time, it is possible that some values equal -1 or "NaN".
* For a given metabolite this class provides methods to extract the appropriate
* times as well as the concentration values from this file.
*
* @since 2.0
* @version
* @author Andreas Dr&auml;ger (draeger) <andreas.draeger@uni-tuebingen.de>
* Copyright (c) ZBiT, University of T&uuml;bingen, Germany Compiler:
* JDK 1.6.0
* @date Sep 6, 2007
*/
public class TimeSeries implements Serializable {
/**
*
*/
private static final long serialVersionUID = 5744947450930268722L;
String dataFile[] = new String[] {
"\"Time\" \"PYR\" \"AKG\" \"ALA\" \"NAD\" \"DHIV\" \"nadp\" \"Glut\" \"2IPM\" \"AcLac\" \"Val\" \"Leu\" \"KIV\" \"KIC\"",
"-3.894 0.69956151035 4.640691888659999 0.8149815245099999 0.43831117728999996 0.12919945973 NaN 39.91322431689 0.01634219825 0.22846321864000002 25.300234279730002 0.31457001595 13.06542276153 0.12828553615000002",
"-3.429 0.6887305946 4.4648219135 0.9733354471500001 0.46283738647 0.09269418599 0.01751164422 34.689755620279996 0.016622587119999997 0.26529057205 27.855794163480002 0.21601742448 12.27325468611 0.08806661914",
"-2.964 0.648489239 5.16446833661 1.08501337472 0.510398731 0.09668719327 0.015292064690000001 35.94424701067 0.0218616059 0.24372308822 27.512009946459997 0.19358187491999998 11.83868901432 0.08060740248 ",
"-2.499 0.66263247645 5.46655875364 1.25007291486 0.54709779337 0.27832465706 0.02017254508 42.09304165779 0.02271131235 0.31096389668 31.734637769419997 0.26547698208000003 9.74938023117 0.09527994438000001 ",
"-2.037 0.78148116407 5.01023940504 1.1274704877 0.54374513457 0.10951589105 0.023434610419999998 38.623872567220005 0.02310058527 0.23193180999000002 28.68948017027 0.27338539200999995 9.8790791622 0.06856701949 ",
"-1.572 0.7976018096 4.50327160849 0.9657423536899999 0.58804343197 0.07731788865 0.021456078269999998 39.65098562534 0.02122962586 NaN 23.23780871601 0.21372010324 7.35589658416 0.04408823098 ",
"-1.107 0.62138120097 5.527992933249999 1.11320796018 0.55468774709 0.19127059402000002 0.02151432978 37.43103867786 0.021760915119999998 0.1961057295 28.06503640484 0.25571800238 7.77390798856 0.08440327591999999 ",
"-0.642 0.61440001723 5.6582676904 1.0934342424799999 0.57892866745 0.29234911798 0.02163427084 41.73288066597 0.02358943064 0.23458068462 31.36134966529 0.28291670151 8.77177024347 0.0732470093 ",
"0.363 0.70849102753 5.6485532671600005 1.07913785266 0.5494837929699999 0.22848890345 0.03264048454 40.837490521439996 0.02034557524 0.25195151103 27.336329975730003 0.1981060288 6.68584901645 0.07329936145 ",
"0.828 0.7284264133299999 5.24081938936 1.20656221781 0.56038053457 0.50828902006 0.02799224444 43.839863948079994 0.02365648322 0.33595864068 30.40658463215 0.25328480297 7.46481961657 0.06727204061 ",
"1.293 2.35072982926 12.865197464340001 2.91425720335 0.6174561459100001 0.51680611101 0.0180555805 45.00192868082 0.02789099302 0.27282017381999996 35.47319021015 0.34012252203000004 12.4841096615 0.12075887125 ",
"1.758 1.9467590874099998 9.85083850897 2.38135380833 0.47990344534 0.36137563687 0.02083824064 39.874833705 0.02603135155 0.24703878422 35.24799025209 0.25499939033 10.58660287792 0.12011356083 ",
"2.220 1.76234822871 12.57168005228 2.535743239 0.58312865514 0.17860360497 0.018047886200000002 48.82282962176 0.02531203769 NaN 31.84083292177 0.21013809416 8.79825645884 0.10474495756 ",
"2.685 1.92439252352 11.2260038878 2.8335955021 0.49220203429 0.16592713605 0.0278326992 39.75506759172 0.02115183034 0.24700121622 29.23941353308 0.22169631684000002 8.94277598226 0.09683684583 ",
