From 42f165d56ce74a4f2aabadf897bf5025b704034b Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Tue, 3 Dec 2013 16:41:18 +0100
Subject: [PATCH] fixed and understand the treatment of best phospho positions
et observed phospho positions
---
.../GroupingProtein/PeptideMass.java | 2 -
.../xtandempipeline/class_msms/Match.java | 2 +-
.../filter_print/swt_table_peptide.java | 4 +-
.../grouping/HashSampleScanSetPhospho.java | 101 +++++++++++++-----
.../grouping/interfaces/GrpProtMatch.java | 9 +-
.../SpreadSheets/OdsPhosphoPeptideOutput.java | 7 +-
.../SpreadSheets/OdsPhosphoSpectraOutput.java | 21 ++--
7 files changed, 98 insertions(+), 48 deletions(-)
diff --git a/src/fr/inra/pappso/xtandempipeline/class_msms/GroupingProtein/PeptideMass.java b/src/fr/inra/pappso/xtandempipeline/class_msms/GroupingProtein/PeptideMass.java
index 25d910d7d..fd484299a 100644
--- a/src/fr/inra/pappso/xtandempipeline/class_msms/GroupingProtein/PeptideMass.java
+++ b/src/fr/inra/pappso/xtandempipeline/class_msms/GroupingProtein/PeptideMass.java
@@ -24,11 +24,9 @@ import java.util.HashMap;
import org.apache.log4j.Logger;
-import fr.inra.pappso.xtandempipeline.Utils;
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
-import fr.inra.pappso.xtandempipeline.grouping.Group;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScan;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSet;
import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
diff --git a/src/fr/inra/pappso/xtandempipeline/class_msms/Match.java b/src/fr/inra/pappso/xtandempipeline/class_msms/Match.java
index 5943a52c3..558feb385 100644
--- a/src/fr/inra/pappso/xtandempipeline/class_msms/Match.java
+++ b/src/fr/inra/pappso/xtandempipeline/class_msms/Match.java
@@ -13,7 +13,6 @@ import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
import fr.inra.pappso.xtandempipeline.grouping.HashProtein;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScan;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
-import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
import fr.inra.pappso.xtandempipeline.grouping.interfaces.GrpPeptide;
import fr.inra.pappso.xtandempipeline.grouping.interfaces.GrpProtMatch;
@@ -352,6 +351,7 @@ public class Match implements Comparable<Match>, GrpProtMatch {
return protein_match;
}
+ @Override
public ArrayList<Peptide> getValidPeptideInPhosphoIsland(
HashSampleScanSetPhospho hashPhospho) throws MSMSException {
ArrayList<Peptide> peps = new ArrayList<Peptide>();
diff --git a/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_peptide.java b/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_peptide.java
index 8a7efa7e8..7d9eaf9fc 100644
--- a/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_peptide.java
+++ b/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_peptide.java
@@ -114,8 +114,8 @@ public class swt_table_peptide extends swt_table_base {
if (pep.getSequence().contains(this.filter_value))
filterPeptideSet.add(hash);
} else if (this.filtercolumn.equals("Sample")) {
- if (hash.getGrpMsSample().getSampleName().contains(
- this.filter_value))
+ if (hash.getGrpMsSample().getSampleName()
+ .contains(this.filter_value))
filterPeptideSet.add(hash);
} else if (this.filtercolumn.equals("Modifs")) {
if (pep.get_Modifs_formater().contains(this.filter_value))
diff --git a/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetPhospho.java b/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetPhospho.java
index e5feea0bc..c638df84b 100644
--- a/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetPhospho.java
+++ b/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetPhospho.java
@@ -1,11 +1,14 @@
package fr.inra.pappso.xtandempipeline.grouping;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.TreeSet;
import org.apache.log4j.Logger;
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+import fr.inra.pappso.xtandempipeline.class_msms.GroupingProtein.PeptideMass;
+import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
import fr.inra.pappso.xtandempipeline.grouping.interfaces.GrpPeptide;
import fr.inra.pappso.xtandempipeline.grouping.interfaces.GrpPhosphoModif;
import fr.inra.pappso.xtandempipeline.grouping.interfaces.GrpProtMatch;
@@ -50,55 +53,95 @@ public class HashSampleScanSetPhospho extends HashSampleScanSetProt {
super.clear();
}
-/*
- @Override
- public int compareTo(HashSampleScanSet o) {
