Examples of com.compomics.util.pride.CvTerm

com.compomics.util.pride.CvTerm

        tabCounter++;


        // the search type
        br.write(getCurrentTabSpace() + "<SearchType>" + System.getProperty("line.separator"));
        tabCounter++;
        writeCvTerm(new CvTerm("PSI-MS", "MS:1001083", "ms-ms search", null));
        tabCounter--;
        br.write(getCurrentTabSpace() + "</SearchType>" + System.getProperty("line.separator"));


        // the search parameters
        br.write(getCurrentTabSpace() + "<AdditionalSearchParams>" + System.getProperty("line.separator"));
        tabCounter++;
        writeCvTerm(new CvTerm("PSI-MS", "MS:1001211", "parent mass type mono", null));
        writeCvTerm(new CvTerm("PSI-MS", "MS:1001256", "fragment mass type mono", null));
        if (mzidVersion1_2) {
            writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX", "peptide-level scoring performed", null)); // @TODO: add correct cv term!
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002497", "Group PSMs by distinct peptide sequence with taking modifications into account", null));
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002489", "Modification localization scoring performed", null));
            if (ptmScoringPreferences.isProbabilitsticScoreCalculation()) {
                writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX", ptmScoringPreferences.getSelectedProbabilisticScore().getName(), null)); // @TODO: add correct cv term!
            }
            writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX", "D-score", null)); // @TODO: add correct cv term!
        }


        // @TODO: list all search parameters from the search engines used?
        tabCounter--;
        br.write(getCurrentTabSpace() + "</AdditionalSearchParams>" + System.getProperty("line.separator"));


        // the modifications
        br.write(getCurrentTabSpace() + "<ModificationParams>" + System.getProperty("line.separator"));
        tabCounter++;


        // iterate and add the ptms
        for (String ptm : searchParameters.getModificationProfile().getAllModifications()) {


            PTM currentPtm = ptmFactory.getPTM(ptm);


            String aminoAcidsAtTarget = "";
            if (currentPtm.getType() == PTM.MODN
                    || currentPtm.getType() == PTM.MODNP
                    || currentPtm.getType() == PTM.MODC
                    || currentPtm.getType() == PTM.MODCP) {
                aminoAcidsAtTarget = ".";
            } else {
                for (Character aa : currentPtm.getPattern().getAminoAcidsAtTarget()) {
                    aminoAcidsAtTarget += aa;
                }
            }


            br.write(getCurrentTabSpace() + "<SearchModification residues=\"" + aminoAcidsAtTarget + "\" massDelta=\"" + currentPtm.getMass()
                    + "\" fixedMod= \"" + searchParameters.getModificationProfile().getFixedModifications().contains(ptm) + "\" >" + System.getProperty("line.separator"));
            tabCounter++;


            CvTerm cvTerm = ptmToPrideMap.getCVTerm(ptm);
            if (cvTerm != null) {
                writeCvTerm(cvTerm);
            } else {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1001460", "unknown modification", null));
            }


            // add modification specificity
            if (currentPtm.getType() == PTM.MODN
                    || currentPtm.getType() == PTM.MODNAA) {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1002057", "modification specificity protein N-term", null));
            } else if (currentPtm.getType() == PTM.MODNP
                    || currentPtm.getType() == PTM.MODNPAA) {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1001189", "modification specificity peptide N-term", null));
            } else if (currentPtm.getType() == PTM.MODC
                    || currentPtm.getType() == PTM.MODCAA) {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1002058", "modification specificity protein C-term", null));
            } else if (currentPtm.getType() == PTM.MODCP
                    || currentPtm.getType() == PTM.MODCPAA) {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1001190", "modification specificity peptide C-term", null));
            }


            tabCounter--;
            br.write(getCurrentTabSpace() + "</SearchModification>" + System.getProperty("line.separator"));
        }


        tabCounter--;
        br.write(getCurrentTabSpace() + "</ModificationParams>" + System.getProperty("line.separator"));


        // enzyme
        br.write(getCurrentTabSpace() + "<Enzymes independent=\"false\">" + System.getProperty("line.separator"));
        // note: if multiple enzymes are specified, independent is set to true if cleavage with different enzymes is performed independently
        tabCounter++;


