From 4fb56465c5b8ebc436b062825244b4550480b8ff Mon Sep 17 00:00:00 2001 From: Fengchao Date: Tue, 23 May 2017 18:52:41 +0800 Subject: [PATCH] Add a "single_chain_t" parameter. --- src/main/java/proteomics/Search/Search.java | 8 ++++++-- src/main/resources/parameter.def | 1 + 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/src/main/java/proteomics/Search/Search.java b/src/main/java/proteomics/Search/Search.java index 3cc6bf5..b74f834 100644 --- a/src/main/java/proteomics/Search/Search.java +++ b/src/main/java/proteomics/Search/Search.java @@ -16,8 +16,6 @@ public class Search { private static final Logger logger = LoggerFactory.getLogger(Search.class); - public static final double single_chain_t = 0.1; - private final int max_common_ion_charge; public final float ms1_tolerance; public final int ms1_tolerance_unit; @@ -28,6 +26,7 @@ public class Search { private final BuildIndex build_index_obj; private int[] C13_correction_range; private Map bin_candidate_num_map; + final double single_chain_t; /////////////////////////////////////////public methods//////////////////////////////////////////////////////////// public Search(BuildIndex build_index_obj, Map parameter_map) { @@ -40,6 +39,11 @@ public Search(BuildIndex build_index_obj, Map parameter_map) { ms1_tolerance = Float.valueOf(parameter_map.get("ms1_tolerance")); bin_seq_map = build_index_obj.getMassBinSeqMap(); bin_candidate_num_map = build_index_obj.getBinCandidateNumMap(); + if (parameter_map.containsKey("single_chain_t")) { + single_chain_t = Float.valueOf(parameter_map.get("single_chain_t")); + } else { + single_chain_t = 0.1; + } String[] temp = parameter_map.get("C13_correction_range").split(","); C13_correction_range = new int[temp.length]; diff --git a/src/main/resources/parameter.def b/src/main/resources/parameter.def index 9764f28..d60bf1c 100644 --- a/src/main/resources/parameter.def +++ b/src/main/resources/parameter.def @@ -10,6 +10,7 @@ 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