- int i = o.size() - this.size();
- if (i != 0)
- return i;
- return (o.hashCode() - this.hashCode());
- }
-*/
- public TreeSet<Integer> getPhosphoPositions(){
- return(phosphoPositions);
+ /*
+ * @Override public int compareTo(HashSampleScanSet o) { int i = o.size() -
+ * this.size(); if (i != 0) return i; return (o.hashCode() -
+ * this.hashCode()); }
+ */
+ public TreeSet<Integer> getPhosphoPositions() {
+ return (phosphoPositions);
}
-
- public String getPhosphoPositionToPrint(){
+
+ public String getPhosphoPositionToPrint() {
String S = "";
- for(Integer value : this.phosphoPositions){
- S = S +" "+ value;
+ for (Integer value : this.phosphoPositions) {
+ S = S + " " + value;
}
S.replaceFirst(" ", "");
- return(S);
+ return (S);
}
-
- public boolean haveMultiPhosphoPeptide() throws MSMSException{
+
+ public boolean haveMultiPhosphoPeptide() throws MSMSException {
boolean multi = false;
- for(HashSampleScan hash: this){
- if(this.match.getBestPeptideToHashSampleScan(hash).getGrpPhosphoModifs().size()>1)
+ for (HashSampleScan hash : this) {
+ if (this.match.getBestPeptideToHashSampleScan(hash)
+ .getGrpPhosphoModifs().size() > 1)
multi = true;
}
- return(multi);
+ return (multi);
}
-
-
+
@Override
public HashKey4GroupsSet getHashKey4GroupsSet() throws Exception {
HashKey4GroupsSet hashPeptideSet = new HashKey4GroupsSet();
HashProtein hashProtein = match.getHashProtein();
-
+
hashPeptideSet.add(hashProtein);
return hashPeptideSet;
}
- public TreeSet<Integer> getAllPositionIncluderedon(HashSampleScan hash) throws MSMSException {
- TreeSet<Integer> posi = new TreeSet<Integer> ();
- for (GrpPeptide pepTemp : this.match.getGrpPeptidesSharingHashSampleScan(hash)) {
- for (GrpPhosphoModif mods : pepTemp.getGrpPhosphoModifs())
- posi.add(mods.getPosi_in_prot());
+ public TreeSet<Integer> getAllPositionIncluderedon(HashSampleScan hash)
+ throws MSMSException {
+ TreeSet<Integer> posi = new TreeSet<Integer>();
+
+ for (GrpPhosphoModif mods : getAllPhosphoPeptideModif(hash)) {
+ posi.add(mods.getPosi_in_prot());
}
+
return posi;
}
+
+ /**
+ * retrieve all Phospho Modifs concerning one Peptide
+ *
+ * @param peptide
+ * @return
+ * @throws MSMSException
+ */
+ public Collection<GrpPhosphoModif> getAllPhosphoPeptideModif(Peptide peptide)
+ throws MSMSException {
+ return getAllPhosphoPeptideModif(peptide.getHashSampleScan());
+ }
+
+ private Collection<GrpPhosphoModif> getAllPhosphoPeptideModif(
+ HashSampleScan hash) throws MSMSException {
+
+ ArrayList<GrpPhosphoModif> modifs = new ArrayList<GrpPhosphoModif>();
+ for (GrpPeptide pepTemp : this.match
+ .getGrpPeptidesSharingHashSampleScan(hash)) {
+ modifs.addAll(pepTemp.getGrpPhosphoModifs());
+ }
+ return modifs;
+ }
+
+ /**
+ * retrieve all Phospho Modifs concerning one PeptideMass
+ *
+ * @param peptideMass
+ * @return
+ * @throws MSMSException
+ */
+
+ public Collection<GrpPhosphoModif> getAllPhosphoModif(
+ PeptideMass peptideMass) throws MSMSException {
+
+ ArrayList<GrpPhosphoModif> modifs = new ArrayList<GrpPhosphoModif>();
+ for (HashSampleScan sampleScan : peptideMass.getHashSampleScanSet()) {
+ modifs.addAll(getAllPhosphoPeptideModif(sampleScan));
+ }
+ return modifs;
+ }
+
}
diff --git a/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpProtMatch.java b/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpProtMatch.java
index 0cb13ed40..7a2b3ca1a 100644
--- a/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpProtMatch.java
+++ b/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpProtMatch.java
@@ -1,20 +1,27 @@
package fr.inra.pappso.xtandempipeline.grouping.interfaces;
+import java.util.ArrayList;
import java.util.Collection;
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
import fr.inra.pappso.xtandempipeline.grouping.HashProtein;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScan;
+import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
public interface GrpProtMatch {
GrpProtein getGrpProtein();
Collection<GrpPeptide> getGrpPeptides() throws MSMSException;
- GrpPeptide getBestPeptideToHashSampleScan(HashSampleScan hash) throws MSMSException;
+ GrpPeptide getBestPeptideToHashSampleScan(HashSampleScan hash)
+ throws MSMSException;
HashProtein getHashProtein() throws MSMSException;
Collection<GrpPeptide> getGrpPeptidesSharingHashSampleScan(
HashSampleScan hash) throws MSMSException;
+
+ public ArrayList<Peptide> getValidPeptideInPhosphoIsland(
