diff --git a/pom.xml b/pom.xml index 711c7f0..bf97bce 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ hk.ust.bioinformatics ECL2 - 2.1.4-dev-201705271641 + 2.1.4-dev-201705281102 jar ECL2 diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java index 2f86115..ca86d06 100644 --- a/src/main/java/proteomics/ECL2.java +++ b/src/main/java/proteomics/ECL2.java @@ -20,12 +20,11 @@ public class ECL2 { - public static final double delta_c_t = 0; public static final int score_point_t = 15000; public static final boolean flankingPeaks = true; private static final Logger logger = LoggerFactory.getLogger(ECL2.class); - public static final String version = "2.1.4-dev-201705271641"; + public static final String version = "2.1.4-dev-201705281102"; public static boolean debug; public static boolean dev; @@ -49,11 +48,17 @@ public static void main(String[] args) { Parameter parameter = new Parameter(parameter_path); Map parameter_map = parameter.returnParameterMap(); int max_common_ion_charge = Integer.valueOf(parameter_map.get("max_common_ion_charge")); + boolean cal_evalue = true; if (parameter_map.containsKey("cal_evalue") && parameter_map.get("cal_evalue").trim().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")); + } + debug = parameter_map.get("debug").contentEquals("1"); dev = parameter_map.get("dev").contentEquals("1"); @@ -112,7 +117,7 @@ public static void main(String[] args) { Search search_obj = new Search(build_index_obj, parameter_map); List> temp_result_list = new LinkedList<>(); for (int scanNum : scanNumArray) { - temp_result_list.add(thread_pool.submit(new SearchWrap(search_obj, num_spectrum_map.get(scanNum), build_index_obj, mass_tool_obj, max_common_ion_charge, build_index_obj.getSeqProMap(), cal_evalue))); + temp_result_list.add(thread_pool.submit(new SearchWrap(search_obj, num_spectrum_map.get(scanNum), build_index_obj, mass_tool_obj, max_common_ion_charge, build_index_obj.getSeqProMap(), cal_evalue, delta_c_t))); } // check progress every minute diff --git a/src/main/java/proteomics/Search/SearchWrap.java b/src/main/java/proteomics/Search/SearchWrap.java index a23e582..f83151f 100644 --- a/src/main/java/proteomics/Search/SearchWrap.java +++ b/src/main/java/proteomics/Search/SearchWrap.java @@ -27,8 +27,9 @@ public class SearchWrap implements Callable { private final PreSpectrum preSpectrumObj; private final Map> seqProMap; private final boolean cal_evalue; + private final float delta_c_t; - public SearchWrap(Search search_obj, SpectrumEntry spectrumEntry, BuildIndex build_index_obj, MassTool mass_tool_obj, int max_common_ion_charge, Map> seqProMap, boolean cal_evalue) { + public SearchWrap(Search search_obj, SpectrumEntry spectrumEntry, BuildIndex build_index_obj, MassTool mass_tool_obj, int max_common_ion_charge, Map> seqProMap, boolean cal_evalue, float delta_c_t) { this.search_obj = search_obj; this.spectrumEntry = spectrumEntry; this.build_index_obj = build_index_obj; @@ -37,6 +38,7 @@ public SearchWrap(Search search_obj, SpectrumEntry spectrumEntry, BuildIndex bui preSpectrumObj = new PreSpectrum(mass_tool_obj); this.seqProMap = seqProMap; this.cal_evalue = cal_evalue; + this.delta_c_t = delta_c_t; } @Override @@ -75,7 +77,7 @@ public FinalResultEntry call() { System.exit(1); } } - if (1 - (resultEntry.getSecondScore() / resultEntry.getScore()) > ECL2.delta_c_t) { + if (1 - (resultEntry.getSecondScore() / resultEntry.getScore()) > delta_c_t) { if (cal_evalue) { float originalTolerance; if (search_obj.ms1_tolerance_unit == 1) { diff --git a/src/main/resources/parameter.def b/src/main/resources/parameter.def index 9bc72f1..ea93b17 100644 --- a/src/main/resources/parameter.def +++ b/src/main/resources/parameter.def @@ -1,4 +1,4 @@ -# 2.1.4-dev-201705271641 +# 2.1.4-dev-201705281102 # The first line is the parameter file version. Do not change it. thread_num = 0 debug = 0 @@ -70,9 +70,10 @@ n = 0 c = 0 # Advanced parameters -single_chain_t = 0 +single_chain_t = 0.1 cal_evalue = 1 ms1_bin_size = 0.001 +delta_c_t = 0.00 # for debug # put interested scan numbers below. One number each line \ No newline at end of file