        Enzyme enzyme = searchParameters.getEnzyme();
        br.write(getCurrentTabSpace() + "<Enzyme "
                + "missedCleavages=\"" + searchParameters.getnMissedCleavages() + "\" "
                + "semiSpecific=\"" + enzyme.isSemiSpecific() + "\" "
                //+ "cTermGain=\"OH\" " // Element formula gained at CTerm
                //+ "nTermGain=\"H\" " // Element formula gained at NTerm
                + "id=\"Enz1\" "
                + "name=\"" + enzyme.getName() + "\">"
                + System.getProperty("line.separator"));
        tabCounter++;


        br.write(getCurrentTabSpace() + "<EnzymeName>" + System.getProperty("line.separator"));
        tabCounter++;
        CvTerm enzymeCvTerm = EnzymeFactory.getEnzymeCvTerm(enzyme);
        if (enzymeCvTerm != null) {
            writeCvTerm(enzymeCvTerm);
        } else {
            writeUserParam(enzyme.getName());
        }
        tabCounter--;
        br.write(getCurrentTabSpace() + "</EnzymeName>" + System.getProperty("line.separator"));


        tabCounter--;
        br.write(getCurrentTabSpace() + "</Enzyme>" + System.getProperty("line.separator"));


        tabCounter--;
        br.write(getCurrentTabSpace() + "</Enzymes>" + System.getProperty("line.separator"));


        // fragment tolerance
        br.write(getCurrentTabSpace() + "<FragmentTolerance>" + System.getProperty("line.separator"));
        tabCounter++;


        br.write(getCurrentTabSpace() + "<cvParam "
                + "accession=\"MS:1001412\" "
                + "cvRef=\"PSI-MS\" "
                + "unitCvRef=\"UO\" "
                + "unitName=\"dalton\" "
                + "unitAccession=\"UO:0000221\" "
                + "value=\"" + searchParameters.getFragmentIonAccuracy() + "\" "
                + "name=\"search tolerance plus value\" />"
                + System.getProperty("line.separator"));
        br.write(getCurrentTabSpace() + "<cvParam "
                + "accession=\"MS:1001413\" "
                + "cvRef=\"PSI-MS\" "
                + "unitCvRef=\"UO\" "
                + "unitName=\"dalton\" "
                + "unitAccession=\"UO:0000221\" "
                + "value=\"" + searchParameters.getFragmentIonAccuracy() + "\" "
                + "name=\"search tolerance minus value\" />"
                + System.getProperty("line.separator"));
        tabCounter--;
        br.write(getCurrentTabSpace() + "</FragmentTolerance>" + System.getProperty("line.separator"));


        // precursor tolerance
        br.write(getCurrentTabSpace() + "<ParentTolerance>" + System.getProperty("line.separator"));
        tabCounter++;


        if (searchParameters.isPrecursorAccuracyTypePpm()) {
            br.write(getCurrentTabSpace() + "<cvParam "
                    + "accession=\"MS:1001412\" "
                    + "cvRef=\"PSI-MS\" "
                    + "unitCvRef=\"UO\" "
                    + "unitName=\"parts per million\" "
                    + "unitAccession=\"UO:0000169\" "
                    + "value=\"" + searchParameters.getPrecursorAccuracy() + "\" "
                    + "name=\"search tolerance plus value\" />"
                    + System.getProperty("line.separator"));
            br.write(getCurrentTabSpace() + "<cvParam "
                    + "accession=\"MS:1001413\" "
                    + "cvRef=\"PSI-MS\" "
                    + "unitCvRef=\"UO\" "
                    + "unitName=\"parts per million\" "
                    + "unitAccession=\"UO:0000169\" "
                    + "value=\"" + searchParameters.getPrecursorAccuracy() + "\" "
                    + "name=\"search tolerance minus value\" />"
                    + System.getProperty("line.separator"));
        } else {
            br.write(getCurrentTabSpace() + "<cvParam "
                    + "accession=\"MS:1001412\" "
                    + "cvRef=\"PSI-MS\" "
                    + "unitCvRef=\"UO\" "
                    + "unitName=\"dalton\" "
                    + "unitAccession=\"UO:0000221\" "
                    + "value=\"" + searchParameters.getPrecursorAccuracy() + "\" "
                    + "name=\"search tolerance plus value\" />"
                    + System.getProperty("line.separator"));
            br.write(getCurrentTabSpace() + "<cvParam "
                    + "accession=\"MS:1001413\" "
                    + "cvRef=\"PSI-MS\" "
                    + "unitCvRef=\"UO\" "
                    + "unitName=\"dalton\" "
                    + "unitAccession=\"UO:0000221\" "
                    + "value=\"" + searchParameters.getPrecursorAccuracy() + "\" "
                    + "name=\"search tolerance minus value\" />"
                    + System.getProperty("line.separator"));
        }


