diff --git a/src/fr/inra/pappso/xtandempipeline/Utils.java b/src/fr/inra/pappso/xtandempipeline/Utils.java
index 2f09b492030f329f27efc3fc950073b91cc26896..7820da745b0c61f922329cd8bdf6aa1ddc6342a0 100644
--- a/src/fr/inra/pappso/xtandempipeline/Utils.java
+++ b/src/fr/inra/pappso/xtandempipeline/Utils.java
@@ -26,9 +26,12 @@ import java.util.Collection;
import org.apache.log4j.Logger;
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+import fr.inra.pappso.xtandempipeline.class_msms.Protein;
import fr.inra.pappso.xtandempipeline.class_msms.GroupingProtein.PeptideMass;
import fr.inra.pappso.xtandempipeline.grouping.Group;
+import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
+import fr.inra.pappso.xtandempipeline.grouping.interfaces.GrpProtMatch;
public class Utils {
private static final Logger logger = Logger.getLogger(Utils.class);
@@ -132,7 +135,8 @@ public class Utils {
}
public static String getPappsoPhosphoIslandId(Group group, SubGroup sg,
- int k) throws MSMSException {
- return getPappsoGroupingNumber(group, sg, k);
+ HashSampleScanSetPhospho phospho) throws MSMSException {
+ Protein prot = (Protein) phospho.getGrpProtMatch().getGrpProtein();
+ return getPappsoGroupingNumber(group, sg, prot.getPhosphoId());
}
}
diff --git a/src/fr/inra/pappso/xtandempipeline/class_msms/Protein.java b/src/fr/inra/pappso/xtandempipeline/class_msms/Protein.java
index 45ac5ca00fd4a0bd8818367b8f39f5f4695e5f55..5c3236f4f46f3573b5cad8ee284b5e5881b30622 100644
--- a/src/fr/inra/pappso/xtandempipeline/class_msms/Protein.java
+++ b/src/fr/inra/pappso/xtandempipeline/class_msms/Protein.java
@@ -16,6 +16,8 @@ public class Protein implements GrpProtein {
private float mw;
+ private Integer phosphoId;
+
private int PAI_count;
private String description;
@@ -342,4 +344,34 @@ public class Protein implements GrpProtein {
return this.PAI_count;
}
+ /**
+ * get the protein identifier of this protein usefull in the PhosphoIsland
+ * context to get a unique PhosphoIsland ID
+ *
+ * @return int
+ * @throws MSMSException
+ */
+ public int getPhosphoId() throws MSMSException {
+ if (this.phosphoId == null) {
+ String error = "phosphoId is null";
+ logger.debug(error);
+ throw new MSMSException(error);
+ }
+ return this.phosphoId.intValue();
+ }
+
+ /**
+ * set the protein identifier of this protein usefull in the PhosphoIsland
+ * context to get a unique PhosphoIsland ID the developper MUST give an id
+ * number for each protein of PhosphoIslands
+ *
+ * @param i
+ */
+ public void setPhosphoId(int i) {
+ if (this.phosphoId == null) {
+ this.phosphoId = i;
+ }
+
+ }
+
}
diff --git a/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoProteinOutput.java b/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoProteinOutput.java
index 3b2278c3e8e72d8d68b0af6eb2f6d598ab1cbc2d..c7febcf92d9f5ee80c2e15356cbef7b388318777 100644
--- a/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoProteinOutput.java
+++ b/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoProteinOutput.java