"3.150 1.92008237217 10.682979534100001 2.63737602928 0.36735949621999997 0.1546055768 0.01515236183 39.012881840679995 NaN 0.46143297886 35.812552779769995 0.28387244697 14.20243053826 0.10933158105 ",
"4.620 1.81992606678 11.067551454270001 2.70934921435 0.40725580208999995 0.24849740356 0.027964720069999997 40.42309102465 0.0170493166 0.42824885292 37.17528380543 0.33573709864 15.33969385816 0.10861095009 ",
"5.085 1.45412618172 8.37506633272 2.5510691881399996 0.5402956812899999 0.29017599822 0.029667666019999997 52.86610489844 0.01551224716 0.37018809756000004 42.07773461152 0.32912302835999996 16.97282365372 0.1127063518 ",
"5.550 1.7963431670299999 10.9951402722 3.2730762781499996 0.49909124182 0.36584625016 0.031689318279999996 49.69757534082 0.030182574599999998 0.50230756817 44.18764066063 0.34318150693 14.45568137413 0.13087029789 ",
"6.015 1.79488675167 10.58210664143 2.82815659112 0.42028499769 0.33884287302 0.02904992542 47.618463449870006 0.02065291348 0.38243112459999995 41.68555649409 0.31270596242 14.18407754513 0.12297689406000001 ",
"6.477 1.71658915979 13.051632359080001 2.86429255047 0.69044126446 0.2906864281 0.02542790495 52.905505205989996 0.0363051233 0.46612294623 51.36020781111 0.52323119427 15.99708653385 0.13462198459000002 ",
"6.942 1.70200349375 11.29511994965 2.47410519106 0.61838724543 0.74141022319 0.02954918008 52.05561320903 0.03626130189 0.36020464648 47.08381733066 0.39496256108 15.29065040412 0.12714131781000002 ",
"7.407 1.4797133761099999 10.85092666902 2.73282139173 0.60893255673 0.91712444816 0.031866304570000004 54.69762263264 0.034354864900000004 0.50457338093 42.85485451463 0.35559022922000005 11.0783278302 0.11004224548000001 ",
"7.872 1.9687388421799998 12.632535436100001 3.38129932903 0.6733727859399999 1.19712426006 0.02287925851 69.03104100976 0.0346858365 0.6115046939 52.213982982809995 0.44352030561 14.17030298056 0.11817042216 ",
"8.877 1.66191235556 10.202950777509999 2.7018080554500004 0.65431385574 0.8630518573 0.03842550936 55.18740808596 0.03100906854 0.43636326995 44.94372991982 0.39590424030000004 11.87915174242 0.12055380252 ",
"9.342 1.79446423883 9.223736902639999 2.82086676673 0.46928184702 0.25036756575999997 0.0261580927 44.218411563610005 0.02307492312 0.37136132062 34.8715067452 0.23048150172999998 9.83227607934 0.08369892896 ",
"9.807 2.02936743557 10.926146897779999 3.40942786382 0.4943626997 0.41616779600000003 0.020775668350000002 57.63290012324 0.02453204368 0.59384364452 41.567799898539995 0.37314942280999996 11.524438278929999 0.10958751164 ",
"10.272 1.96339182674 11.26182399865 3.6725323889699997 0.51033452936 0.38195138421 0.02349833226 68.82889744295 0.02130776115 0.56596184217 43.85824526299 0.3563165939 10.882216090570001 0.11761378372 ",
"10.734 1.69522699956 9.28644900764 3.09521900994 0.46748976233 0.25486955073 0.024124165519999997 56.23949510944 0.01806823073 NaN 36.05982284756 0.25298007274 8.86586676025 0.07157556397999999 ",
"11.199 1.87021691917 9.68208305253 3.2919709268000004 0.5270903229299999 0.42322311943 0.0327964463 59.54087126072 0.022691202100000002 0.47737124454999996 41.842194656909996 0.28466758982 11.91006067162 0.09872917755999999 ",
"11.664 2.23471175262 12.19887299453 3.6051454388299997 0.54389398527 0.54313316601 0.01479252184 63.04737515095 0.02776861734 0.48410774037 46.409590689800005 0.44546516811 12.6862786223 0.10475246765999999 ",
"12.129 1.58626042008 9.99097297113 3.7513050785999997 0.42925918395999996 0.44080053731999996 0.013039703409999999 54.332315720649994 0.02735050961 0.31900140121 39.37877381533 0.32147277213000003 10.09758737431 0.08824555916 ",
