diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRun.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRun.java
index bf927ea3a675867696994b8b2473bd6a6045454e..157df11fba1e6f5676a1ed96847480a891898500 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRun.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRun.java
@@ -46,11 +46,9 @@ public class MsRun implements Comparable<MsRun> {
if (this.sample.equals(msRunCompare.sample)) {
return true;
}
-
else {
logger.debug("msRun COLLISION on " + sample + " compared to "
+ msRunCompare.sample);
-
}
}
return false;
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java
index adede18de9f7f9d592f15e610864a78fffbdf0c0..7d30ca40565d07b719d24dd1c80982dc03d550bd 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java
@@ -15,7 +15,8 @@ public class HashPeptideSet extends HashKey4GroupsSet {
*/
private static final Logger logger = Logger.getLogger(HashPeptideSet.class);
- private HashMap<HashPeptide, HashPeptide> mapHashPeptide = new HashMap<HashPeptide, HashPeptide>(
+ // Uique String to be sur that wath is use for key!!!
+ private HashMap<String, HashPeptide> mapHashPeptide = new HashMap<String, HashPeptide>(
0);
public HashPeptideSet() {
@@ -24,6 +25,7 @@ public class HashPeptideSet extends HashKey4GroupsSet {
@Override
public void clear() {
+ mapHashPeptide = new HashMap<String, HashPeptide>(0);
super.clear();
}
@@ -33,15 +35,14 @@ public class HashPeptideSet extends HashKey4GroupsSet {
throw new Exception("sampleScan is null");
}
HashPeptide temp = new HashPeptide(sampleScan, sequence);
-
+ String tmpString = temp.getMsRun().getSampleName()+temp.getScan()+temp.getSequence();
if (this.add(temp)) {
// this HashPeptide is new
- this.mapHashPeptide.put(temp, temp);
+ this.mapHashPeptide.put(tmpString, temp);
return (temp);
} else {
// find the existing instance of the same peptide scan :
- return this.mapHashPeptide.get(temp);
+ return this.mapHashPeptide.get(tmpString);
}
}
-
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java
index 182d2e77b6b1bfb1f459d46bb82f1bf259399471..49618edc118795bea646f787cecd3ad9efa313fb 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java
@@ -16,7 +16,8 @@ public class HashProteinSet extends HashKey4GroupsSet {
*/
private static final Logger logger = Logger.getLogger(HashProteinSet.class);
- private HashMap<HashProtein, HashProtein> mapHashProtein = new HashMap<HashProtein, HashProtein>(
+ //Accession is String key for ensure unique protein!
+ private HashMap<String, HashProtein> mapHashProtein = new HashMap<String, HashProtein>(
0);
public HashProteinSet() {
@@ -27,16 +28,17 @@ public class HashProteinSet extends HashKey4GroupsSet {
HashProtein temp = new HashProtein(accession);
if (this.add(temp)) {
// this HashProtein is new
- this.mapHashProtein.put(temp, temp);
+ this.mapHashProtein.put(accession, temp);
return (temp);
} else {
// find the existing instance of the same protein :
- return this.mapHashProtein.get(temp);
+ return this.mapHashProtein.get(accession);
}
}
@Override
public void clear() {
+ mapHashProtein = new HashMap<String, HashProtein>(0);
super.clear();
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java
index 76bd0bb868c2d777d9ecaec132f4df227e4b78d7..62de0aa3362d090a4a8535d0e28a458e6715f335 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java
@@ -17,7 +17,9 @@ public class HashSampleScanSet extends HashSet<HashSampleScan> implements
private static final long serialVersionUID = -9055338154900110371L;
private static final Logger logger = Logger
.getLogger(HashSampleScanSet.class);
- private HashMap<HashSampleScan, HashSampleScan> mapHashSampleScan = new HashMap<HashSampleScan, HashSampleScan>(
+
+ //String to unique key for sample scan
+ private HashMap<String, HashSampleScan> mapHashSampleScan = new HashMap<String, HashSampleScan>(
0);
public HashSampleScanSet() {
@@ -32,14 +34,14 @@ public class HashSampleScanSet extends HashSet<HashSampleScan> implements
public HashSampleScan getInstance(int scan, MsRun msRun) {
HashSampleScan temp = new HashSampleScan(scan, msRun);
-
+ String tempString = msRun.getSampleName()+scan;
if (this.add(temp)) {
// this HashSampleScan is new
- this.mapHashSampleScan.put(temp, temp);
+ this.mapHashSampleScan.put(tempString, temp);
return (temp);
} else {
// find the existing instance of the same sample scan :
- return this.mapHashSampleScan.get(temp);
+ return this.mapHashSampleScan.get(tempString);
}
}
@@ -67,6 +69,7 @@ public class HashSampleScanSet extends HashSet<HashSampleScan> implements
