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Commit a8788c8d authored by Olivier Langella's avatar Olivier Langella
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phosphopeptide ods output revision

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src/fr/inra/pappso/xtandempipeline/Utils.java
+ 22
− 0
View file @ a8788c8d
......@@ -59,6 +59,28 @@ public class Utils {
+ getPappsoGroupingId(k);
}
static public String getPappsoPhosphoPeptideMassId(Group group,
SubGroup sg, PeptideMass peptideMass) throws MSMSException {
if (peptideMass == null) {
String message = "peptideMass is null";
logger.error(message);
throw new MSMSException(message);
}
if (group == null) {
String message = "group is null";
logger.error(message);
throw new MSMSException(message);
}
if (sg == null) {
String message = "sg is null";
logger.error(message);
throw new MSMSException(message);
}
return "pep" + getPappsoGroupingId(group.getNumber())
+ getPappsoGroupingId(sg.getNumber())
+ getPappsoGroupingId(peptideMass.getNumber());
}
static public String getPappsoPeptideMassId(Group group,
PeptideMass peptideMass) throws MSMSException {
if (peptideMass == null) {
......
src/fr/inra/pappso/xtandempipeline/class_msms/Match.java
+ 12
− 0
View file @ a8788c8d
......@@ -13,6 +13,7 @@ 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;
......@@ -350,4 +351,15 @@ public class Match implements Comparable<Match>, GrpProtMatch {
public Protein getGrpProtein() {
return protein_match;
}
public ArrayList<Peptide> getValidPeptideInPhosphoIsland(
HashSampleScanSetProt hashPhospho) throws MSMSException {
ArrayList<Peptide> peps = new ArrayList<Peptide>();
for (HashSampleScan sampleScanPhospho : hashPhospho
.getHashSampleScanList()) {
peps.addAll(this
.getAllValidPeptideToHashSampleScan(sampleScanPhospho));
}
return (peps);
}
}
src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoPeptideOutput.java
+ 29
− 25
View file @ a8788c8d
......@@ -64,7 +64,7 @@ public class OdsPhosphoPeptideOutput {
throws MSMSException {
try {
odsTable = new OdsDocWriter(outputStream);
odsTable.writeSheet("peptides");
odsTable.writeSheet("phosphopeptides");
} catch (IOException e) {
String message = "IOException " + e.getMessage();
logger.error(message);
......@@ -87,7 +87,7 @@ public class OdsPhosphoPeptideOutput {
public OdsPhosphoPeptideOutput(OdsDocWriter odsTable) throws MSMSException {
try {
this.odsTable = odsTable;
odsTable.writeSheet("peptides");
odsTable.writeSheet("phosphopeptides");
} catch (XMLStreamException e) {
String message = "XMLStreamException " + e.getMessage();
logger.error(message);
......@@ -118,16 +118,17 @@ public class OdsPhosphoPeptideOutput {
odsTable.writeLine();
odsTable.writeCell("Group ID");
odsTable.writeCell("Peptide ID");
odsTable.writeCell("Sub-group ID");
odsTable.writeCell("Phosphopeptide ID");
odsTable.writeCell("Sequence");
odsTable.writeCell("Modifs");
odsTable.writeCell("Number of phosphorylations");
odsTable.writeCell("Number of phosphorylations (phosphosites)");
odsTable.writeCell("Best Position in sequence");
odsTable.writeCell("All positions");
odsTable.writeCell("Charges");
odsTable.writeCell("MH+ theo");
odsTable.writeCell("Number of subgroups");
odsTable.writeCell("Subgroup ids");
odsTable.writeCell("Number of proteins");
//odsTable.writeCell("Protein ids");
odsTable.writeCell("Number of spectra");
// odsTable.writeCell("Delta-ppm");
} catch (XMLStreamException e) {
......@@ -148,16 +149,16 @@ public class OdsPhosphoPeptideOutput {
this.writeHeaders(ident);
for (Group group : ident.getGrouping().getGroupList()) {
PeptideMassSet pepMassSet = new PeptideMassSet();
HashMap<PeptideMass, HashSet<Peptide>> hashPeptideMass2Peptides = new HashMap<PeptideMass, HashSet<Peptide>>();
int nbpeptide = 0;
for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
PeptideMassSet pepMassSet = new PeptideMassSet();
HashMap<PeptideMass, HashSet<Peptide>> hashPeptideMass2Peptides = new HashMap<PeptideMass, HashSet<Peptide>>();
int nbpeptide = 0;
for (HashSampleScanSetProt hashProt : sg
.getHashSampleScanSetProtList()) {
