From 20d7186be0e9bd915ab5c4b0e1c6f6d682c93cad Mon Sep 17 00:00:00 2001
From: Fengchao <fyuab@connect.ust.hk>
Date: Tue, 23 May 2017 18:50:03 +0800
Subject: [PATCH] Eliminate "min_peak_num" parameter.

---
 src/main/java/proteomics/Spectrum/PreSpectra.java | 6 ------
 src/main/resources/parameter.def                  | 1 -
 2 files changed, 7 deletions(-)

diff --git a/src/main/java/proteomics/Spectrum/PreSpectra.java b/src/main/java/proteomics/Spectrum/PreSpectra.java
index 78296d1..5ced01c 100644
--- a/src/main/java/proteomics/Spectrum/PreSpectra.java
+++ b/src/main/java/proteomics/Spectrum/PreSpectra.java
@@ -29,7 +29,6 @@ public PreSpectra(MzXMLFile spectra_parser, BuildIndex build_index_obj, Map<Stri
         int max_ms1_charge = Integer.valueOf(parameter_map.get("max_ms1_charge"));
         float min_precursor_mass =  Float.valueOf(parameter_map.get("min_precursor_mass"));
         float max_precursor_mass = Float.valueOf(parameter_map.get("max_precursor_mass"));
-        int min_peak_num = Integer.valueOf(parameter_map.get("min_peak_num"));
 
         //  In DEBUG mode, filter out unlisted scan num
         if (ECL2.debug) {
@@ -97,11 +96,6 @@ public void write(int b) throws IOException {}
                     }
                 }
 
-                if (raw_mz_intensity_map.size() < min_peak_num) {
-                    logger.debug("Scan {} doesn't contain enough peak number ({}). Skip.", spectrum.getId(), min_peak_num);
-                    continue;
-                }
-
                 int scan_num = Integer.valueOf(spectrum.getId());
 
                 Scan scan = spectra_parser.getScanByNum((long) scan_num);
diff --git a/src/main/resources/parameter.def b/src/main/resources/parameter.def
index 5fe4f5f..9764f28 100644
--- a/src/main/resources/parameter.def
+++ b/src/main/resources/parameter.def
@@ -15,7 +15,6 @@ max_chain_length = 50
 min_ms1_charge = 3
 max_ms1_charge = 7
 max_common_ion_charge = 3
-min_peak_num = 20
 C13_correction_range = 0
 
 # Tolerance