validation

compomics · Feb 26, 2018 · d5fcd22 · d5fcd22
1 parent 717aa17
commit d5fcd22
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Showing 11 changed files with 570 additions and 91 deletions.
diff --git a/src/main/java/com/compomics/coss/Controller/MainFrameController.java b/src/main/java/com/compomics/coss/Controller/MainFrameController.java
@@ -53,7 +53,6 @@
 public class MainFrameController implements UpdateListener {
 
     private static final Logger LOG = Logger.getLogger(MainFrameController.class);
-    private SwingWorkerThread workerThread;
 
     /**
      * Objects of the views
@@ -66,6 +65,7 @@ public class MainFrameController implements UpdateListener {
     // private ConfigHolder config = new ConfigHolder();
     Matching matching;
     private static List<ArrayList<ComparisonResult>> res;
+    int cutoff_index;
     ConfigData configData;
     public boolean cencelled = false;
     public boolean isBussy = false;
@@ -76,6 +76,7 @@ public class MainFrameController implements UpdateListener {
     public DefaultComboBoxModel cmbModel;
 
     private int targSpectrumNum, resultNumber;
+    private boolean isValidation;
 
     /**
      * Initialize objects, variables and components.
@@ -143,9 +144,13 @@ public void showMainFrame() {
      */
     public void stopSearch() {
 
-        this.cencelled = true;
-        matching.stopMatching();
+        if (matching != null) {
+            this.cencelled = true;
+            matching.stopMatching();
 
+        } else {
+            LOG.info("Nothing to cancel! Matching process is not running");
+        }
     }
 
     /**
@@ -166,11 +171,11 @@ public void startSearch() {
             readSpectra();
             this.cencelled = false;
             this.isBussy = true;
-            matching = new UseMsRoben(this, configData.getExperimentalSpecFile(), configData.getSpecLibraryFile());
-            // matching = new Cascade(this);
 
+            isValidation=false;
+            matching = new UseMsRoben(this, configData.getExpSpecReader(), configData.getExpSpectraIndex(), configData.getLibSpecReader(), "target");
             mainView.prgProgress.setValue(0);
-            workerThread = new SwingWorkerThread();
+            SwingWorkerThread workerThread = new SwingWorkerThread();
             workerThread.execute();
 
         }
@@ -183,6 +188,44 @@ public void startSearch() {
 
     }
 
+    /**
+     * start search against decoy database
+     */
+    private void validateResult(File decoydbFile) {
+
+        SpectrumReader rdDecoy=null;
+        List<IndexKey> decoyindxList=null;
+        try {
+            Indexer giExp = new Indexer(decoydbFile);            
+            decoyindxList = giExp.generate();
+            Collections.sort(decoyindxList);
+
+            //reader for decoy spectrum file
+
+            if (decoydbFile.getName().endsWith("mgf")) {
+                rdDecoy = new MgfReader(decoydbFile, decoyindxList);
+
+
+            } else if (decoydbFile.getName().endsWith("msp")) {
+                rdDecoy = new MspReader(decoydbFile, decoyindxList);
+
+            }
+
+        } catch (IOException ex) {
+            LOG.info(ex);
+        }
+
+
+
+        isValidation = true;
+        matching = new UseMsRoben(this, configData.getExpSpecReader(), configData.getExpSpectraIndex(), rdDecoy, "decoy");
+        mainView.prgProgress.setValue(0);
+        SwingWorkerThread workerThread = new SwingWorkerThread();
+        workerThread.execute();
+
+
+    }
+
     /**
      * Read user input from GUI
      *
@@ -214,7 +257,7 @@ private void readSpectra() {
             // List<Spectrum> experimentalSpectra;
             Indexer giExp = new Indexer(configData.getExperimentalSpecFile());
             List<IndexKey> indxList = giExp.generate();
-            Collections.sort(indxList);
+            //Collections.sort(indxList);
             configData.setExpSpectraIndex(indxList);
 
             //Read spectra library
@@ -689,17 +732,24 @@ public void spectrumDisplay(int specIndex) {
 
     }
 
+
+
     /**
      * swing thread to start the search and it runs on background
      */
     private class SwingWorkerThread extends SwingWorker<Void, Void> {
+
+        List<ArrayList<ComparisonResult>> tempRes;
+
 
         @Override
         protected Void doInBackground() throws Exception {
 
             matching.InpArgs(Integer.toString(configData.getMsRobinOption()), Integer.toString(configData.getIntensityOption()), Double.toString(configData.getfragTol()));
-            res = new ArrayList<>();
-            res = matching.compare(configData.getExpSpecReader(), configData.getExpSpectraIndex(), configData.getLibSpecReader(), configData.getSpectraLibraryIndex(), LOG);
+            tempRes = new ArrayList<>();
+            tempRes = matching.compare(LOG);
+
+
             return null;
         }
 
@@ -718,14 +768,25 @@ protected void done() {
                     mainView.prgProgress.setValue(100);
                     mainView.prgProgress.setString(Integer.toString(100) + "%");
 
-                    if (res != null && res.size() > 0) {
+                    if (tempRes != null && tempRes.size() > 0) {
 