        tabCounter--;
        br.write(getCurrentTabSpace() + "</ParentTolerance>" + System.getProperty("line.separator"));


        // thresholds
        br.write(getCurrentTabSpace() + "<Threshold>" + System.getProperty("line.separator"));
        tabCounter++;


        boolean targetDecoy = sequenceFactory.concatenatedTargetDecoy();


        if (!targetDecoy) {
            writeCvTerm(new CvTerm("PSI-MS", "MS:1001494", "no threshold", null));
        } else {


            // Initial global thresholds
            writeCvTerm(new CvTerm("PSI-MS", "MS:1001364", "distinct peptide-level global FDR", Double.toString(Util.roundDouble(processingPreferences.getPeptideFDR(), CONFIDENCE_DECIMALS))));
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", "PSM-level global FDR", Double.toString(Util.roundDouble(processingPreferences.getPsmFDR(), CONFIDENCE_DECIMALS))));
            if (ptmScoringPreferences.isProbabilitsticScoreCalculation()) {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", ptmScoringPreferences.getSelectedProbabilisticScore().getName() + " threshold", ptmScoringPreferences.getProbabilisticScoreThreshold() + ""));
            }
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", "D-score threshold", "95")); //@TODO: avoid this hard coded value


//            // peptideshaker maps
//            PSMaps psMaps = new PSMaps();
//            psMaps = (PSMaps) identification.getUrParam(psMaps);
//
//            // peptide level threshold
//            PeptideSpecificMap peptideSpecificMap = psMaps.getPeptideSpecificMap();
//            ArrayList<String> peptideGroupsKeys = peptideSpecificMap.getKeys();
//
//            for (String key : peptideGroupsKeys) { // @TODO: find a way of annotating all thresholds..?
//                TargetDecoyMap targetDecoyMap = peptideSpecificMap.getTargetDecoyMap(key);
//                TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
//                double threshold = targetDecoyResults.getUserInput() / 100;
//                int thresholdType = targetDecoyResults.getInputType();
//                if (peptideGroupsKeys.size() > 1) {
//                    String peptideClass = PeptideSpecificMap.getKeyName(searchParameters.getModificationProfile(), key);
//                    // @TODO: somehow indicate the class of peptide thresholded?
//                }
//                if (thresholdType == 0) {
//                    writeCvTerm(new CvTerm("PSI-MS", "MS:1002463", "distinct peptide-level global confidence", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // confidence
//                } else if (targetDecoyResults.getInputType() == 1) {
//                    writeCvTerm(new CvTerm("PSI-MS", "MS:1001364", "distinct peptide-level global FDR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FDR
//                } else if (targetDecoyResults.getInputType() == 2) {
//                    writeCvTerm(new CvTerm("PSI-MS", "MS:1002462", "distinct peptide-level global FNR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FNR
//                }
//            }
//
//            // psm level threshold
//            ArrayList<Integer> chargesWithFileSpecificity = new ArrayList<Integer>();
//            PsmSpecificMap psmSpecificMap = psMaps.getPsmSpecificMap();
//
//            for (Integer charge : psmSpecificMap.getPossibleCharges()) {
//                for (String file : psmSpecificMap.getFilesAtCharge(charge)) {
//                    if (!psmSpecificMap.isFileGrouped(charge, file)) { // @TODO: find a way of annotating all thresholds..?
//                        chargesWithFileSpecificity.add(charge);
//                        TargetDecoyMap targetDecoyMap = psMaps.getPsmSpecificMap().getTargetDecoyMap(charge, file);
//                        TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
//                        double threshold = targetDecoyResults.getUserInput() / 100;
//                        int thresholdType = targetDecoyResults.getInputType();
//                        String psmClass = "Charge " + charge + " of file " + file; // @TODO: annotate class?
//                        if (thresholdType == 0) {
//                            writeCvTerm(new CvTerm("PSI-MS", "MS:1002465", "PSM-level global confidence", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // confidence
//                        } else if (targetDecoyResults.getInputType() == 1) {
//                            writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", "PSM-level global FDR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FDR
//                        } else if (targetDecoyResults.getInputType() == 2) {
//                            writeCvTerm(new CvTerm("PSI-MS", "MS:1002464", "PSM-level global FNR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FNR
//                        }
//                    }
//                }
//            }
            //@TODO: set the PSM group label
