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