@@ -36,6 +36,7 @@ import fr.inra.pappso.xtandempipeline.Utils;
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
import fr.inra.pappso.xtandempipeline.class_msms.Identification;
import fr.inra.pappso.xtandempipeline.class_msms.Match;
+import fr.inra.pappso.xtandempipeline.class_msms.Protein;
import fr.inra.pappso.xtandempipeline.grouping.Group;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
@@ -142,7 +143,11 @@ public class OdsPhosphoProteinOutput {
for (HashSampleScanSetProt hashProt : sg
.getHashSampleScanSetProtList()) {
k++;
- this.writeOnePhosphoProtein(hashProt, group, sg, k);
+ Protein prot = (Protein) hashProt.getGrpProtMatch()
+ .getGrpProtein();
+ prot.setPhosphoId(k);
+ this.writeOnePhosphoProtein(
+ (HashSampleScanSetPhospho) hashProt, group, sg);
}
}
}
@@ -162,14 +167,13 @@ public class OdsPhosphoProteinOutput {
}
}
- private void writeOnePhosphoProtein(HashSampleScanSetProt hashProt,
- Group group, SubGroup sg, int k) throws MSMSException {
+ private void writeOnePhosphoProtein(HashSampleScanSetPhospho phospho,
+ Group group, SubGroup sg) throws MSMSException {
try {
logger.debug("writeOnePhosphoProtein begin " + group + sg);
odsTable.writeLine();
- Match top = (Match) hashProt.getGrpProtMatch();
- HashSampleScanSetPhospho phospho = (HashSampleScanSetPhospho) hashProt;
+ Match top = (Match) phospho.getGrpProtMatch();
// odsTable.writeCell("Group ID");
odsTable.writeCell(Utils.getPappsoGroupId(group));
@@ -178,7 +182,8 @@ public class OdsPhosphoProteinOutput {
odsTable.writeCell(Utils.getPappsoSubGroupId(group, sg));
// odsTable.writeCell("Phosphosite ID");
- odsTable.writeCell(Utils.getPappsoPhosphoIslandId(group, sg, k));
+ odsTable.writeCell(Utils.getPappsoPhosphoIslandId(group, sg,
+ phospho));
// odsTable.writeCell("Description");
odsTable.writeCell(top.get_protein_match().get_description());
diff --git a/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoSpectraOutput.java b/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoSpectraOutput.java
index bb18a2878a426123e1588884f5a49f074f426a62..345d3fbbf21eb0607f6452054d3f18b020d59080 100644
--- a/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoSpectraOutput.java
+++ b/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoSpectraOutput.java
@@ -162,8 +162,13 @@ public class OdsPhosphoSpectraOutput {
HashMap<PeptideMass, HashSet<Peptide>> hashPeptideMass2Peptides = new HashMap<PeptideMass, HashSet<Peptide>>();
int nbpeptide = 0;
+ int k = 0;
for (HashSampleScanSetProt hashPhospho : sg
.getHashSampleScanSetProtSet()) {
+ k++;
+ Protein prot = (Protein) hashPhospho.getGrpProtMatch()
+ .getGrpProtein();
+ prot.setPhosphoId(k);
for (Peptide peptide : ((Match) hashPhospho
.getGrpProtMatch())
.getValidPeptideInPhosphoIsland((HashSampleScanSetPhospho) hashPhospho)) {
@@ -195,10 +200,11 @@ public class OdsPhosphoSpectraOutput {
logger.debug("pepMassSet numbering");
pepMassSet.numbering();
+ HashSet<HashSampleScan> uniqueHashSampleScan = new HashSet<HashSampleScan>();
