From 840dfd440ea3c54cd3a4b3ab071d3aeb43f038a6 Mon Sep 17 00:00:00 2001 From: Fengchao Date: Mon, 29 May 2017 11:04:25 +0800 Subject: [PATCH] Add flanking_peaks as a parameter. --- pom.xml | 2 +- src/main/java/proteomics/ECL2.java | 10 +++++++--- src/main/java/proteomics/Search/SearchWrap.java | 4 ++-- src/main/java/proteomics/Spectrum/PreSpectra.java | 2 -- src/main/java/proteomics/Spectrum/PreSpectrum.java | 6 ++++-- src/main/resources/parameter.def | 3 ++- 6 files changed, 16 insertions(+), 11 deletions(-) diff --git a/pom.xml b/pom.xml index bf97bce..e478eeb 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ hk.ust.bioinformatics ECL2 - 2.1.4-dev-201705281102 + 2.1.4-dev-201705291100 jar ECL2 diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java index ca86d06..5009144 100644 --- a/src/main/java/proteomics/ECL2.java +++ b/src/main/java/proteomics/ECL2.java @@ -21,10 +21,9 @@ public class ECL2 { 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-201705281102"; + public static final String version = "2.1.4-dev-201705291100"; public static boolean debug; public static boolean dev; @@ -59,6 +58,11 @@ public static void main(String[] args) { 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")) { + flankingPeaks = false; + } + debug = parameter_map.get("debug").contentEquals("1"); dev = parameter_map.get("dev").contentEquals("1"); @@ -117,7 +121,7 @@ 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, delta_c_t))); + 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, flankingPeaks))); } // check progress every minute diff --git a/src/main/java/proteomics/Search/SearchWrap.java b/src/main/java/proteomics/Search/SearchWrap.java index f83151f..e9b1783 100644 --- a/src/main/java/proteomics/Search/SearchWrap.java +++ b/src/main/java/proteomics/Search/SearchWrap.java @@ -29,13 +29,13 @@ public class SearchWrap implements Callable { 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, 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, float delta_c_t, boolean flankingPeaks) { this.search_obj = search_obj; this.spectrumEntry = spectrumEntry; this.build_index_obj = build_index_obj; this.mass_tool_obj = mass_tool_obj; this.max_common_ion_charge = max_common_ion_charge; - preSpectrumObj = new PreSpectrum(mass_tool_obj); + preSpectrumObj = new PreSpectrum(mass_tool_obj, flankingPeaks); this.seqProMap = seqProMap; this.cal_evalue = cal_evalue; this.delta_c_t = delta_c_t; diff --git a/src/main/java/proteomics/Spectrum/PreSpectra.java b/src/main/java/proteomics/Spectrum/PreSpectra.java index 5ced01c..862307a 100644 --- a/src/main/java/proteomics/Spectrum/PreSpectra.java +++ b/src/main/java/proteomics/Spectrum/PreSpectra.java @@ -40,8 +40,6 @@ public PreSpectra(MzXMLFile spectra_parser, BuildIndex build_index_obj, Map peaks_map, float precursor_mass, int scanNum) { @@ -76,7 +78,7 @@ private SparseVector prepareXcorr(double[] pl_array) { for (int i = 1; i < pl_array.length; ++i) { double temp = pl_array[i] - tempArray[i]; - if (ECL2.flankingPeaks) { + if (flankingPeaks) { temp += (pl_array[i - 1] - tempArray[i - 1]) * 0.5; if (i + 1 < pl_array.length) { temp += (pl_array[i + 1] - tempArray[i + 1]) * 0.5; diff --git a/src/main/resources/parameter.def b/src/main/resources/parameter.def index ea93b17..2e47fa3 100644 --- a/src/main/resources/parameter.def +++ b/src/main/resources/parameter.def @@ -1,4 +1,4 @@ -# 2.1.4-dev-201705281102 +# 2.1.4-dev-201705291100 # The first line is the parameter file version. Do not change it. thread_num = 0 debug = 0 @@ -74,6 +74,7 @@ single_chain_t = 0.1 cal_evalue = 1 ms1_bin_size = 0.001 delta_c_t = 0.00 +flanking_peaks = 1 # for debug # put interested scan numbers below. One number each line \ No newline at end of file