//            for (int charge : psmSpecificMap.getChargesFromGroupedFiles()) {
//                int correctedCharge = psmSpecificMap.getCorrectedCharge(charge);
//                if (correctedCharge == charge) {
//                    TargetDecoyMap targetDecoyMap = pSMaps.getPsmSpecificMap().getTargetDecoyMap(charge, null);
//                    TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
//                    double threshold = targetDecoyResults.getUserInput() / 100;
//                    int thresholdType = targetDecoyResults.getInputType();
//                    // @TODO: check the cv terms used!!!
//                    if (thresholdType == 0) {
//                        writeCvTerm(new CvTerm("PSI-MS", "MS:1002465", "PSM-level global confidence", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // confidence
//                    } else if (targetDecoyResults.getInputType() == 1) {
//                        writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", "PSM-level global FDR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FDR
//                    } else if (targetDecoyResults.getInputType() == 2) {
//                        writeCvTerm(new CvTerm("PSI-MS", "MS:1002464", "PSM-level global FNR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FNR
//                    }
//                }
//            }
//
            // @TODO: re-add psm ptm thresholds
//            PsmPTMMap psmPTMMap = pSMaps.getPsmPTMMap();
//            if (psmPTMMap != null) { // backward compatibility: information only present in versions 0.28.2 and later
//                for (Double ptmMass : psmPTMMap.getModificationsScored()) {
//                    for (int mapKey : psmPTMMap.getKeys(ptmMass).keySet()) {
//                        TargetDecoyMap targetDecoyMap = psmPTMMap.getTargetDecoyMap(ptmMass, mapKey);
//                        TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
//                        double threshold = targetDecoyResults.getUserInput() / 100;
//                        int thresholdType = targetDecoyResults.getInputType(); // For now only FDR is implemented but others will follow after my next transatlantic flight :)
//                        String ptmClass = "Modification of mass " + ptmMass;
//                        //@TODO: find cv terms
//                    }
//                }
//            }
            // @TODO: one for ptm scores, one per ptm per charge state per file
            // match quality thresholds 
            // @TODO: match quality thresholds?? some are per file...
        }


        tabCounter--;
        br.write(getCurrentTabSpace() + "</Threshold>" + System.getProperty("line.separator"));


        tabCounter--;
        br.write(getCurrentTabSpace() + "</SpectrumIdentificationProtocol>" + System.getProperty("line.separator"));


        // add ProteinDetectionProtocol
        br.write(getCurrentTabSpace() + "<ProteinDetectionProtocol "
                + "analysisSoftware_ref=\"ID_software\" id=\"PeptideShaker_1\">" + System.getProperty("line.separator"));
        tabCounter++;


//        br.write(getCurrentTabSpace() + "<AnalysisParams>" + System.getProperty("line.separator"));
//        tabCounter++;
        // @TODO: add cv terms? (children of MS:1001302)
//        tabCounter--;
//        br.write(getCurrentTabSpace() + "</AnalysisParams>" + System.getProperty("line.separator"));
        // protein level threshold
        br.write(getCurrentTabSpace() + "<Threshold>" + System.getProperty("line.separator"));
        tabCounter++;


        if (!targetDecoy) {
            writeCvTerm(new CvTerm("PSI-MS", "MS:1001494", "no threshold", null));
        } else {
            PSMaps psMaps = new PSMaps();
            psMaps = (PSMaps) identification.getUrParam(psMaps);
            ProteinMap proteinMap = psMaps.getProteinMap();
            TargetDecoyMap targetDecoyMap = proteinMap.getTargetDecoyMap();
            TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();


            double threshold = targetDecoyResults.getUserInput() / 100;
            int thresholdType = targetDecoyResults.getInputType();


            if (thresholdType == 0) {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1002461", "protein group-level global confidence", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // confidence
            } else if (targetDecoyResults.getInputType() == 1) {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1002369", "protein group-level global FDR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FDR
            } else if (targetDecoyResults.getInputType() == 2) {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1002460", "protein group-level global FNR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FNR
            }
        }
        tabCounter--;
        br.write(getCurrentTabSpace() + "</Threshold>" + System.getProperty("line.separator"));