+
for (HashSampleScanSetProt hashPprot : sg
.getHashSampleScanSetProtSet()) {
HashSampleScanSetPhospho hashPhospho = (HashSampleScanSetPhospho) hashPprot;
- HashSet<HashSampleScan> uniqueHashSampleScan = new HashSet<HashSampleScan>();
Protein prot = (Protein) hashPhospho.getGrpProtMatch()
.getGrpProtein();
@@ -326,12 +332,11 @@ public class OdsPhosphoSpectraOutput {
HashSet<HashSampleScanSetProt> phosphoIslandList = sg
.getHashSampleScanSetProtSet();
Collection<String> phosphoIslandsIds = new TreeSet<String>();
- int k = 0;
+
for (HashSampleScanSetProt hashProt : phosphoIslandList) {
HashSampleScanSetPhospho phosphoIsland = (HashSampleScanSetPhospho) hashProt;
- k++;
phosphoIslandsIds.add(Utils.getPappsoPhosphoIslandId(group, sg,
- k));
+ phosphoIsland));
}
// odsTable.writeCell("Number of subgroups");
odsTable.writeCell(phosphoIslandsIds.size());
diff --git a/src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java
index e7b3da84d9a913a9a27e6645b2ee38ca587e2e68..56234bf0bbffac4476bdbbdf7e44d523f8aef6e3 100644
--- a/src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java
+++ b/src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java
@@ -29,7 +29,7 @@ public class Mascot {
private MascotDatfile mascotDatfile;
- //private Peptide peptide;
+ // private Peptide peptide;
private Protein prot_;
@@ -102,18 +102,16 @@ public class Mascot {
protected void addPeptideToIdentification(PeptideHit pep, Query query,
boolean reversed) throws MSMSException {
-
+
// mapping proteinHit to protein && peptideHit to peptide
for (Object obj : pep.getProteinHits()) {
ProteinHit prot = (ProteinHit) obj;
-
-
- //peptide = PeptideStore.getInstance().newPeptide();
+
+ // peptide = PeptideStore.getInstance().newPeptide();
Peptide pep_ = PeptideStore.getInstance().newPeptide();
pep_.set_sample_id(
- identification_.getMsRunSet()
- .getInstance(sample_), sample_);
+ identification_.getMsRunSet().getInstance(sample_), sample_);
pep_.set_charge((int) round(
(pep.getPeptideMr() / query.getPrecursorMZ()), 0));
@@ -123,14 +121,14 @@ public class Mascot {
+ pep.getDeltaMass() + 1.007825));
pep_.set_mhplus_theo((float) (pep.getPeptideMr() + 1.007825));
pep_.set_sequence(pep.getSequence());
-
- if(XtandemPipelineSession.getInstance().getConfig().get_mascot_evalue_theoritical()){
- //Evalue theoritical
+ if (XtandemPipelineSession.getInstance().getConfig()
+ .get_mascot_evalue_theoritical()) {
+ // Evalue theoritical
pep_.set_evalue((float) pep.getExpectancy());
- }else{
- //Evalue experimental
- double eval = (pep.getIonsScore()-pep.getHomologyThreshold())/10;
+ } else {
+ // Evalue experimental
+ double eval = (pep.getIonsScore() - pep.getHomologyThreshold()) / 10;
eval = 0.05 / Math.pow(10, eval);
pep_.set_evalue((float) eval);
}
@@ -180,7 +178,7 @@ public class Mascot {
// modified posi in prot of the peptide
pep_.set_start(prot.getStart());
pep_.set_stop(prot.getStop());
-
+
// modifs add with position in prot!!!
