Delete min_precursor_mass and max_precursor_mass parameters. Delete a…

… unnecessary filter.
fcyu · Jan 30, 2018 · b7ef385 · b7ef385
1 parent 1e0dd6b
commit b7ef385
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Showing 3 changed files with 23 additions and 47 deletions.
diff --git a/src/main/java/proteomics/Index/BuildIndex.java b/src/main/java/proteomics/Index/BuildIndex.java
@@ -39,7 +39,6 @@ public BuildIndex(Map<String, String> parameter_map) throws IOException {
         int missed_cleavage = Integer.valueOf(parameter_map.get("missed_cleavage"));
         float mz_bin_size = Float.valueOf(parameter_map.get("mz_bin_size"));
         float one_minus_bin_offset = 1 - Float.valueOf(parameter_map.get("mz_bin_offset"));
-        float max_precursor_mass = Float.valueOf(parameter_map.get("max_precursor_mass"));
         ms1_bin_size = Float.valueOf(parameter_map.get("ms1_bin_size"));
         inverseMs1BinSize = 1 / ms1_bin_size;
 
@@ -146,18 +145,16 @@ public BuildIndex(Map<String, String> parameter_map) throws IOException {
             Set<Short> linkSiteSet = getLinkSiteSet(seq, proteinNTerm, proteinCTerm, linker_type);
             if (!linkSiteSet.isEmpty()) {
                 float totalMass = (float) (mass_tool_obj.calResidueMass(seq) + MassTool.H2O);
-                if (totalMass < max_precursor_mass - linker_mass) {
-                    int bin = massToBin(totalMass);
-                    if (bin_seq_map.containsKey(bin)) {
-                        bin_seq_map.get(bin).add(seq);
-                    } else {
-                        Set<String> temp = new HashSet<>();
-                        temp.add(seq);
-                        bin_seq_map.put(bin, temp);
-                    }
-                    ChainEntry chainEntry = new ChainEntry(seq, totalMass, linkSiteSet, proteinNTerm, proteinCTerm, "0".hashCode());
-                    seq_entry_map.put(seq, chainEntry);
+                int bin = massToBin(totalMass);
+                if (bin_seq_map.containsKey(bin)) {
+                    bin_seq_map.get(bin).add(seq);
+                } else {
+                    Set<String> temp = new HashSet<>();
+                    temp.add(seq);
+                    bin_seq_map.put(bin, temp);
                 }
+                ChainEntry chainEntry = new ChainEntry(seq, totalMass, linkSiteSet, proteinNTerm, proteinCTerm, "0".hashCode());
+                seq_entry_map.put(seq, chainEntry);
             }
 
             // mod containing
@@ -167,24 +164,22 @@ public BuildIndex(Map<String, String> parameter_map) throws IOException {
                 linkSiteSet.add(varSeq.linkSite);
                 if (!linkSiteSet.isEmpty()) {
                     float totalMass = (float) (mass_tool_obj.calResidueMass(varSeq.seq) + MassTool.H2O);
-                    if (totalMass < max_precursor_mass - linker_mass) {
-                        int bin = massToBin(totalMass);
-                        if (bin_seq_map.containsKey(bin)) {
-                            bin_seq_map.get(bin).add(varSeq.seq);
-                        } else {
-                            Set<String> temp = new HashSet<>();
-                            temp.add(varSeq.seq);
-                            bin_seq_map.put(bin, temp);
-                        }
-                        ChainEntry chainEntry = new ChainEntry(varSeq.seq, totalMass, linkSiteSet, proteinNTerm, proteinCTerm, varSeq.binaryModType);
-                        if (seq_entry_map.containsKey(varSeq.seq)) {
-                            // Binary mod has the higher priority
-                            if (seq_entry_map.get(varSeq.seq).binaryModType == "0".hashCode()) {
-                                seq_entry_map.put(varSeq.seq, chainEntry);
-                            }
-                        } else {
+                    int bin = massToBin(totalMass);
+                    if (bin_seq_map.containsKey(bin)) {
+                        bin_seq_map.get(bin).add(varSeq.seq);
+                    } else {
+                        Set<String> temp = new HashSet<>();
+                        temp.add(varSeq.seq);
+                        bin_seq_map.put(bin, temp);
+                    }
+                    ChainEntry chainEntry = new ChainEntry(varSeq.seq, totalMass, linkSiteSet, proteinNTerm, proteinCTerm, varSeq.binaryModType);
+                    if (seq_entry_map.containsKey(varSeq.seq)) {
+                        // Binary mod has the higher priority
+                        if (seq_entry_map.get(varSeq.seq).binaryModType == "0".hashCode()) {
                             seq_entry_map.put(varSeq.seq, chainEntry);
                         }
+                    } else {
+                        seq_entry_map.put(varSeq.seq, chainEntry);
                     }
                 }
             }

diff --git a/src/main/java/proteomics/Spectrum/PreSpectra.java b/src/main/java/proteomics/Spectrum/PreSpectra.java
@@ -29,9 +29,6 @@ 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) throws MzXMLParsingException, IOException {
-        float min_precursor_mass =  Float.valueOf(parameter_map.get("min_precursor_mass"));
-        float max_precursor_mass = Float.valueOf(parameter_map.get("max_precursor_mass"));
-
         //  In DEBUG mode, filter out unlisted scan num
         if (ECL2.debug) {
             for (String k : parameter_map.keySet()) {
@@ -62,22 +59,8 @@ public PreSpectra(JMzReader spectra_parser, BuildIndex build_index_obj, Map<Stri
             double precursor_mz = spectrum.getPrecursorMZ();
             float precursor_mass = (float) (precursor_mz * precursor_charge - precursor_charge * 1.00727646688);
 
-            if ((precursor_mass > max_precursor_mass) || (precursor_mass < min_precursor_mass)) {
-                continue;
-            }
-
             Map<Double, Double> raw_mz_intensity_map = spectrum.getPeakList();
 
-            int peakCount = 0;
-            for (double intensity : raw_mz_intensity_map.values()) {
-                if (intensity > 1e-6) {
-                    ++peakCount;
-                }
-            }
-            if (peakCount < 10) {
-                continue;
-            }
-
             if (ECL2.debug) {
                 BufferedWriter writer = new BufferedWriter(new FileWriter(Integer.valueOf(spectrum.getId()) + ".raw.spectrum.csv"));
                 writer.write("mz,intensity\n");

diff --git a/src/main/resources/parameter.def b/src/main/resources/parameter.def
@@ -8,8 +8,6 @@ dev = 0 # Output development information.
 db = small+random50.fasta # The protein database.
 database_type = UniProt # Different types have different fasta header patterns. Available values: UniProt, SwissProt, TAIR, Others
 missed_cleavage = 2 # Maximum number of allowed missed cleavage.
-min_precursor_mass = 1000
-max_precursor_mass = 12000
 min_chain_length = 5 # Minimum length of a peptide chain.
 max_chain_length = 50