View Full Code Here

                    }
                }


                // add main protein cv terms
                if (accession.equalsIgnoreCase(mainAccession)) {
                    writeCvTerm(new CvTerm("PSI-MS", "MS:1001591", "anchor protein", null));
                    //writeCvTerm(new CvTerm("PSI-MS", "MS:1001594", "sequence same-set protein", null));
                } else {
                    writeCvTerm(new CvTerm("PSI-MS", "MS:1001594", "sequence same-set protein", null)); // @TODO: validate these cv terms!! (children of MS:1001101)
                }


                // add protein coverage cv term
                //writeCvTerm(new CvTerm("PSI-MS", "MS:1001093", "sequence coverage", null)); // @TODO: sequence coverage?? (need for MIAPE)
                // add protein score
                // @TODO: add protein scores? don't think we have these..?
                // children off MS:1001153 or MS:1001116
                tabCounter--;
                br.write(getCurrentTabSpace() + "</ProteinDetectionHypothesis>" + System.getProperty("line.separator"));
            }


            // add protein group cv terms
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002470", "PeptideShaker protein group score", Double.toString(Util.roundDouble(psParameter.getProteinScore(), CONFIDENCE_DECIMALS))));
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002471", "PeptideShaker protein group confidence", Double.toString(Util.roundDouble(psParameter.getProteinConfidence(), CONFIDENCE_DECIMALS))));


            tabCounter--;
            br.write(getCurrentTabSpace() + "</ProteinAmbiguityGroup>" + System.getProperty("line.separator"));


            waitingHandler.increasePrimaryProgressCounter();

View Full Code Here

                if (ionMatch.ion.getType() == IonType.PEPTIDE_FRAGMENT_ION
                        || ionMatch.ion.getType() == IonType.IMMONIUM_ION) { // @TODO: add PRECURSOR_ION and REPORTER_ION
//                    || ionMatch.ion.getType() == IonType.PRECURSOR_ION
//                    || ionMatch.ion.getType() == IonType.REPORTER_ION) {


                    CvTerm fragmentIonTerm = ionMatch.ion.getPrideCvTerm(); // @TODO: replace by PSI-MS mappings...
                    Integer charge = ionMatch.charge.value;


                    if (fragmentIonTerm != null) {
                        if (!allFragmentIons.containsKey(fragmentIonTerm.getName())) {
                            allFragmentIons.put(fragmentIonTerm.getName(), new HashMap<Integer, ArrayList<IonMatch>>());
                        }
                        if (!allFragmentIons.get(fragmentIonTerm.getName()).containsKey(charge)) {
                            allFragmentIons.get(fragmentIonTerm.getName()).put(charge, new ArrayList<IonMatch>());
                        }
                        allFragmentIons.get(fragmentIonTerm.getName()).get(charge).add(ionMatch);
                    }
                }
            }


            if (!allFragmentIons.isEmpty()) {


                br.write(getCurrentTabSpace() + "<Fragmentation>" + System.getProperty("line.separator"));
                tabCounter++;


                // add the fragment ions
                Iterator<String> fragmentTypeIterator = allFragmentIons.keySet().iterator();


                while (fragmentTypeIterator.hasNext()) {


                    String fragmentType = fragmentTypeIterator.next();
                    Iterator<Integer> chargeTypeIterator = allFragmentIons.get(fragmentType).keySet().iterator();


                    while (chargeTypeIterator.hasNext()) {


                        Integer fragmentCharge = chargeTypeIterator.next();
                        ArrayList<IonMatch> ionMatches = allFragmentIons.get(fragmentType).get(fragmentCharge);
                        CvTerm fragmentIonTerm = ionMatches.get(0).ion.getPrideCvTerm();