Modification[] mods = pep.getModifications();
for (int i = 0; i < mods.length; i++) {
@@ -194,7 +192,7 @@ public class Mascot {
posi--;
}
if (mod != null) {
- pep_.set_Modifs(mod.getLocation(), posi+prot.getStart(),
+ pep_.set_Modifs(mod.getLocation(), posi + prot.getStart(),
(float) mod.getMass());
identification_.add_modifs_to_liste(new Modifs((float) mod
.getMass()));
diff --git a/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java
index d191efcf5bd605efe0f45bae06e0ec19b893402a..3a45992d002dfbcdc5b7aec6d170617a67dabe7b 100644
--- a/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java
+++ b/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java
@@ -172,8 +172,9 @@ public class XtandemPhospho extends org.xml.sax.helpers.DefaultHandler {
pep_ = peptide;
// valeur généric du scan
try {
- pep_.set_sample_id(identification_.getMsRunSet().getInstance(
- sample_), sample_);
+ pep_.set_sample_id(
+ identification_.getMsRunSet().getInstance(sample_),
+ sample_);
} catch (MSMSException e) {
throw new SAXException(e);
}
@@ -202,9 +203,9 @@ public class XtandemPhospho extends org.xml.sax.helpers.DefaultHandler {
this.peptide = PeptideStore.getInstance().newPeptide();
}
pep_ = peptide;
- pep_.set_Modifs(attrs.getValue("type"), Integer.parseInt(attrs
- .getValue("at")), Float.valueOf(attrs.getValue("modified"))
- .floatValue());
+ pep_.set_Modifs(attrs.getValue("type"),
+ Integer.parseInt(attrs.getValue("at")),
+ Float.valueOf(attrs.getValue("modified")).floatValue());
// modifs liste for isotopic analysis
identification_.add_modifs_to_liste(new Modifs(Float.valueOf(
attrs.getValue("modified")).floatValue()));
@@ -232,8 +233,9 @@ public class XtandemPhospho extends org.xml.sax.helpers.DefaultHandler {
match_ = (Match) identification_.get_match(prot_);
prot_ = match_.get_protein_match();
}
- prot_.set_evalue(identification_.getMsRunSet().getInstance(
- sample_), Float.valueOf(_evalue_prot).floatValue());
+ prot_.set_evalue(
+ identification_.getMsRunSet().getInstance(sample_),
+ Float.valueOf(_evalue_prot).floatValue());
}
if (spectre_number) {
String tmp = C_data.replaceAll(" ", "");
diff --git a/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java
index 56d42086a2e2df19477bb99779ecdcf03f31435b..a8b1390a46838fcac45d0d6c75e2af403c5dc935 100644
--- a/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java
+++ b/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java
@@ -168,8 +168,9 @@ public class xtandem extends org.xml.sax.helpers.DefaultHandler {
}
pep_ = this.peptide;
try {
- pep_.set_sample_id(identification_.getMsRunSet().getInstance(
- sample_), sample_);
+ pep_.set_sample_id(
+ identification_.getMsRunSet().getInstance(sample_),
+ sample_);
} catch (MSMSException e) {
throw new SAXException(e);
}
@@ -198,9 +199,9 @@ public class xtandem extends org.xml.sax.helpers.DefaultHandler {
this.peptide = PeptideStore.getInstance().newPeptide();
}
pep_ = peptide;
- pep_.set_Modifs(attrs.getValue("type"), Integer.parseInt(attrs
- .getValue("at")), Float.valueOf(attrs.getValue("modified"))
- .floatValue());
+ pep_.set_Modifs(attrs.getValue("type"),
+ Integer.parseInt(attrs.getValue("at")),
+ Float.valueOf(attrs.getValue("modified")).floatValue());
// modifs liste for isotopic analysis
identification_.add_modifs_to_liste(new Modifs(Float.valueOf(
attrs.getValue("modified")).floatValue()));
@@ -228,16 +229,20 @@ public class xtandem extends org.xml.sax.helpers.DefaultHandler {
match_ = (Match) identification_.get_match(prot_);
prot_ = match_.get_protein_match();
}
- prot_.set_evalue(identification_.getMsRunSet().getInstance(
- sample_), Float.valueOf(_evalue_prot).floatValue());
+ prot_.set_evalue(
+ identification_.getMsRunSet().getInstance(sample_),
+ Float.valueOf(_evalue_prot).floatValue());
}
if (spectre_number) {
String tmp = C_data.replaceAll(" .*", "");
String[] split = tmp.split("-");
if (split.length == 2) {
try {
- int scan = Integer.parseInt(split[0].replaceAll("ScanNumber:", ""));
- float rtime = Float.valueOf(split[1].replaceAll("RtInSec:", "")).floatValue();
+ int scan = Integer.parseInt(split[0].replaceAll(
+ "ScanNumber:", ""));
+ float rtime = Float.valueOf(
+ split[1].replaceAll("RtInSec:", ""))
+ .floatValue();
correction_scan.put("" + _scan, "" + scan);
correction_time.put("" + scan, "" + rtime);
logger.debug("" + scan + " = " + rtime);