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Update from master #6

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Update from master #6

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44bd33d
Fixed support for idXML from Comet
julianu Jul 29, 2021
32efad7
incresae version number
julianu Jul 29, 2021
47a0210
Merge pull request #166 from julianu/master
julianu Jul 29, 2021
77c01f1
Merge branch 'master' into update
ypriverol Jul 29, 2021
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55 changes: 36 additions & 19 deletions src/main/java/de/mpc/pia/intermediate/compiler/parser/IdXMLFileParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -150,7 +150,7 @@ public static boolean getDataFromIdXMLFile(String name, String fileName,
LOGGER.error("This identification has no protein information, so PIA cannot use it.");
break;
}

// create the analysis software and add it to the compiler
AnalysisSoftware topp = new AnalysisSoftware();
topp.setId("topp");
Expand Down Expand Up @@ -339,6 +339,11 @@ private static int[] processPeptideIdentification(PeptideIdentification pepID, P
// nothing given in this file, create an ID using M/Z and RT
sourceID = pepID.getMZ() + "__" + pepID.getRT();
}

String searchEngine = idRun.getSearchEngine();
if ((searchEngine != null) && searchEngine.trim().isEmpty()) {
searchEngine = null;
}

// the distinct PSMs in this pepID
List<PeptideSpectrumMatch> hitsPSMs = new ArrayList<>();
Expand Down Expand Up @@ -381,7 +386,7 @@ private static int[] processPeptideIdentification(PeptideIdentification pepID, P
specNr++;

// set the main score
parsePeptideHitMainScore(psm, pepID, pepHit);
parsePeptideHitMainScore(psm, pepID, pepHit, searchEngine);


// add additional userParams Scores
Expand Down Expand Up @@ -452,8 +457,6 @@ private static String getSpectrumSourceIDFromUserParams(List<UserParamIdXML> use
private static String getSpectrumSourceIDFromSpectrumReference(String spectrumReference) {
String sourceID = null;

LOGGER.debug("spectrumReference: " + spectrumReference);

if (spectrumReference != null) {
Matcher matcher = MzIdentMLTools.patternScanInTitle.matcher(spectrumReference);
if (matcher.matches()) {
Expand All @@ -472,18 +475,27 @@ private static String getSpectrumSourceIDFromSpectrumReference(String spectrumRe
* @param pepHit
*/
private static void parsePeptideHitMainScore(PeptideSpectrumMatch psm, PeptideIdentification pepID,
PeptideHit pepHit) {
PeptideHit pepHit, String searchEngine) {
ScoreModel score;
ScoreModelEnum scoreModel = ScoreModelEnum.getModelByDescription(pepID.getScoreType() + "_openmsmainscore");

ScoreModelEnum scoreModel = ScoreModelEnum.UNKNOWN_SCORE;

if (searchEngine != null) {
scoreModel = ScoreModelEnum.getModelByDescription(searchEngine + ScoreModelEnum.OPENMS_MAINSCORE_PREFIX);
}

if (scoreModel.equals(ScoreModelEnum.UNKNOWN_SCORE)) {
// first way did not work, try this
scoreModel = ScoreModelEnum.getModelByDescription(pepID.getScoreType() + ScoreModelEnum.OPENMS_MAINSCORE_PREFIX);
}

if (!scoreModel.equals(ScoreModelEnum.UNKNOWN_SCORE)) {
score = new ScoreModel(
// looks weird, but so the decimals are correct
Double.parseDouble(String.valueOf(pepHit.getScore())),
scoreModel);
psm.addScore(score);
} else {
// try another way
// try as search engines main score way
scoreModel = ScoreModelEnum.getModelByDescription(pepID.getScoreType());

if (!scoreModel.equals(ScoreModelEnum.UNKNOWN_SCORE)) {
Expand All @@ -495,7 +507,7 @@ private static void parsePeptideHitMainScore(PeptideSpectrumMatch psm, PeptideId
} else {
score = new ScoreModel(
Double.parseDouble(String.valueOf(pepHit.getScore())),
pepID.getScoreType() + "_openmsmainscore",
pepID.getScoreType() + ScoreModelEnum.OPENMS_MAINSCORE_PREFIX,
pepID.getScoreType());
psm.addScore(score);
}
Expand Down Expand Up @@ -545,8 +557,12 @@ private static boolean addFloatValueUserParam(PeptideSpectrumMatch psm, UserPara

// try to add it as a score
ScoreModel score;
ScoreModelEnum scoreModel = ScoreModelEnum.getModelByDescription(
idRun.getSearchEngine() + '_' + userParam.getName());
ScoreModelEnum scoreModel = ScoreModelEnum.getModelByDescription(userParam.getName());

if (scoreModel.equals(ScoreModelEnum.UNKNOWN_SCORE)) {
scoreModel = ScoreModelEnum.getModelByDescription(
idRun.getSearchEngine() + '_' + userParam.getName());
}

// if the score was not found with this, try another way
if (scoreModel.equals(ScoreModelEnum.UNKNOWN_SCORE)
Expand All @@ -556,13 +572,14 @@ private static boolean addFloatValueUserParam(PeptideSpectrumMatch psm, UserPara
scoreModel = ScoreModelEnum.getModelByDescription(userParam.getName());
}

if (!scoreModel.equals(ScoreModelEnum.UNKNOWN_SCORE)) {
// a valid score was found now
score = new ScoreModel(
Double.parseDouble(userParam.getValue()),
scoreModel);
psm.addScore(score);
paramAdded = true;
if (!scoreModel.equals(ScoreModelEnum.UNKNOWN_SCORE) &&
(psm.getScore(scoreModel.getName()) == null)) {
// a valid score was found now and not yet in the scores
score = new ScoreModel(
Double.parseDouble(userParam.getValue()),
scoreModel);
psm.addScore(score);
paramAdded = true;
}

return paramAdded;
Expand All @@ -585,7 +602,7 @@ private static int connectProteins(List<Object> proteinRefs, PIACompiler compile

// filter for correct references and connect them
proteinRefs.stream()
.filter(ref -> ref instanceof ProteinHit)
.filter(ProteinHit.class::isInstance)
.forEach(protHit -> addedAccs.addAndGet(connectProtein((ProteinHit)protHit, compiler, peptide, fileID, searchDbID))
);

Expand Down
3 changes: 0 additions & 3 deletions src/main/java/de/mpc/pia/modeller/exporter/IdXMLExporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -463,9 +463,6 @@ private void writeIdentificationRun(XMLStreamWriter streamWriter, Long fileID,
streamWriter.writeEndElement(); // PeptideIdentification
}


LOGGER.debug("peptides: " + peptideIdentifications.size());

streamWriter.writeEndElement(); // IdentificationRun
}

Expand Down
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