@Override
public void clear() {
+ mapHashSampleScan = new HashMap<String, HashSampleScan>(0);
super.clear();
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQmlWriter.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQmlWriter.java
index 2d727c3c12096132f5aed6b9dd8ac10a72a23484..098ebe4d54ce836e07759385cd49eda22f10500e 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQmlWriter.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQmlWriter.java
@@ -84,7 +84,6 @@ public class MassChroQmlWriter {
this.writePeptides(ident);
this.writeIsotopes(isotopic_mods);
- this.writeIsotopes(isotopic_mods);
// ajout des methodes
this.writeAlignement();
@@ -110,20 +109,18 @@ public class MassChroQmlWriter {
// Element result = doc.createElement("quantification_results");
writer.writeStartElement("quantification_results");
// Element output = doc.createElement("quantification_result");
- writer.writeStartElement("quantification_result");
+ writer.writeEmptyElement("quantification_result");
writer.writeAttribute("output_file", "XIC_result");
writer.writeAttribute("format", "tsv");
- writer.writeEndElement();// quantification_result
writer.writeEndElement();// quantification_results
// Element trace = doc.createElement("quantification_traces");
writer.writeStartElement("quantification_traces");
// Element peptides_traces = doc.createElement("peptide_traces");
- writer.writeStartElement("peptide_traces");
+ writer.writeEmptyElement("peptide_traces");
writer.writeAttribute("peptide_ids", "pep0 pep1");
writer.writeAttribute("output_dir", "peplist_xics_traces/");
writer.writeAttribute("format", "tsv");
- writer.writeEndElement();// peptide_traces
writer.writeEndElement();// quantification_traces
// Element quantify = doc.createElement("quantify");
@@ -133,7 +130,7 @@ public class MassChroQmlWriter {
writer.writeAttribute("quantification_method_id", "quant1");
// Element peptides_in_peptide_list = doc
// .createElement("peptides_in_peptide_list");
- writer.writeStartElement("peptides_in_peptide_list");
+ writer.writeEmptyElement("peptides_in_peptide_list");
writer.writeAttribute("mode", "real_or_mean");
// ajout des labels isotopics dans la methode
@@ -144,7 +141,6 @@ public class MassChroQmlWriter {
}
writer.writeAttribute("isotope_label_refs", label.trim());
}
- writer.writeEndElement();// peptides_in_peptide_list
writer.writeEndElement();// quantify
writer.writeEndElement();// quantification
@@ -173,11 +169,10 @@ public class MassChroQmlWriter {
// selection
// Element ppm_range = doc.createElement("ppm_range");
- writer.writeStartElement("ppm_range");
+ writer.writeEmptyElement("ppm_range");
writer.writeAttribute("min", "10");
writer.writeAttribute("max", "10");
writer.writeComment("For XIC extraction on Da use: mz_range");
- writer.writeEndElement();// ppm_range
writer.writeEndElement();// xic_extraction
@@ -186,15 +181,13 @@ public class MassChroQmlWriter {
writer.writeStartElement("xic_filters");
// Element anti_spike = doc.createElement("anti_spike");
- writer.writeStartElement("anti_spike");
+ writer.writeEmptyElement("anti_spike");
writer.writeAttribute("half", "5");
- writer.writeEndElement();// anti_spike
// Element background = doc.createElement("background");
- writer.writeStartElement("background");
+ writer.writeEmptyElement("background");
writer.writeAttribute("half_mediane", "5");
writer.writeAttribute("half_min_max", "20");
- writer.writeEndElement();// background
writer.writeEndElement();// xic_filters
@@ -233,7 +226,8 @@ public class MassChroQmlWriter {
writer.writeEndElement();// detection_zivy
writer.writeEndElement();// peak_detection
-
+
+ writer.writeEndElement();// quantification_method
writer.writeEndElement();// quantification_methods
} catch (Exception e) {
logger.error(e.getMessage());
@@ -283,11 +277,10 @@ public class MassChroQmlWriter {
// groupe d'alignement
// Element align = doc.createElement("align");
- writer.writeStartElement("align");
+ writer.writeEmptyElement("align");
writer.writeAttribute("group_id", this.groupe_id);
writer.writeAttribute("method_id", "ms2_1");
writer.writeAttribute("reference_data_id", "samp0");
- writer.writeEndElement();// align
writer.writeEndElement();// alignments
} catch (Exception e) {
@@ -308,14 +301,13 @@ public class MassChroQmlWriter {
// balise rawdata
// Element data_file = doc.createElement("data_file");
- writer.writeStartElement("data_file");
+ writer.writeEmptyElement("data_file");
