Improve the procedure of generating theoretical fragment ions and cal…

…culating XCorr.
fcyu · Jan 30, 2018 · a212c13 · a212c13
1 parent 82cd63f
commit a212c13
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Showing 2 changed files with 15 additions and 17 deletions.
diff --git a/src/main/java/proteomics/Search/Search.java b/src/main/java/proteomics/Search/Search.java
@@ -279,11 +279,8 @@ public FinalResultEntry convertResultEntry(int scanNum, ResultEntry result_entry
 
     private void linearScan(SpectrumEntry spectrumEntry, SparseVector xcorrPL, 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);
-
-            // Calculate dot produce
-            double dot_product = theo_mz.dot(xcorrPL) * 0.005;
+            // generate theoretical fragment ion bins and calculate XCorr.
+            double dot_product = mass_tool_obj.generateTheoFragmentAndCalXCorr(chainEntry.seq, link_site_1, spectrumEntry.precursor_mass - chainEntry.chain_mass, spectrumEntry.precursor_charge, xcorrPL);
 
             if (ECL2.debug) {
                 debugEntryList.add(new DebugEntry(chainEntry.seq, link_site_1, chainEntry.chain_mass, dot_product));

diff --git a/src/main/java/proteomics/TheoSeq/MassTool.java b/src/main/java/proteomics/TheoSeq/MassTool.java
@@ -2,6 +2,7 @@
 
 import proteomics.Types.AA;
 import proteomics.Types.SparseBooleanVector;
+import proteomics.Types.SparseVector;
 
 import java.util.*;
 import java.util.regex.*;
@@ -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) {
+    public double generateTheoFragmentAndCalXCorr(String seq, short linkSite, float additional_mass, int precursor_charge, SparseVector xcorrPL) {
         linkSite = (short) Math.max(1, linkSite);
 
         int localMaxCharge = Math.min(max_charge, Math.max(precursor_charge - 1, 1));
@@ -118,62 +119,62 @@ public SparseBooleanVector buildTheoVector(String seq, short linkSite, float add
             inverseChargeArray[charge - 1] = (double) 1 / (double) charge;
         }
 
-        SparseBooleanVector outputVector = new SparseBooleanVector();
-
         AA[] aaArray = seqToAAList(seq);
 
+        double xcorr = 0;
+
         // traverse the sequence to get b-ion
         double bIonMass = mass_table.get(aaArray[0].aa) + aaArray[0].delta_mass; // add N-term modification
         for (int i = 1; i < aaArray.length - 2; ++i) {
             bIonMass += mass_table.get(aaArray[i].aa) + aaArray[i].delta_mass;
             if (i < linkSite) {
                 for (double inverseCharge : inverseChargeArray) {
-                    outputVector.put(mzToBin(bIonMass * inverseCharge + 1.00727646688));
+                    xcorr += xcorrPL.get(mzToBin(bIonMass * inverseCharge + 1.00727646688));
                 }
             } else {
                 for (double inverseCharge : inverseChargeArray) {
-                    outputVector.put(mzToBin((bIonMass + additional_mass) * inverseCharge + 1.00727646688));
+                    xcorr += xcorrPL.get(mzToBin((bIonMass + additional_mass) * inverseCharge + 1.00727646688));
                 }
             }
         }
         // calculate the last b-ion with C-term modification
         bIonMass +=  mass_table.get(aaArray[aaArray.length - 2].aa) + aaArray[aaArray.length - 2].delta_mass + mass_table.get(aaArray[aaArray.length - 1].aa) + aaArray[aaArray.length - 1].delta_mass;
         for (double inverseCharge : inverseChargeArray) {
-            outputVector.put(mzToBin((bIonMass + additional_mass) * inverseCharge + 1.00727646688)); // for the fragment containing all amino acids, the additional mass is always included.
+            xcorr += xcorrPL.get(mzToBin((bIonMass + additional_mass) * inverseCharge + 1.00727646688)); // for the fragment containing all amino acids, the additional mass is always included.
         }
 
         // traverse the sequence with reversed order to get y-ion
         // the whole sequence
         double yIonMass = bIonMass + H2O;
         for (double inverseCharge : inverseChargeArray) {
-            outputVector.put(mzToBin((yIonMass + additional_mass) * inverseCharge + 1.00727646688)); // for the fragment containing all amino acids, the additional mass is always included.
+            xcorr += xcorrPL.get(mzToBin((yIonMass + additional_mass) * inverseCharge + 1.00727646688)); // for the fragment containing all amino acids, the additional mass is always included.
         }
         // delete the first amino acid and N-term modification
         yIonMass -= mass_table.get(aaArray[0].aa) + aaArray[0].delta_mass + mass_table.get(aaArray[1].aa) + aaArray[1].delta_mass;
         if (1 >= linkSite) {
             for (double inverseCharge : inverseChargeArray) {
-                outputVector.put(mzToBin(yIonMass * inverseCharge + 1.00727646688));
+                xcorr += xcorrPL.get(mzToBin(yIonMass * inverseCharge + 1.00727646688));
             }
         } else {
             for (double inverseCharge : inverseChargeArray) {
-                outputVector.put(mzToBin((yIonMass + additional_mass) * inverseCharge + 1.00727646688));
+                xcorr += xcorrPL.get(mzToBin((yIonMass + additional_mass) * inverseCharge + 1.00727646688));
             }
         }
         // rest of the sequence
         for (int i = 2; i < aaArray.length - 2; ++i) {
             yIonMass -= mass_table.get(aaArray[i].aa) + aaArray[i].delta_mass;
             if (i >= linkSite) { // caution: here, it is different from b-ion
                 for (double inverseCharge : inverseChargeArray) {
-                    outputVector.put(mzToBin(yIonMass * inverseCharge + 1.00727646688));
+                    xcorr += xcorrPL.get(mzToBin(yIonMass * inverseCharge + 1.00727646688));
                 }
             } else {
                 for (double inverseCharge : inverseChargeArray) {
-                    outputVector.put(mzToBin((yIonMass + additional_mass) * inverseCharge + 1.00727646688));
+                    xcorr += xcorrPL.get(mzToBin((yIonMass + additional_mass) * inverseCharge + 1.00727646688));
                 }
             }
         }
 
-        return outputVector;
+        return xcorr * 0.005;
     }
 
     public static AA[] seqToAAList(String seq) {