spectrum title removed from key and mzml file added

src/main/java/com/compomics/coss/Controller/ConfigSpecReaders.java

@@ -0,0 +1,153 @@
+/*
+ * 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.ms2io.IndexKey;
+import com.compomics.ms2io.Indexer;
+import java.io.File;
+import java.io.IOException;
+import java.util.Collections;
+import java.util.List;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import com.compomics.coss.Model.*;
+import com.compomics.ms2io.MgfReader;
+import com.compomics.ms2io.MspReader;
+import com.compomics.ms2io.SpectraReader;
+import java.util.concurrent.ExecutionException;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+/**
+ *This class generate index file for both experimental and library spectra and 
+ * configures spectrum reader object to read them
+ * @author Genet
+ */
+public class ConfigSpecReaders {
+
+    private final File fileExperimnt;
+    private final File fileLibrary;
+    private boolean isCanceled;
+
+    public ConfigSpecReaders(File expFile, File libFile) {
+        this.fileExperimnt = expFile;
+        this.fileLibrary = libFile;
+        isCanceled=false;
+    }
+
+    public void cancelConfig(boolean cncl){
+        isCanceled=cncl;
+
+    }
+
+    public boolean readFile(ConfigData cfData) {
+
+        try {
+            ExecutorService executors = Executors.newFixedThreadPool(2);
+            Future[] fut = new Future[2];
+
+            //Generate Index for experimental spectrum
+            InputHandler ipHandler = new InputHandler(this.fileExperimnt, "spectrum");
+            fut[0] = executors.submit(ipHandler);
+
+
+            //generating index for library spectrum if it doesn't exist and read if it does.
+           // String libname = this.fileLibrary.getName().substring(0, this.fileLibrary.getName().lastIndexOf("."));
+           // File lib_indxfile = new File(this.fileLibrary.getParent(), libname + ".idx");
+           // if(!lib_indxfile.exists()){
+                ipHandler = new InputHandler(this.fileLibrary, "spectrum" );
+
+//            }
+//            
+//            else{
+//                ipHandler = new InputHandler(this.fileLibrary, "index" );
+//                
+//            }
+            fut[1] = executors.submit(ipHandler);
+            executors.shutdown();
+
+            cfData.setExpSpectraIndex((List<IndexKey>) fut[0].get());
+            cfData.setSpectralLibraryIndex((List<IndexKey>) fut[1].get());
+
+            //sort library spectrum
+            Collections.sort(cfData.getSpectraLibraryIndex());
+
+
+
+
+            //reader for experimental spectrum file
+            if (cfData.getExperimentalSpecFile().getName().endsWith("mgf")) {
+                SpectraReader rd = new MgfReader(cfData.getExperimentalSpecFile(), cfData.getExpSpectraIndex());
+                cfData.setExpSpecReader(rd);
+
+            } else if (cfData.getExperimentalSpecFile().getName().endsWith("msp")) {
+                SpectraReader rd = new MspReader(cfData.getExperimentalSpecFile(), cfData.getExpSpectraIndex());
+                cfData.setExpSpecReader(rd);
+
+            }
+
+            //reader for spectral library file
+            if (cfData.getSpecLibraryFile().getName().endsWith("mgf")) {
+                SpectraReader rd = new MgfReader(cfData.getSpecLibraryFile(), cfData.getSpectraLibraryIndex());
+                cfData.setLibSpecReader(rd);
+
+            } else if (cfData.getSpecLibraryFile().getName().endsWith("msp")) {
+                SpectraReader rd = new MspReader(cfData.getSpecLibraryFile(), cfData.getSpectraLibraryIndex());
+                cfData.setLibSpecReader(rd);
+            }
+
+
+
+
+
+
+        } catch (InterruptedException ex) {
+            Logger.getLogger(ConfigSpecReaders.class.getName()).log(Level.SEVERE, null, ex);
+        } catch (ExecutionException ex) {
+            Logger.getLogger(ConfigSpecReaders.class.getName()).log(Level.SEVERE, null, ex);
+        }
+
+        return true;
+    }
+
+    private class InputHandler implements Callable<List<IndexKey>> {
+
+        private final File file;
+        private final String aboutFile;
+
+        public InputHandler(File file, String aboutFile) {
+            this.file = file;
+            this.aboutFile=aboutFile;
+        }
+
+
+
+        @Override
+        public List<IndexKey> call() throws Exception {
+            List<IndexKey> indxList = null;
+
+            try {
+                if (this.aboutFile.equals("spectrum")) {
+                    Indexer giExp = new Indexer(this.file);
+                    indxList = giExp.generate();
+                }
+                else if(this.aboutFile.equals("index")){
+                    Indexer indxer = new Indexer();
+                    indxList = indxer.readFromFile(this.file);
+                }
+
+            } catch (IOException e) {
+                e.printStackTrace();
+            }
+
+            return indxList;
+        }
+
+    }
+
+}