// data_file.setAttribute("id", id_samp);
writer.writeAttribute("id", id_samp);
- writer.writeAttribute("type", "profile");
writer.writeAttribute("format", "mzxml");
writer.writeAttribute("path", "" + sample.getSampleName()
+ ".mzXML");
- writer.writeEndElement();
+ writer.writeAttribute("type", "profile");
}
writer.writeEndElement();
@@ -333,7 +325,7 @@ public class MassChroQmlWriter {
// //balise groups
// Element group = doc.createElement("group");
- writer.writeStartElement("group");
+ writer.writeEmptyElement("group");
writer.writeAttribute("id", this.groupe_id);
String raw_list = "";
for (MsRun sample : ident.get_samples().getMsRunList()) {
@@ -363,10 +355,9 @@ public class MassChroQmlWriter {
String prot_id = this.getSubGroupGroupNumber(group, sg);
// Element protein = doc.createElement("protein");
- writer.writeStartElement("protein");
+ writer.writeEmptyElement("protein");
writer.writeAttribute("id", prot_id);
writer.writeAttribute("desc", top.get_description());
- writer.writeEndElement();
}
}
@@ -390,15 +381,17 @@ public class MassChroQmlWriter {
try {
writer.writeStartElement("peptide_list");
Hashtable<String, HashSet<String>> seqMod2protIds;
- Hashtable<String, String> seqMod2xmlPeptideId;
+ Hashtable<String, String> xmlPeptideId2seqMod;
Hashtable<String, ArrayList<Peptide>> seqMod2PeptideList;
+ ArrayList<String> peptideId;
int i = 0;
for (Group group : ident.getGrouping().getGroupList()) {
seqMod2protIds = new Hashtable<String, HashSet<String>>();
- seqMod2xmlPeptideId = new Hashtable<String, String>();
+ xmlPeptideId2seqMod = new Hashtable<String, String>();
seqMod2PeptideList = new Hashtable<String, ArrayList<Peptide>>();
+ peptideId = new ArrayList<String>();
for (HashSampleScan hash : group.getHashSampleScanSet()
.getHashSampleScanList()) {
@@ -412,15 +405,16 @@ public class MassChroQmlWriter {
String seqMod = pep.get_LI_sequenceModifsWithoutMs3();
if (seqMod2protIds.containsKey(seqMod)) {
} else {
- seqMod2xmlPeptideId.put(seqMod, "pep" + i++);
+ //Add new peptide id
+ String pepid = "pep" + i++;
+ xmlPeptideId2seqMod.put(pepid,seqMod);
+ peptideId.add(pepid);
/*
* <peptide id="pep0" mh="1463.626" mods="114.08"
* prot_ids="P1.1" seq="TCVADESHAGCEK">
*/
// table temporaire pour prot_id
HashSet<String> temp = new HashSet<String>();
- // Hashtable<String, String> temp = new
- // Hashtable<String, String>();
seqMod2protIds.put(seqMod, temp);
seqMod2PeptideList
@@ -434,17 +428,19 @@ public class MassChroQmlWriter {
temp.add(this.getSubGroupGroupNumber(group, sgTemp));
}
}// end loop on each scan for one group
-
- for (String seqMod : seqMod2xmlPeptideId.keySet()) {
+
+ //iterated current pepid to write buffer peptide element
+ for (String pepid : peptideId) {
+ String seqMod = xmlPeptideId2seqMod.get(pepid);
ArrayList<Peptide> peptideList = seqMod2PeptideList
.get(seqMod);
writer.writeStartElement("peptide");
- writer.writeAttribute("id", seqMod2xmlPeptideId.get(seqMod));
+ writer.writeAttribute("id", pepid);
Peptide peptide = peptideList.get(0);
// this.seq_to_element.put(seqMod, peptide);
- writer.writeAttribute("seq", peptide.get_sequence());
writer.writeAttribute("mh",
"" + peptide.get_mh_theo_without_isotope(true));
+ writer.writeAttribute("seq", peptide.get_sequence());
writer.writeAttribute("mods",
"" + peptide.get_Modifs_formater_without_isotope());
@@ -458,17 +454,16 @@ public class MassChroQmlWriter {
for (Peptide peptideScan : peptideList) {
// Element observed = doc.createElement("observed_in");
- writer.writeStartElement("observed_in");
+ writer.writeEmptyElement("observed_in");
// eda choisir mode export
// observed.setAttribute("rt", "" +
// peps[j].get_RT_in_sec());
- writer.writeAttribute("scan",
- "" + peptideScan.get_scan());
writer.writeAttribute("data",
this.sample2xmlId.get(peptideScan.getMsRun()));
+ writer.writeAttribute("scan",
+ "" + peptideScan.get_scan());
writer.writeAttribute("z",
"" + peptideScan.get_charge());
- writer.writeEndElement();
}
writer.writeEndElement();
@@ -502,11 +497,10 @@ public class MassChroQmlWriter {
writer.writeStartElement("isotope_label");
writer.writeAttribute("id", "iso" + (i + 1));
// Element mod = doc.createElement("mod");
- writer.writeStartElement("mod");
+ writer.writeEmptyElement("mod");
writer.writeAttribute("value", "" + mds[i].get_modvalue());
writer.writeAttribute("at", "Nter,Cter,A,K,L...");
- // isotope_label.appendChild(mod);
- writer.writeEndElement();
+
// isotopes.appendChild(isotope_label);
writer.writeEndElement();
}