"13.134 1.09179740401 6.491353226309999 2.26052958713 0.5481437170200001 NaN 0.01664214786 49.99620609066 0.02341309598 NaN 32.90242406736 0.29822072293 7.4630383928 0.0570285326 ",
"13.599 1.3879954566700001 9.38597812226 3.67292411291 0.41493699655 0.35712124297000003 0.01725904447 49.842043735 0.025759816390000002 0.40749356039 36.65749859265 0.31221753187 8.49907762956 0.08041935436999999 ",
"14.064 1.46398956252 9.514586394050001 3.8008622291900003 0.48941052945 0.43946239095 0.01718538349 54.47374486523 0.02895368422 0.48952197341 40.26813532416 0.40474806982 9.42390966864 0.07994405853 ",
"14.529 1.38755206855 8.484590611449999 3.2508142214399998 0.4940005127 0.48337445569 0.01893519951 47.84282639242 0.026125384369999997 0.4407703548 41.362606442570005 0.27053364357 11.06193869222 0.1028701703 ",
"14.991 0.88675119894 6.09938485345 2.0966046727900003 0.51403159937 0.25811120551 0.0228857864 44.11169057688 0.021193232819999998 NaN 31.027494313570003 0.22906790417 7.52510837768 0.053950203 ",
"15.456 1.8352414024800001 8.469270941569999 3.3301897663099997 0.4957035248 0.26361946777 0.025116875570000002 36.08517318062 0.025039514409999998 0.38916760052 38.21581762714 0.2746950311 11.731711424339998 0.12009641433 ",
"15.921 1.3283163392300001 8.17980680802 3.0409809543 0.38135485122 0.31612171511000003 0.01517163163 32.72595199009 0.02671292861 0.34622186149 42.07802536984 0.2542175654 12.23730313735 0.13746139785 ",
"16.386 1.0127505969 4.742491586150001 1.84597095725 0.34553761760999996 NaN NaN 23.37116254961 NaN NaN NaN 0.15254582637 6.9247716185999995 0.07113160166999999 ",
"17.391 1.3310395982 7.94156759798 2.53879431682 0.48983728463 0.28795700924 0.026527055879999997 26.57827416636 0.02478540202 0.32631108383999996 33.95632215865 0.23618178628 10.48083524196 0.12515650878 ",
"17.856 0.95469028533 6.2343780867100005 2.17715476263 0.38729195765999996 0.28723013923 0.02123345169 24.49108607053 0.02618426224 0.29861161455 32.8592195428 0.2472225415 10.106162722479999 0.10923677735 ",
"18.321 NaN 5.49182392648 1.46886777519 0.34474738841999997 0.40646871383 0.01547566737 20.63720807926 0.02820014831 0.24058040600000002 40.71516409524 0.24270642545999999 14.12503277772 0.12899961175000002 ",
"18.786 0.82619105906 5.95530539146 2.299362329 0.44373946309 0.41075036223 0.02555677606 38.20802369971 0.02900285112 0.32959703389 34.213028316030005 0.25023635697 9.12222153162 0.10197379988000001 ",
"19.248 1.25881942787 6.53214282703 2.7302141736600003 0.50467802709 0.41526312678 0.02242466065 36.837815626659996 0.02483324467 0.38040913803 33.23783851764 0.23737761148 9.48079376972 0.11263783924000001 ",
"19.713 1.18507811227 5.4310205666 2.1360162267800002 0.46222885974 NaN 0.03397622205 28.19338823663 0.02104977904 NaN 25.47234120703 0.14638363385 7.60817737184 0.08542327693999999 ",
"20.178 0.98680703323 6.8729957498 2.34703189167 0.36189835991 0.35197395012 0.0170510439 26.43911126279 0.03024185129 0.30588350463 36.72827117308 0.23660664184000002 13.6943897464 0.16017717532 ",
"20.643 0.97377667062 6.15710096877 2.10492373702 0.46580796436000005 0.38984610765 0.020551778160000003 28.19084298145 0.02817732147 0.31660453741 33.563565688000004 0.17354025424 11.137671980450001 0.11278907400999999" };
private int dataFileLineCnt = dataFile.length;
private Map<String, Object> names;
public static void main(String args[]) {
new TimeSeries();
}
/**
* This constructs a new instance of this class from the given file. All
* entries of the given file are stored in a <java>String</java> matrix.
