Change "/" to "*" to increase speed.

fcyu · Feb 2, 2018 · fd9494a · fd9494a
1 parent b0c7fa3
commit fd9494a
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Showing 3 changed files with 11 additions and 7 deletions.
diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java
@@ -145,7 +145,7 @@ private ECL2(String parameter_path, String spectra_path, String dbName) throws I
             thread_num = 1;
         }
         ExecutorService thread_pool = Executors.newFixedThreadPool(thread_num);
-        Search search_obj = new Search(build_index_obj, parameter_map);
+        Search search_obj = new Search(build_index_obj, parameter_map, ms1Tolerance, leftInverseMs1Tolerance, rightInverseMs1Tolerance, ms1ToleranceUnit);
         List<Future<Boolean>> taskList = new LinkedList<>();
         Connection sqlConnection = DriverManager.getConnection(sqlPath);
         Statement sqlStatement = sqlConnection.createStatement();

diff --git a/src/main/java/proteomics/Search/Search.java b/src/main/java/proteomics/Search/Search.java
@@ -13,6 +13,8 @@
 public class Search {
 
     public final double ms1_tolerance;
+    public final double leftInverseMs1Tolerance;
+    public final double rightInverseMs1Tolerance;
     public final int ms1_tolerance_unit;
     private final Map<String, ChainEntry> chain_entry_map;
     private final MassTool mass_tool_obj;
@@ -23,12 +25,14 @@ public class Search {
     private final boolean cal_evalue;
 
     /////////////////////////////////////////public methods////////////////////////////////////////////////////////////
-    public Search(BuildIndex build_index_obj, Map<String, String> parameter_map) {
+    public Search(BuildIndex build_index_obj, Map<String, String> parameter_map, double ms1_tolerance, double leftInverseMs1Tolerance, double rightInverseMs1Tolerance, int ms1ToleranceUnit) {
         this.build_index_obj = build_index_obj;
         chain_entry_map = build_index_obj.getSeqEntryMap();
         mass_tool_obj = build_index_obj.returnMassTool();
-        ms1_tolerance_unit = Integer.valueOf(parameter_map.get("ms1_tolerance_unit"));
-        ms1_tolerance = Double.valueOf(parameter_map.get("ms1_tolerance"));
+        this.ms1_tolerance = ms1_tolerance;
+        this.leftInverseMs1Tolerance = leftInverseMs1Tolerance;
+        this.rightInverseMs1Tolerance = rightInverseMs1Tolerance;
+        this.ms1_tolerance_unit = ms1ToleranceUnit;
         bin_seq_map = build_index_obj.getMassBinSeqMap();
         single_chain_t = Double.valueOf(parameter_map.get("single_chain_t"));
         if (parameter_map.get("cal_evalue").contentEquals("0")) {
@@ -57,8 +61,8 @@ ResultEntry doSearch(SparseVector xcorrPL, TreeMap<Integer, List<Double>> binSco
         double leftMs1Tol = ms1_tolerance;
         double rightMs1Tol = ms1_tolerance;
         if (ms1_tolerance_unit == 1) {
-            leftMs1Tol = precursorMass - (precursorMass / (1 + ms1_tolerance * 1e-6));
-            rightMs1Tol = (precursorMass / (1 - ms1_tolerance * 1e-6)) - precursorMass;
+            leftMs1Tol = precursorMass - (precursorMass * leftInverseMs1Tolerance);
+            rightMs1Tol = (precursorMass * rightInverseMs1Tolerance) - precursorMass;
         }
 
         // for debug

diff --git a/src/main/java/proteomics/Spectrum/PreSpectra.java b/src/main/java/proteomics/Spectrum/PreSpectra.java
@@ -25,7 +25,7 @@ public class PreSpectra {
     private static final Pattern scanNumPattern2 = Pattern.compile("scan=([0-9]+)", Pattern.CASE_INSENSITIVE);
     private static final Pattern scanNumPattern3 = Pattern.compile("^[^.]+\\.([0-9]+)\\.[0-9]+\\.[0-9]");
 
-    public PreSpectra(JMzReader spectra_parser, BuildIndex build_index_obj, Map<String, String> parameter_map, String ext, String sqlPath) throws MzXMLParsingException, IOException, SQLException {
+    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<>();
         //  In DEBUG mode, filter out unlisted scan num
         if (ECL2.debug) {