From 012c18aacaccb2b404b6dc700ed5a21a8adb08a6 Mon Sep 17 00:00:00 2001
From: Genet Abay <genetabay.shiferaw@vib-ugent.be>
Date: Tue, 13 Apr 2021 16:19:39 +0200
Subject: [PATCH] command line error fixed

---
 .../controller/MainConsoleController.java     | 38 ++++++++++++++-----
 .../coss/controller/MainFrameController.java  | 26 +++++++++----
 .../coss/controller/rescoring/Rescore.java    |  1 +
 3 files changed, 49 insertions(+), 16 deletions(-)

diff --git a/src/main/java/com/compomics/coss/controller/MainConsoleController.java b/src/main/java/com/compomics/coss/controller/MainConsoleController.java
index 7f8cf17..c3b11b2 100644
--- a/src/main/java/com/compomics/coss/controller/MainConsoleController.java
+++ b/src/main/java/com/compomics/coss/controller/MainConsoleController.java
@@ -2,6 +2,7 @@
 
 import com.compomics.coss.controller.decoyGeneration.*;
 import com.compomics.coss.controller.SpectrumAnnotation.Annotation;
+import com.compomics.coss.controller.rescoring.Rescore;
 import com.compomics.coss.model.ComparisonResult;
 import com.compomics.coss.model.ConfigHolder;
 import java.io.File;
@@ -39,6 +40,8 @@ public class MainConsoleController implements UpdateListener {
     public void startRunning(String[] args) {
         try {
 
+            System.out.println("Starting COSS-V2");
+            System.out.println("Rescoring with Percolator is set on by default in this version");
             int lenArgs = args.length;
             String arg1 = args[0];
             if (lenArgs <= 1 || lenArgs > 5) {
@@ -75,14 +78,13 @@ public void startRunning(String[] args) {
             } else if (lenArgs == 3 && (arg1.startsWith("-a"))) {
 
                 System.out.println("Annotating spectral library file...");
-                double fragTol=0.5;
-                try{
-                    fragTol= Double.parseDouble(args[2]);
-                }catch(NumberFormatException ex){
+                double fragTol = 0.5;
+                try {
+                    fragTol = Double.parseDouble(args[2]);
+                } catch (NumberFormatException ex) {
                     LOG.info("check the fragment tolearnce input: " + ex.toString());
                 }
-                
-                
+
                 annotateLibrary(fragTol, args[1]);
                 Runtime.getRuntime().exit(0);
 
@@ -109,8 +111,8 @@ public void startRunning(String[] args) {
 
                     startMatching();
 
-                    ImportExport exp = new ImportExport(result, configData);
-                    exp.saveResult_CL(2);
+//                    ImportExport exp = new ImportExport(result, configData);
+//                    exp.saveResult_CL(2);
                 }
 
             }
@@ -227,9 +229,27 @@ private void startMatching() {
 
         dispatcher = new Dispatcher(this.configData, this, LOG);
         result = dispatcher.dispatch();
+        
         if (configData.isDecoyAvailable() && result != null) {
             validateResult();
-            LOG.info("Number of validated identified spectra: " + Integer.toString(result.size()));
+            LOG.info("Number of validated identified spectra by COSS: " + Integer.toString(result.size()));
+
+            LOG.info("starting rescoring the result with Percolator ... ");
+            Rescore rescore = new Rescore(result);
+            try {
+                boolean finished = rescore.start_rescoring(configData.getExperimentalSpecFile().toString());
+                if (finished) {
+                    LOG.info("Percolator finishes scoring and result is stored in the directory of input file ");
+                } else {
+                    LOG.info("Percolator exits with error. Result not rescored ");
+                    if (!rescore.error_msg.isEmpty()) {
+                        LOG.info(rescore.error_msg);
+                    }
+                }
+            } catch (IOException ex) {
+                java.util.logging.Logger.getLogger(MainFrameController.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
+            }
+
         } else {
             LOG.info("No decoy spectra found in library");
         }
diff --git a/src/main/java/com/compomics/coss/controller/MainFrameController.java b/src/main/java/com/compomics/coss/controller/MainFrameController.java
index f0dd459..f35e145 100644
--- a/src/main/java/com/compomics/coss/controller/MainFrameController.java
+++ b/src/main/java/com/compomics/coss/controller/MainFrameController.java
@@ -535,7 +535,7 @@ private void fillExpSpectraTable() {
             int resultSize = 0;
             resultSize = result.size();// configData.getExpSpectraIndex().size();
             Spectrum expSpec;
-            Object[] row = new Object[13];
+            Object[] row = new Object[15];
             ComparisonResult res;
             MatchedLibSpectra matchedSpec;
             int row_index;
@@ -616,6 +616,9 @@ public void fillBestmatchTable(int target) {
                 row[11] = Double.toString(mSpec.getSumMatchedInt_Lib());
                 row[12] = Double.toString(mSpec.getNumMatchedPeaks());
                 tblModelResult.addRow(row);
+                if(mainView.chkboxPercolator.isSelected()){
+                    break;
+                }
 
             }
 
@@ -971,22 +974,31 @@ protected void done() {
                                 }
                             } catch (IOException ex) {
                                 java.util.logging.Logger.getLogger(MainFrameController.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
-                            }finally{
-                                
+                            }finally{ 
                                 List<ComparisonResult> temp = new ArrayList<>();                                
                                 List<Integer> newIndex= new ArrayList<Integer>(rescore.rescored_result.keySet()) ;
                                 double rescored_score;
                                 double q_val;
                                 String[] splits;
-                                for(int i=0;i<newIndex.size();i++){
-                                    
+                                for(int i=0;i<newIndex.size();i++){                                    
                                     temp.add(i, result.get(newIndex.get(i)));
                                     splits = rescore.rescored_result.get(newIndex.get(i)).split(",");
-                                    rescored_score = Double.parseDouble(splits[0]);
-                                    q_val = Double.parseDouble(splits[1]);
+                                    try{
+                                        rescored_score = Double.parseDouble(splits[0]);
+                                    }catch(NumberFormatException ex){
+                                        rescored_score = 0.0;
+                                    }
+                                    try{
+                                        q_val = Double.parseDouble(splits[1]);
+                                        
+                                    }catch(NumberFormatException ex){
+                                        
+                                        q_val = 0.0;
+                                    }                                   
                                     
                                     temp.get(i).setTopScore(rescored_score);
                                     temp.get(i).setQval(q_val);
+                                    temp.get(i).getMatchedLibSpec().get(0).setScore(rescored_score);
                                 }
                                 
                                 result=temp;
diff --git a/src/main/java/com/compomics/coss/controller/rescoring/Rescore.java b/src/main/java/com/compomics/coss/controller/rescoring/Rescore.java
index 0ab4c70..b23e008 100644
--- a/src/main/java/com/compomics/coss/controller/rescoring/Rescore.java
+++ b/src/main/java/com/compomics/coss/controller/rescoring/Rescore.java
@@ -81,6 +81,7 @@ public boolean start_rescoring(String output_path) throws IOException {
                     id=title.substring(title.indexOf("Index")).split("=")[1];
                     int index=Integer.parseInt(id);
                     rescored_result.put(index, sb.toString());
+                    sb.setLength(0);
                     
                     
                 }else if(line.contains("percolator finished")){