Add some advanced parameters.

fcyu · May 26, 2017 · e6b5baf · e6b5baf
1 parent d9fd9c9
commit e6b5baf
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Showing 2 changed files with 13 additions and 3 deletions.
diff --git a/src/main/java/proteomics/Index/BuildIndex.java b/src/main/java/proteomics/Index/BuildIndex.java
@@ -16,7 +16,6 @@
 public class BuildIndex {
 
     private static final Logger logger = LoggerFactory.getLogger(BuildIndex.class);
-    private static final float ms1_bin_size = 0.001f;
     private static final Pattern varModParamPattern = Pattern.compile("([0-9.-]+)\\s+([A-Znc]+)");
     private static final int globalVarModMaxNum = 5; // Do not change this value. Otherwise, change generateLocalIdxModMassMap accordingly.
     private static final float varModMassResolution = 0.01f;
@@ -32,6 +31,7 @@ public class BuildIndex {
     private Map<String, boolean[]> seq_term_map = new HashMap<>();
     private Set<String> for_check_duplicate = new HashSet<>();
     private Map<String, Set<String>> seqProMap;
+    private final float ms1_bin_size ;
 
     public BuildIndex(Map<String, String> parameter_map) {
         // initialize parameters
@@ -43,6 +43,12 @@ public BuildIndex(Map<String, String> parameter_map) {
         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"));
 
+        if (parameter_map.containsKey("ms1_bin_size")) {
+            ms1_bin_size = Float.valueOf(parameter_map.get("ms1_bin_size"));
+        } else {
+            ms1_bin_size = 0.001f;
+        }
+
         // Read fix modification
         fix_mod_map.put('G', Float.valueOf(parameter_map.get("G")));
         fix_mod_map.put('A', Float.valueOf(parameter_map.get("A")));

diff --git a/src/main/resources/parameter.def b/src/main/resources/parameter.def
@@ -9,7 +9,6 @@ min_precursor_mass = 1000
 max_precursor_mass = 12000
 min_chain_length = 5 # minimum length of a peptide chain
 max_chain_length = 50
-single_chain_t = 0
 
 # Spectrum
 min_ms1_charge = 3
@@ -66,5 +65,10 @@ O = 0
 n = 0
 c = 0
 
+# Advanced parameters
+single_chain_t = 0
+cal_evalue = 1
+ms1_bin_size = 0.001
+
 # for debug
-# put interested scan numbers below. One number each line
+# put interested scan numbers below. One number each line