* The names of the metabolites are stored in a hash for easy retrival.
*
* @param fileName
*/
public TimeSeries() {
try {
int i = 0, j = 0;
this.names = new HashMap<String, Object>();
StringTokenizer st = new StringTokenizer(dataFile[0]);
// Lesen zum ersten Mal und initialisieren Matrix.
for (j = 0; st.hasMoreElements(); st.nextElement(), j++)
;
String data[][] = new String[dataFileLineCnt - 1][j];
// Jetzt in Matrix einlesen.
for (i = 0; i < dataFileLineCnt; i++) {
j = 0;
st = new StringTokenizer(dataFile[i]);
while (st.hasMoreElements())
if (i > 0) {
data[i - 1][j++] = st.nextElement().toString();
}
else {
names.put(st.nextElement().toString().replaceAll("\"",
""), new Integer(j++));
}
}
/*
* for (i=0; i<data.length; i++) {
* System.out.print("\n"+data[i][0]+" "); for (j=1; j<data[0].length;
* j++) { double val = Double.parseDouble(data[i][j])/1000;
* System.out.print(val+"\t"); } }
*/
/*
* names becomes a hash pointing to matrices.
*/
Iterator<String> iter = names.keySet().iterator();
while (iter.hasNext())
try {
double values[][];
int tcol = 0, count = 0;
String name = iter.next().toString();
i = 0;
j = ((Integer) names.get(name)).intValue();
for (i = 0; i < data.length; i++) {
if (!data[i][j].equals("-1")
&& !data[i][j].equals("NaN")) {
count++;
}
}
values = new double[2][count];
// /*
// * The times are supposed to be the first column. However,
// this
// * enables the times to be any column.
// */
// try {
// tcol = ((Integer) this.names.get("Time")).intValue();
// } catch (Exception exc) {
// };
for (i = 0, count = 0; i < data.length; i++) {
if (!data[i][j].equals("-1")
&& !data[i][j].equals("NaN")) {
values[0][count] = Double
.parseDouble(data[i][tcol]);
values[1][count++] = Double.parseDouble(data[i][j]);
}
}
names.put(name, values);
} catch (Exception exc) {
exc.printStackTrace();
}
data = null;
} catch (Exception exc) {
exc.printStackTrace();
}
}
/**
* With this method one retrives the time data of the given metabolite or
* throws an <java>exception</java> if the given metabolite does not exist.
*
* @param metabolite
* The name of the metabolite, whose time data are desired.
* @return The time data.
* @throws Exception
* @throws If
* there is no entry for the desired metabolite, an exeption is
* thrown.
*/
public double[] getTimes(String metabolite) throws Exception {
if (names == null) {
System.err.println("getTimes: names is null");
}
if (!names.containsKey(metabolite)) {
throw new Exception("No data measured for this metabolite");
}
if (names.get(metabolite) == null) {
System.err.println("get(metabolite) is null");
}
return ((double[][]) names.get(metabolite))[0];
}
/**
* This method returns all measured times.
*
* @return An array containing all measurement times.
* @throws Exception
* If there is no column called "Time" in the data matrix.
*/
public double[] getTimes() throws Exception {
return getTimes("Time");
}
/**
* This method returns the concentration values of the given metabolite or
* throws an exception if there is no measurement for the desired
* metabolite.
*
* @param metabolite
* The name of the desired metabolite.
* @return an array of concentration values.
* @throws Exception
* @throws If
* there is no entry for the desired metabolite, an exception is
* thrown.
*/
public double[] getValues(String metabolite) throws Exception {
if (!names.containsKey(metabolite)) {
throw new Exception("No data measured for this metabolite");
}
return ((double[][]) names.get(metabolite))[1];
}
/**
* With this method it can be checked wheather measurements have been
* perforemd for the given metabolite.
*
* @param name
* The name of the metabolite
* @return <code>true</code> if an entry for this metabolite exists or
* <code>false</code> otherwise.
*/
public boolean containsMetabolite(String name) {
return names.keySet().contains(name);
}
/**
* Returns the number of measurements taken for this specific metabolite or
* zero if there are no measurements.
*
* @param name
* The name of the metabolite
* @return The number of available measurement data for this metabolite
*/
public int numberOfMeasurements(String name) {
try {
return getTimes(name).length;
} catch (Exception exc) {
return 0;
}
}
public Iterator<String> namesIterator() {
return this.names.keySet().iterator();
}
public int size() {
return names.keySet().size();
}
}