DataSetFDR added

tested

Author: cctsou

CrossLinker/nbproject/private/private.properties

@@ -4,4 +4,4 @@ do.depend=false
 do.jar=true
 javac.debug=true
 javadoc.preview=true
-user.properties.file=C:\\Users\\Tsou\\AppData\\Roaming\\NetBeans\\8.1\\build.properties
+user.properties.file=C:\\Users\\Cct\\AppData\\Roaming\\NetBeans\\8.1\\build.properties

DIA-Umpire/src/MSUmpire/DIA/DIAPack.java

@@ -641,27 +641,27 @@ public void SetPepXMLPath(){
     public void ParsePepXML(DBSearchParam searchPara, LCMSID refID) throws ParserConfigurationException, SAXException, IOException, XmlPullParserException, ClassNotFoundException, InterruptedException {
 
         SetPepXMLPath();
-        IDsummary = new LCMSID(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename),searchPara.DecoyPrefix,searchPara.FastaPath);        
+        IDsummary = new LCMSID(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename), searchPara.DecoyPrefix, searchPara.FastaPath);
         for (String pepxml : iProphPepXMLs) {
-            LCMSID pepxmlid = new LCMSID(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename),searchPara.DecoyPrefix,searchPara.FastaPath);
+            LCMSID pepxmlid = new LCMSID(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename), searchPara.DecoyPrefix, searchPara.FastaPath);
             PepXMLParser pepxmlparser = new PepXMLParser(pepxmlid, pepxml, 0f);
             if (refID == null) {
                 pepxmlid.FilterByPepDecoyFDR(searchPara.DecoyPrefix, searchPara.PepFDR);
             }
             Logger.getRootLogger().info("No. of peptide ions:" + pepxmlid.GetPepIonList().size() + "; Peptide level threshold: " + pepxmlid.PepProbThreshold);
             for (PepIonID pepID : pepxmlid.GetPepIonList().values()) {
                 if (refID != null) {
-                    if(refID.GetPepIonList().containsKey(pepID.GetKey())){
+                    if (refID.GetPepIonList().containsKey(pepID.GetKey())) {
                         IDsummary.AddPeptideID(pepID);
-                    }                    
+                    }
                 } else {
                     IDsummary.AddPeptideID(pepID);
                 }
             }
         }
         IDsummary.ReMapProPep();
         Logger.getRootLogger().info("Total number of peptide ions:" + IDsummary.GetPepIonList().size());
-        CheckPSMRT();        
+        CheckPSMRT();
         if (MS1FeatureMap != null) {
             this.MS1FeatureMap.IDsummary = IDsummary;
         }

DIA-Umpire/src/MSUmpire/LCMSPeakStructure/LCMSPeakMS1.java

@@ -32,7 +32,6 @@
 import MSUmpire.PeptidePeakClusterDetection.PDHandlerMS1;
 import MSUmpire.SearchResultParser.PepXMLParser;
 import MSUmpire.SpectrumParser.SpectrumParserBase;
-import MSUmpire.SpectrumParser.mzXMLParser;
 import java.awt.BasicStroke;
 import java.awt.Color;
 import java.awt.geom.Ellipse2D;

DIA-Umpire/src/MSUmpire/MathPackage/ChiSquareGOF.java

@@ -33,15 +33,15 @@ public class ChiSquareGOF {
     public static ChiSquared[] chimodels;
     public static ReadWriteLock lock = new ReentrantReadWriteLock();    
 
-    private ChiSquareGOF(int maxpeak) {        
+    private ChiSquareGOF(int maxpeak) {      
         chimodels = new ChiSquared[maxpeak-1];
-        for (int i = 1; i <= maxpeak; i++) {
-            chimodels[i - 1] = new ChiSquared(i);
+        for (int i = 1; i < maxpeak; i++) {
+            chimodels[i-1] = new ChiSquared(i);
         }
     }
 
     public static ChiSquareGOF GetInstance(int maxpeak) {
-        if (models == null || (maxpeak>1 && maxpeak >= chimodels.length)) {
+        if (models == null) {
             lock.writeLock().lock();
             try {
                 if (models == null) {
@@ -57,17 +57,22 @@ public static ChiSquareGOF GetInstance(int maxpeak) {
     public float GetGoodNessOfFitProb(float[] expected, float[] observed) {
         float gof = 0f;
         int nopeaks = 0;
-        for (int i = 0; i < Math.min(observed.length,expected.length); i++) {
+        for (int i = 0; i < Math.min(observed.length, expected.length); i++) {
             if (observed[i] > 0) {
                 float error = expected[i] - observed[i];
                 gof += (error * error) / (expected[i] * expected[i]);
                 nopeaks++;
             }
         }
-        if (Float.isNaN(gof) || nopeaks<2){
+        if (Float.isNaN(gof) || nopeaks < 2) {
             return 0f;
         }
-        float prob = 1 - (float) chimodels[nopeaks-2].cdf(gof);
+        
+        if(chimodels[nopeaks-2]==null){
+            System.out.println("");
+        }
+        
+        float prob = 1 - (float) chimodels[nopeaks - 2].cdf(gof);
         return prob;
     }
-}
+}

DIA_Umpire_ProtQuant/nbproject/private/private.properties

@@ -4,4 +4,4 @@ do.depend=false
 do.jar=true
 javac.debug=true
 javadoc.preview=true
-user.properties.file=C:\\Users\\Tsou\\AppData\\Roaming\\NetBeans\\8.1\\build.properties
+user.properties.file=C:\\Users\\Cct\\AppData\\Roaming\\NetBeans\\8.1\\build.properties