Change the factor in fount of xcorr

fcyu · May 21, 2017 · e86ee1e · e86ee1e
1 parent fcd901a
commit e86ee1e
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/src/main/java/proteomics/Search/CalEValue.java b/src/main/java/proteomics/Search/CalEValue.java
@@ -226,8 +226,8 @@ private int generateRandomRandomScores(int gap_num) {
                         String[] temp = seq_1_link_site.split("-");
                         String seq_1 = temp[0];
                         short link_site = Short.valueOf(temp[1]);
-                        double score1 = theo_mz_1.dot(pl_map_xcorr) * 0.25;
                         SparseBooleanVector theo_mz_1 = mass_tool_obj.buildTheoVector(MassTool.seqToAAList(seq_1), link_site, precursor_mass - mass_1, result_entry.charge, max_common_ion_charge, pl_map_xcorr.getMaxIdx());
+                        double score1 = theo_mz_1.dot(pl_map_xcorr) * 0.005;
                         if (score1 > Search.single_chain_t) {
                             gap_num = generateMoreScoresSub(sub_map, seq_1, score1, precursor_mass, gap_num);
                             if (gap_num < 0) {
@@ -248,8 +248,8 @@ private int generateMoreScoresSub(NavigableMap<Float, Set<String>> sub_map, Stri
                 String seq_2 = temp[0];
                 short link_site = Short.valueOf(temp[1]);
                 if (!seq_1.contentEquals(seq_2)) {
-                    double score2 = theo_mz_2.dot(pl_map_xcorr) * 0.25;
                     SparseBooleanVector theo_mz_2 = mass_tool_obj.buildTheoVector(MassTool.seqToAAList(seq_2), link_site, precursor_mass - mass_2, result_entry.charge, max_common_ion_charge, pl_map_xcorr.getMaxIdx());
+                    double score2 = theo_mz_2.dot(pl_map_xcorr) * 0.005;
                     if (score2 > Search.single_chain_t) {
                         double score = score1 + score2;
                         result_entry.addToScoreHistogram(score);

diff --git a/src/main/java/proteomics/Search/Search.java b/src/main/java/proteomics/Search/Search.java
@@ -290,7 +290,7 @@ private void linearScan(SpectrumEntry spectrumEntry, SparseVector xcorrPL, Chain
             SparseBooleanVector theo_mz = mass_tool_obj.buildTheoVector(chainEntry.aaArray, link_site_1, spectrumEntry.precursor_mass - chainEntry.chain_mass, precursor_charge, max_common_ion_charge, xcorrPL.getMaxIdx());
 
             // Calculate dot produce
-            double dot_product = theo_mz.dot(xcorrPL) * 0.25;
+            double dot_product = theo_mz.dot(xcorrPL) * 0.005;
 
             if (ECL2.debug) {
                 debugEntryList.add(new DebugEntry(chainEntry.seq, link_site_1, chainEntry.chain_mass, dot_product));