Change some LinkedList to ArrayList for a higher speed.

src/main/java/proteomics/ECL2.java

@@ -166,7 +166,7 @@ private ECL2(String parameter_path, String spectra_path, String dbName) throws I
         }
         ExecutorService thread_pool = Executors.newFixedThreadPool(thread_num);
         Search search_obj = new Search(build_index_obj, parameter_map, ms1Tolerance, leftInverseMs1Tolerance, rightInverseMs1Tolerance, ms1ToleranceUnit);
-        List<Future<Boolean>> taskList = new LinkedList<>();
+        ArrayList<Future<SearchWrap.Entry>> taskList = new ArrayList<>(preSpectra.getUsefulSpectraNum() + 10);
         Connection sqlConnection = DriverManager.getConnection(sqlPath);
         Statement sqlStatement = sqlConnection.createStatement();
         ResultSet sqlResultSet = sqlStatement.executeQuery("SELECT scanId, precursorCharge, massWithoutLinker, precursorMass FROM spectraTable");
@@ -188,8 +188,8 @@ private ECL2(String parameter_path, String spectra_path, String dbName) throws I
         int count = 0;
         while (count < totalCount) {
             // record search results and delete finished ones.
-            List<Future<Boolean>> toBeDeleteTaskList = new LinkedList<>();
             for (Future<Boolean> task : taskList) {
+            List<Future<SearchWrap.Entry>> toBeDeleteTaskList = new ArrayList<>(totalCount - count);
                 if (task.isDone()) {
                     if (task.get()) {
                         ++resultCount;
@@ -201,6 +201,7 @@ private ECL2(String parameter_path, String spectra_path, String dbName) throws I
             }
             count += toBeDeleteTaskList.size();
             taskList.removeAll(toBeDeleteTaskList);
+            taskList.trimToSize();
 
             int progress = count * 20 / totalCount;
             if (progress != lastProgress) {
@@ -270,20 +271,20 @@ private static void saveTargetResult(Map<String, CalFDR.Entry> result, Map<Strin
             interTargetWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,\n");
             interDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,\n");
         }
-        List<CalFDR.Entry> entryList = new LinkedList<>(result.values());
+        List<CalFDR.Entry> entryList = new ArrayList<>(result.values());
         entryList.sort(Comparator.reverseOrder());
         for (CalFDR.Entry entry : entryList) {
             sqlResultSet = sqlStatement.executeQuery(String.format(Locale.US, "SELECT scanNum, precursorMz, precursorMass, rt, isotopeCorrectionNum, ms1PearsonCorrelationCoefficient, precursorCharge, theoMass, score, deltaC, ppm, seq1, linkSite1, seq2, linkSite2, proId1, proId2, eValue, mgfTitle, candidateNum, pointCount, rSquare, slope, intercept, startIdx, endIdx, chainScore1, chainRank1, chainScore2, chainRank2, hitType, clType FROM spectraTable WHERE scanId='%s'", entry.scanId));
             if (sqlResultSet.next()) {
-                List<String> proAnnotationList1 = new LinkedList<>();
+                List<String> proAnnotationList1 = new ArrayList<>();
                 for (String s : sqlResultSet.getString("proId1").split(";")) {
                     if (s.startsWith("DECOY_")) {
                         proAnnotationList1.add("DECOY");
                     } else {
                         proAnnotationList1.add(pro_annotate_map.get(s));
                     }
                 }
-                List<String> proAnnotationList2 = new LinkedList<>();
+                List<String> proAnnotationList2 = new ArrayList<>();
                 for (String s : sqlResultSet.getString("proId2").split(";")) {
                     if (s.startsWith("DECOY_")) {
                         proAnnotationList2.add("DECOY");

src/main/java/proteomics/Spectrum/PreSpectra.java

@@ -28,6 +28,7 @@ public class PreSpectra {
     private static final Pattern scanNumPattern3 = Pattern.compile("^[^.]+\\.([0-9]+)\\.[0-9]+\\.[0-9]");
 
     private Map<Integer, TreeMap<Integer, TreeSet<DevEntry>>> scanDevEntryMap = new HashMap<>();
+    private int usefulSpectraNum = 0;
 
     public PreSpectra(JMzReader spectra_parser, double ms1Tolerance, double leftInverseMs1Tolerance, double rightInverseMs1Tolerance, int ms1ToleranceUnit, BuildIndex build_index_obj, Map<String, String> parameter_map, String ext, String sqlPath) throws MzXMLParsingException, IOException, SQLException, JMzReaderException {
         Set<Integer> debug_scan_num_set = new HashSet<>();
@@ -52,7 +53,6 @@ public PreSpectra(JMzReader spectra_parser, double ms1Tolerance, double leftInve
 
         PreparedStatement sqlPrepareStatement = sqlConnection.prepareStatement("INSERT INTO spectraTable (scanNum, scanId, precursorCharge, precursorMz, precursorMass, rt, massWithoutLinker, mgfTitle, isotopeCorrectionNum, ms1PearsonCorrelationCoefficient) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)");
         sqlConnection.setAutoCommit(false);
-        int usefulSpectraNum = 0;
 
         Iterator<Spectrum> spectrumIterator = spectra_parser.getSpectrumIterator();
         String parentId = null;
@@ -154,6 +154,10 @@ public Map<Integer, TreeMap<Integer, TreeSet<DevEntry>>> getScanDevEntryMap() {
         return scanDevEntryMap;
     }
 
+    public int getUsefulSpectraNum() {
+        return usefulSpectraNum;
+    }
+
     private Entry getIsotopeCorrectionNum(double precursorMz, int charge, double inverseCharge, TreeMap<Double, Double> parentPeakList, double ms1Tolerance, double leftInverseMs1Tolerance, double rightInverseMs1Tolerance, int ms1ToleranceUnit, IsotopeDistribution isotopeDistribution, TreeMap<Integer, TreeSet<DevEntry>> chargeDevEntryMap) {
         Entry entry = new Entry(0, 0);
         double leftTol = ms1Tolerance * 2;

src/main/java/proteomics/Types/SparseVector.java

@@ -43,13 +43,13 @@ public Set<Integer> getIdxSet() {
     }
 
     double getMaxValue() {
-        List<Double> intensity_list = new LinkedList<>(sparse_vector.values());
+        List<Double> intensity_list = new ArrayList<>(sparse_vector.values());
         intensity_list.sort(Collections.reverseOrder());
         return intensity_list.get(0);
     }
 
     double getMinValue() {
-        List<Double> intensity_list = new LinkedList<>(sparse_vector.values());
+        List<Double> intensity_list = new ArrayList<>(sparse_vector.values());
         Collections.sort(intensity_list);
         return intensity_list.get(0);
     }