Delete three unimportant parameters.

fcyu · Jan 29, 2018 · 72ba36b · 72ba36b
1 parent 924f103
commit 72ba36b
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Showing 6 changed files with 7 additions and 21 deletions.
diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java
@@ -57,7 +57,6 @@ public static void main(String[] args) {
         // Get the parameter map
         Parameter parameter = new Parameter(parameter_path);
         Map<String, String> parameter_map = parameter.returnParameterMap();
-        int max_common_ion_charge = Integer.valueOf(parameter_map.get("max_common_ion_charge"));
 
         // print all parameters
         logger.info("Parameters:");
@@ -140,7 +139,7 @@ public static void main(String[] args) {
         Search search_obj = new Search(build_index_obj, parameter_map);
         List<Future<FinalResultEntry>> taskList = new LinkedList<>();
         for (int scanNum : scanNumArray) {
-            taskList.add(thread_pool.submit(new SearchWrap(search_obj, num_spectrum_map.get(scanNum), build_index_obj, mass_tool_obj, max_common_ion_charge, build_index_obj.getSeqProMap(), cal_evalue, delta_c_t, flankingPeaks)));
+            taskList.add(thread_pool.submit(new SearchWrap(search_obj, num_spectrum_map.get(scanNum), build_index_obj, mass_tool_obj, build_index_obj.getSeqProMap(), cal_evalue, delta_c_t, flankingPeaks)));
         }
 
         // check progress every minute, record results,and delete finished tasks.

diff --git a/src/main/java/proteomics/Search/Search.java b/src/main/java/proteomics/Search/Search.java
@@ -16,7 +16,6 @@ public class Search {
 
     private static final Logger logger = LoggerFactory.getLogger(Search.class);
 
-    private final int max_common_ion_charge;
     public final float ms1_tolerance;
     public final int ms1_tolerance_unit;
     private final Map<String, ChainEntry> chain_entry_map;
@@ -35,7 +34,6 @@ public Search(BuildIndex build_index_obj, Map<String, String> parameter_map) {
         chain_entry_map = build_index_obj.getSeqEntryMap();
         fix_mod_map = build_index_obj.getFixModMap();
         mass_tool_obj = build_index_obj.returnMassTool();
-        max_common_ion_charge = Integer.valueOf(parameter_map.get("max_common_ion_charge"));
         ms1_tolerance_unit = Integer.valueOf(parameter_map.get("ms1_tolerance_unit"));
         ms1_tolerance = Float.valueOf(parameter_map.get("ms1_tolerance"));
         bin_seq_map = build_index_obj.getMassBinSeqMap();
@@ -319,7 +317,7 @@ public FinalResultEntry convertResultEntry(int scanNum, ResultEntry result_entry
     private void linearScan(SpectrumEntry spectrumEntry, SparseVector xcorrPL, int specMaxBinIdx, ChainEntry chainEntry, int binInx, TreeMap<Integer, ChainResultEntry> binChainMap, List<DebugEntry> debugEntryList, Map<String, Double> devChainScoreMap) {
         for (short link_site_1 : chainEntry.link_site_set) {
             int precursor_charge = spectrumEntry.precursor_charge;
-            SparseBooleanVector theo_mz = mass_tool_obj.buildTheoVector(chainEntry.seq, link_site_1, spectrumEntry.precursor_mass - chainEntry.chain_mass, precursor_charge, max_common_ion_charge, specMaxBinIdx);
+            SparseBooleanVector theo_mz = mass_tool_obj.buildTheoVector(chainEntry.seq, link_site_1, spectrumEntry.precursor_mass - chainEntry.chain_mass, precursor_charge, specMaxBinIdx);
 
             // Calculate dot produce
             double dot_product = theo_mz.dot(xcorrPL) * 0.005;

diff --git a/src/main/java/proteomics/Search/SearchWrap.java b/src/main/java/proteomics/Search/SearchWrap.java
@@ -23,18 +23,16 @@ public class SearchWrap implements Callable<FinalResultEntry> {
     private final SpectrumEntry spectrumEntry;
     private final BuildIndex build_index_obj;
     private final MassTool mass_tool_obj;
-    private final int max_common_ion_charge;
     private final PreSpectrum preSpectrumObj;
     private final Map<String, Set<String>> seqProMap;
     private final boolean cal_evalue;
     private final float delta_c_t;
 
