Add delta_c_t as an option.

fcyu · May 28, 2017 · 91b4444 · 91b4444
1 parent 26962e2
commit 91b4444
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Showing 4 changed files with 16 additions and 8 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-201705271641</version>
+    <version>2.1.4-dev-201705281102</version>
     <packaging>jar</packaging>
 
     <name>ECL2</name>

diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java
@@ -20,12 +20,11 @@
 
 public class ECL2 {
 
-    public static final double delta_c_t = 0;
     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-201705271641";
+    public static final String version = "2.1.4-dev-201705281102";
 
     public static boolean debug;
     public static boolean dev;
@@ -49,11 +48,17 @@ public static void main(String[] args) {
         Parameter parameter = new Parameter(parameter_path);
         Map<String, String> parameter_map = parameter.returnParameterMap();
         int max_common_ion_charge = Integer.valueOf(parameter_map.get("max_common_ion_charge"));
+
         boolean cal_evalue = true;
         if (parameter_map.containsKey("cal_evalue") && parameter_map.get("cal_evalue").trim().contentEquals("0")) {
             cal_evalue = false;
         }
 
+        float delta_c_t = 0;
+        if (parameter_map.containsKey("delta_c_t")) {
+            delta_c_t = Float.valueOf(parameter_map.get("delta_c_t"));
+        }
+
         debug = parameter_map.get("debug").contentEquals("1");
         dev = parameter_map.get("dev").contentEquals("1");
 
@@ -112,7 +117,7 @@ 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)));
+            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)));
         }
 
         // check progress every minute

diff --git a/src/main/java/proteomics/Search/SearchWrap.java b/src/main/java/proteomics/Search/SearchWrap.java
@@ -27,8 +27,9 @@ public class SearchWrap implements Callable<FinalResultEntry> {
     private final PreSpectrum preSpectrumObj;
     private final Map<String, Set<String>> seqProMap;
     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) {
+    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) {
         this.search_obj = search_obj;
         this.spectrumEntry = spectrumEntry;
         this.build_index_obj = build_index_obj;
@@ -37,6 +38,7 @@ public SearchWrap(Search search_obj, SpectrumEntry spectrumEntry, BuildIndex bui
         preSpectrumObj = new PreSpectrum(mass_tool_obj);
         this.seqProMap = seqProMap;
         this.cal_evalue = cal_evalue;
+        this.delta_c_t = delta_c_t;
     }
 
     @Override
@@ -75,7 +77,7 @@ public FinalResultEntry call() {
                     System.exit(1);
                 }
             }
-            if (1 - (resultEntry.getSecondScore() / resultEntry.getScore()) > ECL2.delta_c_t) {
+            if (1 - (resultEntry.getSecondScore() / resultEntry.getScore()) > delta_c_t) {
                 if (cal_evalue) {
                     float originalTolerance;
                     if (search_obj.ms1_tolerance_unit == 1) {

diff --git a/src/main/resources/parameter.def b/src/main/resources/parameter.def
@@ -1,4 +1,4 @@
-# 2.1.4-dev-201705271641
+# 2.1.4-dev-201705281102
 # The first line is the parameter file version. Do not change it.
 thread_num = 0
 debug = 0
@@ -70,9 +70,10 @@ n = 0
 c = 0
 
 # Advanced parameters
-single_chain_t = 0
+single_chain_t = 0.1
 cal_evalue = 1
 ms1_bin_size = 0.001
+delta_c_t = 0.00
 
 # for debug
 # put interested scan numbers below. One number each line