for (Peptide peptide : ((Match) hashProt
for (HashSampleScanSetProt hashPhospho : sg
.getHashSampleScanSetProtSet()) {
for (Peptide peptide : ((Match) hashPhospho
.getGrpProtMatch())
.get_peptide_order_inclus_redon()) {
.getValidPeptideInPhosphoIsland(hashPhospho)) {
// first pass to index each ScanSample and give it a
// PeptideMass
nbpeptide++;
......@@ -177,17 +178,17 @@ public class OdsPhosphoPeptideOutput {
peptideList.add(peptide);
}
}
}
logger.debug("nb peptide : " + nbpeptide);
logger.debug("nb peptide : " + nbpeptide);
logger.debug("pepMassSet size : " + pepMassSet.size());
logger.debug("pepMassSet size : " + pepMassSet.size());
logger.debug("pepMassSet numbering");
pepMassSet.numbering();
logger.debug("pepMassSet numbering");
pepMassSet.numbering();
for (PeptideMass pepMass : pepMassSet) {
this.writeOnePeptideMass(ident, group, pepMass,
hashPeptideMass2Peptides.get(pepMass));
for (PeptideMass pepMass : pepMassSet) {
this.writeOnePeptideMass(ident, group, sg, pepMass,
hashPeptideMass2Peptides.get(pepMass));
}
}
}
......@@ -208,7 +209,7 @@ public class OdsPhosphoPeptideOutput {
}
private void writeOnePeptideMass(Identification ident, Group group,
PeptideMass pepMass, HashSet<Peptide> peptideSet)
SubGroup sg, PeptideMass pepMass, HashSet<Peptide> peptideSet)
throws MSMSException {
try {
logger.debug("writeOnePeptideMass begin " + group + pepMass);
......@@ -226,8 +227,9 @@ public class OdsPhosphoPeptideOutput {
*/
// odsTable.writeCell("Group ID");
odsTable.writeCell(Utils.getPappsoGroupId(group));
odsTable.writeCell(Utils.getPappsoSubGroupId(group, sg));
// odsTable.writeCell("Peptide ID");
odsTable.writeCell(Utils.getPappsoPeptideMassId(group, pepMass));
odsTable.writeCell(Utils.getPappsoPhosphoPeptideMassId(group,sg, pepMass));
// odsTable.writeCell("Sequence");
odsTable.writeCell(pepMass.getSequenceLi());
// odsTable.writeCell("Modifs");
......@@ -267,16 +269,18 @@ public class OdsPhosphoPeptideOutput {
// odsTable.writeCell("MH+ theo");
odsTable.writeCell(bestPeptide.get_mhplus_theo());
SubGroupSet sgList = pepMass.getSubGroupSet();
//SubGroupSet sgList = pepMass.getSubGroupSet();
// odsTable.writeCell("Number of subgroups");
odsTable.writeCell(sgList.size());
odsTable.writeCell(sg.getHashSampleScanSetProtSet().size());
/*
TreeSet<String> sgIds = new TreeSet<String>();
for (SubGroup sg : sgList) {
sgIds.add(Utils.getPappsoSubGroupId(group, sg));
}
// odsTable.writeCell("Subgroup ids");
odsTable.writeCell(Utils.collectionToString(sgIds));
*/
// odsTable.writeCell("Number of spectra");
odsTable.writeCell(pepMass.getHashSampleScanSet().size());
......
src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoProteinOutput.java
+ 5
− 5
View file @ a8788c8d
......@@ -55,7 +55,7 @@ public class OdsPhosphoProteinOutput {
throws MSMSException {
try {
odsTable = new OdsDocWriter(outputStream);
odsTable.writeSheet("proteins");
odsTable.writeSheet("phosphoislands");
} catch (IOException e) {
String message = "IOException " + e.getMessage();
logger.error(message);
......@@ -78,7 +78,7 @@ public class OdsPhosphoProteinOutput {
public OdsPhosphoProteinOutput(OdsDocWriter odsTable) throws MSMSException {
try {
this.odsTable = odsTable;
odsTable.writeSheet("proteins");
odsTable.writeSheet("phosphoislands");
} catch (XMLStreamException e) {
String message = "XMLStreamException " + e.getMessage();
logger.error(message);
......@@ -108,14 +108,14 @@ public class OdsPhosphoProteinOutput {
odsTable.writeLine();
odsTable.writeCell("Group ID");
odsTable.writeCell("Sub-group ID");
odsTable.writeCell("PhosphoIsland ID");
odsTable.writeCell("Phosphosite ID");
odsTable.writeCell("Description");
odsTable.writeCell("MW");
odsTable.writeCell("Positions");
odsTable.writeCell("Phosphosites positions");
odsTable.writeCell("Spectra");
odsTable.writeCell("Uniques");
odsTable.writeCell("number of proteins in this sharing this phosphosite");
odsTable.writeCell("number of proteins sharing these phosphosites");
} catch (XMLStreamException e) {
String message = "XMLStreamException in writeHeaders() "
......
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