+                        if(!isValidation){
+                            res=tempRes;   
+                            cutoff_index=res.size()-1;
+                        }
+                        else{
+                            Validation validation=new Validation();
+                            validation.compareNmerge(res, tempRes);
+                            cutoff_index=validation.validate(res, 0.01);                            
+                            isValidation=false;
+                        }
+
                         fillTargetTable();
                         fillBestmatchTable(0);
                         displayResult();
 
                     } else {
-//                        Log.info("No comparison result.");
+                       LOG.info("No comparison result.");
                     }
 
                 }

diff --git a/src/main/java/com/compomics/coss/Controller/Validation.java b/src/main/java/com/compomics/coss/Controller/Validation.java
@@ -0,0 +1,79 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package com.compomics.coss.Controller;
+
+import com.compomics.coss.Model.ComparisonResult;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+/**
+ *
+ * @author Genet
+ */
+public class Validation {
+
+    public Validation() {
+
+    }
+
+    public void compareNmerge(List<ArrayList<ComparisonResult>> targetResult, List<ArrayList<ComparisonResult>> decoyResult) {
+
+        List<ArrayList<ComparisonResult>> validatedResult = null;
+        //calculate FDR=Ndecoy/Ntargethits
+
+        int c = 0;
+        int decoySSM = 0;
+
+        for (ArrayList<ComparisonResult> rTarget : targetResult) {
+            ArrayList<ComparisonResult> rDecoy = decoyResult.get(c++);
+            if (rTarget.get(0).compareTo(rDecoy.get(0)) < 0) {
+
+                rTarget.clear();
+                rTarget.addAll(rDecoy);
+                decoySSM++;
+
+            }
+
+        }
+        Collections.sort(targetResult, (ArrayList<ComparisonResult> o1, ArrayList<ComparisonResult> o2) -> Double.valueOf(o1.get(0).getScore()).compareTo(o2.get(0).getScore()));
+
+    }
+
+    public int validate(List<ArrayList<ComparisonResult>> result, double threshold) {
+
+        int cutoff_index = 0;
+        int numDecoy = 0;
+        int numTarget = 0;
+        double fdr = 0;
+        //double threshold = 0.01;
+
+        for (ArrayList<ComparisonResult> r : result) {
+            // ArrayList<ComparisonResult> rDecoy=decoyResult.get(c++);
+            if (r.get(0).getResultType().equals("target")) {
+
+                numTarget++;
+
+            } else {
+                numDecoy++;
+            }
+
+            fdr = numDecoy / (double) numTarget;
+
+            if (fdr >= threshold) {
+                break;
+            }
+            cutoff_index++;
+
+        }
+        if(cutoff_index==0)
+            cutoff_index=result.size();
+        return cutoff_index;
+
+    }
+
+}
diff --git a/src/main/java/com/compomics/coss/Model/ComparisonResult.java b/src/main/java/com/compomics/coss/Model/ComparisonResult.java
@@ -12,6 +12,7 @@ public class ComparisonResult implements Comparable<ComparisonResult> {
     private String charge;
     private double score;
     private long spec_pos;
+    private String result_type;//either decoy or target
 
     public long getSpecPosition(){
         return this.spec_pos;
@@ -62,6 +63,15 @@ public double getScore(){
     }
 
 
+    public String getResultType(){
+        return this.result_type;
+    }
+
+    public void setResultType(String resType){
+        this.result_type=resType;
+    }
+
+
 
     @Override
     public int compareTo(ComparisonResult t) {

diff --git a/src/main/java/com/compomics/coss/View/MainGUI.java b/src/main/java/com/compomics/coss/View/MainGUI.java
@@ -25,6 +25,8 @@
 import javax.swing.JScrollPane;
 import javax.swing.JTextArea;
 import javax.swing.WindowConstants;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
 
 
 /**
@@ -129,6 +131,9 @@ private void initComponents() {
         innerControlPanel.add(btnStartSearch);
         innerControlPanel.add(btnCancel);
 
+        JPanel pnlValidationControl = new JPanel(new FlowLayout());
+
+
         pnlCommands.add(innerControlPanel, BorderLayout.NORTH);
         pnlCommands.add(prgProgress, BorderLayout.SOUTH);
 
@@ -269,7 +274,12 @@ public void actionPerformed(ActionEvent e) {
         }
         );
 
-
+        tab.addChangeListener((ChangeEvent e) -> {
+            if (e.getSource() instanceof JTabbedPane) {
+                JTabbedPane pane = (JTabbedPane) e.getSource();
+                changeControlView(pane.getSelectedIndex());
+            }          
+        });
 
         setJMenuBar(menuBar);        
         BorderLayout layout=new BorderLayout();
@@ -306,6 +316,12 @@ public void actionPerformed(ActionEvent e) {
     public JTextArea txtlog;
     private JScrollPane scrLogArea;
     public JProgressBar prgProgress;
+
+    private void changeControlView(int selectedIndex) {
+
+
+
+    }
 
 
 

diff --git a/src/main/java/com/compomics/coss/View/TargetDB_View.java b/src/main/java/com/compomics/coss/View/TargetDB_View.java
@@ -1,8 +1,4 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
+
 package com.compomics.coss.View;
 
 import com.compomics.coss.Controller.MainFrameController;