From e6b5bafa12541bb57d17eb3fea401ceacceca424 Mon Sep 17 00:00:00 2001 From: Fengchao Date: Fri, 26 May 2017 14:19:24 +0800 Subject: [PATCH] Add some advanced parameters. --- src/main/java/proteomics/Index/BuildIndex.java | 8 +++++++- src/main/resources/parameter.def | 8 ++++++-- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/src/main/java/proteomics/Index/BuildIndex.java b/src/main/java/proteomics/Index/BuildIndex.java index 1337402..8407448 100644 --- 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 seq_term_map = new HashMap<>(); private Set for_check_duplicate = new HashSet<>(); private Map> seqProMap; + private final float ms1_bin_size ; public BuildIndex(Map parameter_map) { // initialize parameters @@ -43,6 +43,12 @@ public BuildIndex(Map 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 index 17e9b3d..c8cc9f1 100644 --- 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 \ No newline at end of file