                        String indexes = "";
                        String mzValues = "";
                        String intensityValues = "";
                        String errorValues = "";


                        // get the fragment ion details
                        for (IonMatch ionMatch : ionMatches) {


                            if (ionMatch.ion instanceof PeptideFragmentIon) {
                                indexes += ((PeptideFragmentIon) ionMatch.ion).getNumber() + " ";
                            } else if (ionMatch.ion instanceof ImmoniumIon) {
                                char residue = ImmoniumIon.getResidue(((ImmoniumIon) ionMatch.ion).getSubType());
                                char[] peptideAsArray = peptideSequence.toCharArray();
                                for (int i = 0; i < peptideAsArray.length; i++) {
                                    if (peptideAsArray[i] == residue) {
                                        indexes += (i + 1) + " ";
                                    }
                                }
                            } else {
                                // not yet implemented...
                            }


                            mzValues += ionMatch.peak.mz + " ";
                            intensityValues += ionMatch.peak.intensity + " ";
                            errorValues += ionMatch.getAbsoluteError() + " ";
                        }


                        br.write(getCurrentTabSpace() + "<IonType charge=\"" + fragmentCharge + "\" index=\"" + indexes.trim() + "\">" + System.getProperty("line.separator"));
                        tabCounter++;


                        br.write(getCurrentTabSpace() + "<FragmentArray measure_ref=\"Measure_MZ\" values=\"" + mzValues.trim() + "\"/>" + System.getProperty("line.separator"));
                        br.write(getCurrentTabSpace() + "<FragmentArray measure_ref=\"Measure_Int\" values=\"" + intensityValues.trim() + "\"/>" + System.getProperty("line.separator"));
                        br.write(getCurrentTabSpace() + "<FragmentArray measure_ref=\"Measure_Error\" values=\"" + errorValues.trim() + "\"/>" + System.getProperty("line.separator"));


                        writeCvTerm(new CvTerm(fragmentIonTerm.getOntology(), fragmentIonTerm.getAccession(), fragmentIonTerm.getName(), null));


                        tabCounter--;
                        br.write(getCurrentTabSpace() + "</IonType>" + System.getProperty("line.separator"));
                    }
                }


                tabCounter--;
                br.write(getCurrentTabSpace() + "</Fragmentation>" + System.getProperty("line.separator"));
            }


            // add peptide shaker score and confidence
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002466", "PeptideShaker: PSM score", Double.toString(Util.roundDouble(psmParameter.getPsmScore(), CONFIDENCE_DECIMALS))));
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002467", "PeptideShaker PSM confidence", Double.toString(Util.roundDouble(psmParameter.getPsmConfidence(), CONFIDENCE_DECIMALS))));


            if (mzidVersion1_2) {


                PeptideMatch peptideMatch = identification.getPeptideMatch(bestPeptideKey);
                PSPtmScores psPtmScores = (PSPtmScores) spectrumMatch.getUrParam(new PSPtmScores());
                if (psPtmScores != null) {
                    int modMatchIndex = 0;
                    for (ModificationMatch modMatch : bestPeptideAssumption.getPeptide().getModificationMatches()) {
                        PtmScoring ptmScoring = psPtmScores.getPtmScoring(modMatch.getTheoreticPtm());
                        if (ptmScoring != null) {
                            int site = modMatch.getModificationSite();
                            if (ptmScoringPreferences.isProbabilitsticScoreCalculation()) {
                                double score = ptmScoring.getProbabilisticScore(site);
                                String valid = "true";
                                if (score < ptmScoringPreferences.getProbabilisticScoreThreshold()) {
                                    valid = "false";
                                }
                                writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX",
                                        ptmScoringPreferences.getSelectedProbabilisticScore().getName(),
                                        modMatchIndex + ":" + score + ":" + site + ":" + valid)); // @TODO: add correct cv term!
                            }
                            double score = ptmScoring.getDeltaScore(site);
                            String valid = "true";
                            if (score < 95) { //@TODO: avoid this hard coded value
                                valid = "false";
                            }
                            writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX", "D-score",
                                    modMatchIndex + ":" + score + ":" + site + ":" + valid)); // @TODO: add correct cv term!
                        }
                        modMatchIndex++;
                    }
                }


