Improvement. Assume all advanced parameters are in the parameter.def.…

… Delete unnecessary trim().
fcyu · Jan 30, 2018 · 3209614 · 3209614
1 parent 8040f53
commit 3209614
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Showing 3 changed files with 6 additions and 20 deletions.
diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java
@@ -77,17 +77,14 @@ private ECL2(String parameter_path, String spectra_path) throws IOException, MzX
         }
 
         boolean cal_evalue = true;
-        if (parameter_map.containsKey("cal_evalue") && parameter_map.get("cal_evalue").trim().contentEquals("0")) {
+        if (parameter_map.get("cal_evalue").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"));
-        }
+        float 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")) {
+        if (parameter_map.get("flanking_peaks").contentEquals("0")) {
             flankingPeaks = false;
         }
 

diff --git a/src/main/java/proteomics/Index/BuildIndex.java b/src/main/java/proteomics/Index/BuildIndex.java
@@ -40,12 +40,7 @@ public BuildIndex(Map<String, String> parameter_map) throws IOException {
         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"));
-
-        if (parameter_map.containsKey("ms1_bin_size")) {
-            ms1_bin_size = Float.valueOf(parameter_map.get("ms1_bin_size"));
-        } else {
-            ms1_bin_size = 0.001f;
-        }
+        ms1_bin_size = Float.valueOf(parameter_map.get("ms1_bin_size"));
         inverseMs1BinSize = 1 / ms1_bin_size;
 
         // Read fix modification

diff --git a/src/main/java/proteomics/Search/Search.java b/src/main/java/proteomics/Search/Search.java
@@ -36,14 +36,8 @@ public Search(BuildIndex build_index_obj, Map<String, String> parameter_map) {
         ms1_tolerance_unit = Integer.valueOf(parameter_map.get("ms1_tolerance_unit"));
         ms1_tolerance = Float.valueOf(parameter_map.get("ms1_tolerance"));
         bin_seq_map = build_index_obj.getMassBinSeqMap();
-
-        if (parameter_map.containsKey("single_chain_t")) {
-            single_chain_t = Float.valueOf(parameter_map.get("single_chain_t"));
-        } else {
-            single_chain_t = 0.1f;
-        }
-
-        if (parameter_map.containsKey("cal_evalue") && parameter_map.get("cal_evalue").trim().contentEquals("0")) {
+        single_chain_t = Float.valueOf(parameter_map.get("single_chain_t"));
+        if (parameter_map.get("cal_evalue").contentEquals("0")) {
             cal_evalue = false;
         } else {
             cal_evalue = true;