+ HashSampleScanSetPhospho hashPhospho) throws MSMSException;
}
diff --git a/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoPeptideOutput.java b/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoPeptideOutput.java
index 6953799bc..5bf956940 100644
--- a/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoPeptideOutput.java
+++ b/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoPeptideOutput.java
@@ -48,7 +48,6 @@ import fr.inra.pappso.xtandempipeline.grouping.Group;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
-import fr.inra.pappso.xtandempipeline.grouping.SubGroupSet;
import fr.inra.pappso.xtandempipeline.grouping.interfaces.GrpPhosphoModif;
public class OdsPhosphoPeptideOutput {
@@ -226,6 +225,8 @@ public class OdsPhosphoPeptideOutput {
* hashSampleScanSetPhospho = (HashSampleScanSetPhospho) sgList
* .get(0).getHashSampleScanSetProtList().get(0);
*/
+ HashSampleScanSetPhospho hashSampleScanSetPhospho = (HashSampleScanSetPhospho) sg
+ .getHashSampleScanSetProtList().get(0);
// odsTable.writeCell("Group ID");
odsTable.writeCell(Utils.getPappsoGroupId(group));
odsTable.writeCell(Utils.getPappsoSubGroupId(group, sg));
@@ -253,12 +254,16 @@ public class OdsPhosphoPeptideOutput {
for (Peptide peptide : peptideSet) {
phosphoAllModifs.addAll(peptide.getGrpPhosphoModifs());
}
+
+ phosphoModifs = hashSampleScanSetPhospho
+ .getAllPhosphoModif(pepMass);
obsPhosphoPos = new TreeSet<Integer>();
for (GrpPhosphoModif phosphoModif : phosphoModifs) {
Modifs modif = (Modifs) phosphoModif;
obsPhosphoPos.add(modif.get_posi());
}
// odsTable.writeCell("All positions");
+ // TreeSet<Integer> posi = phospho.getAllPositionIncluderedon(hash);
odsTable.writeCell(Utils.collectionToString(obsPhosphoPos));
TreeSet<Integer> obsCharges = new TreeSet<Integer>();
diff --git a/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoSpectraOutput.java b/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoSpectraOutput.java
index 345d3fbbf..c50b11a5d 100644
--- a/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoSpectraOutput.java
+++ b/src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoSpectraOutput.java
@@ -130,7 +130,7 @@ public class OdsPhosphoSpectraOutput {
odsTable.writeCell("Sequence (top)");
odsTable.writeCell("Modifs (top)");
odsTable.writeCell("Best position in peptide");
- odsTable.writeCell("All Position in sequence");
+ odsTable.writeCell("All observed positions in phosphopeptide");
odsTable.writeCell("Number of phosphoislands");
odsTable.writeCell("Phosphoislands Ids");
odsTable.writeCell("Best e-value");
@@ -206,8 +206,6 @@ public class OdsPhosphoSpectraOutput {
.getHashSampleScanSetProtSet()) {
HashSampleScanSetPhospho hashPhospho = (HashSampleScanSetPhospho) hashPprot;
- Protein prot = (Protein) hashPhospho.getGrpProtMatch()
- .getGrpProtein();
HashSet<PeptideMass> uniquePepMass = new HashSet<PeptideMass>();
for (Peptide peptide : ((Match) hashPhospho
@@ -224,8 +222,10 @@ public class OdsPhosphoSpectraOutput {
.getHashSampleScanSet()) {
if (uniqueHashSampleScan.add(scan)) {
+
this.writeOneHashSampleScan(ident,
- group, sg, prot, pepMass, scan,
+ group, sg, hashPhospho,
+ pepMass, scan,
hashPeptideMass2Peptides
.get(pepMass));
}
@@ -255,9 +255,9 @@ public class OdsPhosphoSpectraOutput {
}
private void writeOneHashSampleScan(Identification ident, Group group,
- SubGroup sg, Protein prot, PeptideMass pepMass,
- HashSampleScan scan, HashSet<Peptide> peptideSet)
- throws MSMSException {
+ SubGroup sg, HashSampleScanSetPhospho hashPhospho,
+ PeptideMass pepMass, HashSampleScan scan,
+ HashSet<Peptide> peptideSet) throws MSMSException {
try {
logger.debug("writeOneHashSampleScan begin " + group + pepMass);
HashSet<Peptide> peptideSetScan = new HashSet<Peptide>();
@@ -317,12 +317,9 @@ public class OdsPhosphoSpectraOutput {
// odsTable.writeCell(pepMass.getSequenceLi());
- HashSet<GrpPhosphoModif> phosphoAllModifs = new HashSet<GrpPhosphoModif>();
- for (Peptide peptide : peptideSet) {
- phosphoAllModifs.addAll(peptide.getGrpPhosphoModifs());
- }
obsPhosphoPos = new TreeSet<Integer>();
- for (GrpPhosphoModif phosphoModif : phosphoModifs) {
+ for (GrpPhosphoModif phosphoModif : hashPhospho
+ .getAllPhosphoModif(pepMass)) {
Modifs modif = (Modifs) phosphoModif;
obsPhosphoPos.add(modif.get_posi());
}
--
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