Change according to ProteomicsLibrary's changes.

src/main/java/proteomics/ECL2.java

@@ -143,21 +143,6 @@ private ECL2(String parameter_path, String spectra_path, String dbName) throws E
 
         PreSpectra preSpectra = new PreSpectra(spectra_parser, ms1Tolerance, leftInverseMs1Tolerance, rightInverseMs1Tolerance, ms1ToleranceUnit, build_index_obj, parameter_map, ext, sqlPath);
 
-        if (dev && parameter_map.get("C13_correction").contentEquals("1")) {
-            BufferedWriter writer = new BufferedWriter(new FileWriter("spectrum.dev.csv"));
-            writer.write("scanNum,charge,finalIsotopeCorrectionNum,isotopeCorrectionNum,pearsonCorrelationCoefficient,expMz1,expMz2,expMz3,expInt1,expInt2,expInt3,theoMz1,theoMz2,theoMz3,theoInt1,theoInt2,theoInt3\n");
-            Map<Integer, TreeMap<Integer, TreeSet<IsotopeDistribution.DevEntry>>> scanDevEntryMap = preSpectra.getScanDevEntryMap();
-            for (int scanNum : scanDevEntryMap.keySet()) {
-                TreeMap<Integer, TreeSet<IsotopeDistribution.DevEntry>> chargeDevEntryMap = scanDevEntryMap.get(scanNum);
-                for (int charge : chargeDevEntryMap.keySet()) {
-                    for (IsotopeDistribution.DevEntry devEntry : chargeDevEntryMap.get(charge)) {
-                        writer.write(String.format(Locale.US, "%d,%d,%d,%d,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f\n", scanNum, charge, devEntry.isotopeCorrectionNum, devEntry.isotopeCorrectionNum, devEntry.pearsonCorrelationCoefficient, devEntry.expMatrix[0][0], devEntry.expMatrix[1][0], devEntry.expMatrix[2][0], devEntry.expMatrix[0][1], devEntry.expMatrix[1][1], devEntry.expMatrix[2][1], devEntry.theoMatrix[0][0], devEntry.theoMatrix[1][0], devEntry.theoMatrix[2][0], devEntry.theoMatrix[0][1], devEntry.theoMatrix[1][1], devEntry.theoMatrix[2][1]));
-                    }
-                }
-            }
-            writer.close();
-        }
-
         logger.info("Start searching...");
 
         int thread_num = Integer.valueOf(parameter_map.get("thread_num"));

src/main/java/proteomics/Index/BuildIndex.java

@@ -99,7 +99,7 @@ public BuildIndex(Map<String, String> parameter_map) throws Exception {
         }
 
         // define a new MassTool object
-        mass_tool_obj = new MassTool(missed_cleavage, fix_mod_map, "KR", "P", true, mz_bin_size * 0.5, one_minus_bin_offset, "N14", "[]");
+        mass_tool_obj = new MassTool(missed_cleavage, fix_mod_map, "KR", "P", true, mz_bin_size * 0.5, one_minus_bin_offset, "N14");
 
         // generate seq_pro_map
         Map<String, boolean[]> seq_term_map = new HashMap<>();
@@ -513,10 +513,10 @@ private List<Map<Integer, Double>> generateLocalIdxModMassMap(int[] idxArray, Ma
     private Set<String> checkKCTermMod(Set<String> varSeqSet) { // eliminate those sequence that the middle amino acids having the same mod mass and the n-term and the first amino acid or the c-term and the last amino acid have the same mod mass. todo: check
         String[] varSeqArray = varSeqSet.toArray(new String[0]);
         Arrays.sort(varSeqArray); // Make sure that nK[].... is before n[]K..., so that n[]K... will be kept.
-        int seqLength = MassTool.seqToAAList(varSeqArray[0], "[]").length;
+        int seqLength = MassTool.seqToAAList(varSeqArray[0]).length;
         AA[][] aaArrays = new AA[varSeqArray.length][seqLength];
         for (int i = 0; i < varSeqArray.length; ++i) {
-            aaArrays[i] = MassTool.seqToAAList(varSeqArray[i], "[]");
+            aaArrays[i] = MassTool.seqToAAList(varSeqArray[i]);
         }
 
         if (aaArrays.length > 1) {
@@ -549,7 +549,7 @@ private Set<String> checkKCTermMod(Set<String> varSeqSet) { // eliminate those s
     }
 
