Add flanking_peaks as a parameter.

fcyu · May 29, 2017 · 840dfd4 · 840dfd4
1 parent 66e517f
commit 840dfd4
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Showing 6 changed files with 16 additions and 11 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>hk.ust.bioinformatics</groupId>
     <artifactId>ECL2</artifactId>
-    <version>2.1.4-dev-201705281102</version>
+    <version>2.1.4-dev-201705291100</version>
     <packaging>jar</packaging>
 
     <name>ECL2</name>

diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java
@@ -21,10 +21,9 @@
 public class ECL2 {
 
     public static final int score_point_t = 15000;
-    public static final boolean flankingPeaks = true;
 
     private static final Logger logger = LoggerFactory.getLogger(ECL2.class);
-    public static final String version = "2.1.4-dev-201705281102";
+    public static final String version = "2.1.4-dev-201705291100";
 
     public static boolean debug;
     public static boolean dev;
@@ -59,6 +58,11 @@ public static void main(String[] args) {
             delta_c_t = Float.valueOf(parameter_map.get("delta_c_t"));
         }
 
+        boolean flankingPeaks = true;
+        if (parameter_map.containsKey("flanking_peaks") && parameter_map.get("flanking_peaks").contentEquals("0")) {
+            flankingPeaks = false;
+        }
+
         debug = parameter_map.get("debug").contentEquals("1");
         dev = parameter_map.get("dev").contentEquals("1");
 
@@ -117,7 +121,7 @@ public static void main(String[] args) {
         Search search_obj = new Search(build_index_obj, parameter_map);
         List<Future<FinalResultEntry>> temp_result_list = new LinkedList<>();
         for (int scanNum : scanNumArray) {
-            temp_result_list.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)));
+            temp_result_list.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)));
         }
 
         // check progress every minute

diff --git a/src/main/java/proteomics/Search/SearchWrap.java b/src/main/java/proteomics/Search/SearchWrap.java
@@ -29,13 +29,13 @@ public class SearchWrap implements Callable<FinalResultEntry> {
     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) {
+    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) {
         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);
+        preSpectrumObj = new PreSpectrum(mass_tool_obj, flankingPeaks);
         this.seqProMap = seqProMap;
         this.cal_evalue = cal_evalue;
         this.delta_c_t = delta_c_t;

diff --git a/src/main/java/proteomics/Spectrum/PreSpectra.java b/src/main/java/proteomics/Spectrum/PreSpectra.java
@@ -40,8 +40,6 @@ public PreSpectra(MzXMLFile spectra_parser, BuildIndex build_index_obj, Map<Stri
             }
         }
 
-        PreSpectrum pre_spectrum_obj = new PreSpectrum(mass_tool_obj);
-
         PrintStream original_stream = System.out;
         PrintStream null_stream = new PrintStream(new OutputStream() {
             @Override

diff --git a/src/main/java/proteomics/Spectrum/PreSpectrum.java b/src/main/java/proteomics/Spectrum/PreSpectrum.java
@@ -17,9 +17,11 @@ public class PreSpectrum {
     private static final int XCORR_OFFSET = 75;
 
     private final MassTool mass_tool_obj;
+    private final boolean flankingPeaks;
 
-    public PreSpectrum(MassTool mass_tool_obj) {
+    public PreSpectrum(MassTool mass_tool_obj, boolean flankingPeaks) {
         this.mass_tool_obj = mass_tool_obj;
+        this.flankingPeaks =flankingPeaks;
     }
 
     public SparseVector preSpectrum (Map<Double, Double> peaks_map, float precursor_mass, int scanNum) {
@@ -76,7 +78,7 @@ private SparseVector prepareXcorr(double[] pl_array) {
 
         for (int i = 1; i < pl_array.length; ++i) {
             double temp = pl_array[i] - tempArray[i];
-            if (ECL2.flankingPeaks) {
+            if (flankingPeaks) {
                 temp += (pl_array[i - 1] - tempArray[i - 1]) * 0.5;
                 if (i + 1 < pl_array.length) {
                     temp += (pl_array[i + 1] - tempArray[i + 1]) * 0.5;

diff --git a/src/main/resources/parameter.def b/src/main/resources/parameter.def
@@ -1,4 +1,4 @@
-# 2.1.4-dev-201705281102
+# 2.1.4-dev-201705291100
 # The first line is the parameter file version. Do not change it.
 thread_num = 0
 debug = 0
@@ -74,6 +74,7 @@ single_chain_t = 0.1
 cal_evalue = 1
 ms1_bin_size = 0.001
 delta_c_t = 0.00
+flanking_peaks = 1
 
 # for debug
 # put interested scan numbers below. One number each line