-    public SearchWrap(Search search_obj, SpectrumEntry spectrumEntry, BuildIndex build_index_obj, MassTool mass_tool_obj, int max_common_ion_charge, Map<String, Set<String>> seqProMap, boolean cal_evalue, float delta_c_t, boolean flankingPeaks) {
+    public SearchWrap(Search search_obj, SpectrumEntry spectrumEntry, BuildIndex build_index_obj, MassTool mass_tool_obj, Map<String, Set<String>> seqProMap, boolean cal_evalue, float delta_c_t, boolean flankingPeaks) {
         this.search_obj = search_obj;
         this.spectrumEntry = spectrumEntry;
         this.build_index_obj = build_index_obj;
         this.mass_tool_obj = mass_tool_obj;
-        this.max_common_ion_charge = max_common_ion_charge;
         preSpectrumObj = new PreSpectrum(mass_tool_obj, flankingPeaks);
         this.seqProMap = seqProMap;
         this.cal_evalue = cal_evalue;
@@ -60,8 +58,8 @@ public FinalResultEntry call() {
         ResultEntry resultEntry =  search_obj.doSearch(spectrumEntry, xcorrPL, specMaxBinIdx);
         if (resultEntry != null) {
             if (ECL2.debug) {
-                SparseBooleanVector chainVector1 = mass_tool_obj.buildTheoVector(resultEntry.getChain1(), (short) resultEntry.getLinkSite1(), spectrumEntry.precursor_mass - (float) (mass_tool_obj.calResidueMass(resultEntry.getChain1()) + MassTool.H2O), spectrumEntry.precursor_charge, max_common_ion_charge, specMaxBinIdx);
-                SparseBooleanVector chainVector2 = mass_tool_obj.buildTheoVector(resultEntry.getChain2(), (short) resultEntry.getLinkSite2(), spectrumEntry.precursor_mass - (float) (mass_tool_obj.calResidueMass(resultEntry.getChain2()) + MassTool.H2O), spectrumEntry.precursor_charge, max_common_ion_charge, specMaxBinIdx);
+                SparseBooleanVector chainVector1 = mass_tool_obj.buildTheoVector(resultEntry.getChain1(), (short) resultEntry.getLinkSite1(), spectrumEntry.precursor_mass - (float) (mass_tool_obj.calResidueMass(resultEntry.getChain1()) + MassTool.H2O), spectrumEntry.precursor_charge, specMaxBinIdx);
+                SparseBooleanVector chainVector2 = mass_tool_obj.buildTheoVector(resultEntry.getChain2(), (short) resultEntry.getLinkSite2(), spectrumEntry.precursor_mass - (float) (mass_tool_obj.calResidueMass(resultEntry.getChain2()) + MassTool.H2O), spectrumEntry.precursor_charge, specMaxBinIdx);
                 try (BufferedWriter writer = new BufferedWriter(new FileWriter(spectrumEntry.scan_num + ".chain.spectrum.csv"))) {
                     writer.write(resultEntry.getChain1() + " bin idx\n");
                     for (int idx : chainVector1.getIdxSet()) {

diff --git a/src/main/java/proteomics/Spectrum/PreSpectra.java b/src/main/java/proteomics/Spectrum/PreSpectra.java
@@ -28,8 +28,6 @@ public class PreSpectra {
     private Set<Integer> debug_scan_num_set = new HashSet<>();
 
     public PreSpectra(JMzReader spectra_parser, BuildIndex build_index_obj, Map<String, String> parameter_map, String ext) {
-        int min_ms1_charge = Integer.valueOf(parameter_map.get("min_ms1_charge"));
-        int max_ms1_charge = Integer.valueOf(parameter_map.get("max_ms1_charge"));
         float min_precursor_mass =  Float.valueOf(parameter_map.get("min_precursor_mass"));
         float max_precursor_mass = Float.valueOf(parameter_map.get("max_precursor_mass"));
 
@@ -61,11 +59,6 @@ public PreSpectra(JMzReader spectra_parser, BuildIndex build_index_obj, Map<Stri
                     continue;
                 }
                 int precursor_charge = spectrum.getPrecursorCharge();
-
-                if ((precursor_charge < min_ms1_charge) || (precursor_charge > max_ms1_charge)) {
-                    continue;
-                }
-
                 double precursor_mz = spectrum.getPrecursorMZ();
                 float precursor_mass = (float) (precursor_mz * precursor_charge - precursor_charge * 1.00727646688);
 

diff --git a/src/main/java/proteomics/TheoSeq/MassTool.java b/src/main/java/proteomics/TheoSeq/MassTool.java
@@ -9,6 +9,7 @@
 public class MassTool {
 
     private static final int max_charge = 6;
+    private static final int max_common_ion_charge = 3;
     private static final Pattern mod_aa_pattern = Pattern.compile("([A-Znc])(\\[([0-9\\.\\-]+)\\])?");
 
     public static final double H2O = 18.010564684;
@@ -109,7 +110,7 @@ public Map<Character, Float> getMassTable() {
         return mass_table;
     }
 
-    public SparseBooleanVector buildTheoVector(String seq, short linkSite, float additional_mass, int precursor_charge, int max_common_ion_charge, int specMaxBinIdx) {
+    public SparseBooleanVector buildTheoVector(String seq, short linkSite, float additional_mass, int precursor_charge, int specMaxBinIdx) {
         linkSite = (short) Math.max(1, linkSite);
 
         int localMaxCharge = Math.min(max_charge, Math.max(precursor_charge - 1, 1));

diff --git a/src/main/resources/parameter.def b/src/main/resources/parameter.def
@@ -14,9 +14,6 @@ min_chain_length = 5 # Minimum length of a peptide chain.
 max_chain_length = 50
 
 # Spectrum
-min_ms1_charge = 3
-max_ms1_charge = 7
-max_common_ion_charge = 3
 C13_correction_range = 0 # Precursor mass correction range. Normally set to -1,0 to consider one C13 error.
 
 # Tolerance