     private Set<Short> getLinkSiteSet(String seq, boolean n_term, boolean c_term, short linker_type) {
-        AA[] aa_list = MassTool.seqToAAList(seq, "[]");
+        AA[] aa_list = MassTool.seqToAAList(seq);
         Set<Short> output = new HashSet<>(5, 1);
         for (int i = 1; i < aa_list.length - 2; ++i) {
             if (linker_type == 1 && aa_list[i].aa == 'K' && (Math.abs(aa_list[i].ptmDeltaMass) < varModMassResolution)) {

src/main/java/proteomics/Search/SearchWrap.java

@@ -220,7 +220,7 @@ private int getC13Num(double exp_mass, double theo_mass) {
 
     private String addFixMod(String seq, int linkSite) {
         Map<Character, Double> fix_mod_map = build_index_obj.getFixModMap();
-        AA[] aaList = MassTool.seqToAAList(seq, "[]");
+        AA[] aaList = MassTool.seqToAAList(seq);
         StringBuilder sb = new StringBuilder(seq.length() * 3);
         for (int i = 0; i < aaList.length; ++i) {
             AA aa = aaList[i];

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

@@ -26,10 +26,9 @@ public class PreSpectra {
     private static final Logger logger = LoggerFactory.getLogger(PreSpectra.class);
     private static final Pattern pattern = Pattern.compile("^[0-9]+$");
 
-    private Map<Integer, TreeMap<Integer, TreeSet<IsotopeDistribution.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 {
+    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 Exception {
         Set<Integer> debug_scan_num_set = new HashSet<>();
         //  In DEBUG mode, filter out unlisted scan num
         if (ECL2.debug) {
@@ -101,10 +100,6 @@ public PreSpectra(JMzReader spectra_parser, double ms1Tolerance, double leftInve
                 int rt = -1;
                 int isotopeCorrectionNum = 0;
                 double pearsonCorrelationCoefficient = -1;
-                TreeMap<Integer, TreeSet<IsotopeDistribution.DevEntry>> chargeDevEntryMap = null;
-                if (ECL2.dev) {
-                    chargeDevEntryMap = new TreeMap<>();
-                }
                 if (ext.toLowerCase().contentEquals("mgf")) {
                     mgfTitle = ((Ms2Query) spectrum).getTitle();
                     scan_num = getScanNum(mgfTitle);
@@ -115,7 +110,7 @@ public PreSpectra(JMzReader spectra_parser, double ms1Tolerance, double leftInve
                     if (parameter_map.get("C13_correction").contentEquals("1")) {
                         TreeMap<Double, Double> parentPeakList = new TreeMap<>(spectra_parser.getSpectrumById(parentId).getPeakList());
                         // We do not try to correct the precursor charge if there is one.
-                        IsotopeDistribution.Entry entry = isotopeDistribution.getIsotopeCorrectionNum(precursor_mz, ms1Tolerance, ms1ToleranceUnit, precursor_charge, parentPeakList, chargeDevEntryMap);
+                        IsotopeDistribution.Entry entry = isotopeDistribution.getIsotopeCorrectionNum(precursor_mz, ms1Tolerance, ms1ToleranceUnit, precursor_charge, parentPeakList);
                         if (entry.pearsonCorrelationCoefficient >= 0.7) { // If the Pearson correlation coefficient is smaller than 0.7, there is not enough evidence to change the original precursor mz.
                             isotopeCorrectionNum = entry.isotopeCorrectionNum;
                             pearsonCorrelationCoefficient = entry.pearsonCorrelationCoefficient;
@@ -136,10 +131,6 @@ public PreSpectra(JMzReader spectra_parser, double ms1Tolerance, double leftInve
                 sqlPrepareStatement.setDouble(10, pearsonCorrelationCoefficient);
                 sqlPrepareStatement.executeUpdate();
                 ++usefulSpectraNum;
-
-                if (ECL2.dev) {
-                    scanDevEntryMap.put(scan_num, chargeDevEntryMap);
-                }
             } catch (RuntimeException ex) {
                 logger.error(ex.toString());
             }
@@ -151,10 +142,6 @@ public PreSpectra(JMzReader spectra_parser, double ms1Tolerance, double leftInve
         logger.info("Useful MS/MS spectra number: {}.", usefulSpectraNum);
     }
 
-    public Map<Integer, TreeMap<Integer, TreeSet<IsotopeDistribution.DevEntry>>> getScanDevEntryMap() {
-        return scanDevEntryMap;
-    }
-
     public int getUsefulSpectraNum() {
         return usefulSpectraNum;
     }