                PSParameter peptideParameter = (PSParameter) identification.getPeptideMatchParameter(bestPeptideKey, psmParameter);
                writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX", "peptide: Confidence", peptideParameter.getPeptideConfidence() + "")); // @TODO: add correct cv term!
                writeCvTerm(new CvTerm("PSI-MS", "MS:1002489", "peptide: Score", peptideParameter.getPeptideScore() + ""));
                writeCvTerm(new CvTerm("PSI-MS", "MS:1002500", "peptide passes threshold", peptideParameter.getMatchValidationLevel().isValidated() + ""));


                psPtmScores = (PSPtmScores) peptideMatch.getUrParam(new PSPtmScores());
                if (psPtmScores != null) {
                    int modMatchIndex = 0;
                    for (ModificationMatch modMatch : peptideMatch.getTheoreticPeptide().getModificationMatches()) {
                        PtmScoring ptmScoring = psPtmScores.getPtmScoring(modMatch.getTheoreticPtm());
                        if (ptmScoring != null) {
                            int site = modMatch.getModificationSite();
                            if (ptmScoringPreferences.isProbabilitsticScoreCalculation()) {
                                double score = ptmScoring.getProbabilisticScore(site);
                                String valid = "true";
                                if (score < ptmScoringPreferences.getProbabilisticScoreThreshold()) {
                                    valid = "false";
                                }
                                writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX", "peptide: "
                                        + ptmScoringPreferences.getSelectedProbabilisticScore().getName(),
                                        modMatchIndex + ":" + score + ":" + site + ":" + valid)); // @TODO: add correct cv term!
                            }
                            double score = ptmScoring.getDeltaScore(site);
                            String valid = "true";
                            if (score < 95) { // @TODO: avoid this hard coded value
                                valid = "false";
                            }
                            writeCvTerm(new CvTerm("PSI-MS", "MS:100XXX",
                                    "peptide: D-score", modMatchIndex
                                    + ":" + score + ":" + site + ":" + valid)); // @TODO: add correct cv term!
                        }
                        modMatchIndex++;
                    }
                }
            }


            // add the individual search engine results
            Double mascotScore = null, msAmandaScore = null;
            HashMap<Integer, Double> scores = new HashMap<Integer, Double>();
            for (Integer tempAdvocate : spectrumMatch.getAdvocates()) {
                ArrayList<Double> eValues = new ArrayList<Double>(spectrumMatch.getAllAssumptions(tempAdvocate).keySet());
                for (double eValue : eValues) {
                    for (SpectrumIdentificationAssumption currentAssumption : spectrumMatch.getAllAssumptions(tempAdvocate).get(eValue)) {
                        if (currentAssumption instanceof PeptideAssumption) {
                            PeptideAssumption peptideAssumption = (PeptideAssumption) currentAssumption;
                            if (peptideAssumption.getPeptide().isSameSequenceAndModificationStatus(
                                    bestPeptideAssumption.getPeptide(), sequenceMatchingPreferences)) {
                                Double currentMinEvalue = scores.get(tempAdvocate);
                                if (currentMinEvalue == null || eValue < currentMinEvalue) {
                                    scores.put(tempAdvocate, eValue);


                                    // save the special advocate scores
                                    if (tempAdvocate == Advocate.mascot.getIndex()) {
                                        mascotScore = ((MascotScore) peptideAssumption.getUrParam(new MascotScore(0))).getScore();
                                    } else if (tempAdvocate == Advocate.msAmanda.getIndex()
                                            && peptideAssumption.getUrParam(new MsAmandaScore()) != null) {
                                        msAmandaScore = ((MsAmandaScore) peptideAssumption.getUrParam(new MsAmandaScore())).getScore();
                                    }
                                }
                            }
                        }
                    }
                }
            }
            ArrayList<Integer> algorithms = new ArrayList<Integer>(scores.keySet());
            Collections.sort(algorithms);
            for (int tempAdvocate : algorithms) {
                double eValue = scores.get(tempAdvocate);
                if (tempAdvocate == Advocate.msgf.getIndex()) {
                    writeCvTerm(new CvTerm("PSI-MS", "MS:1002052", "MS-GF:SpecEValue", Double.toString(eValue)));
                } else if (tempAdvocate == Advocate.mascot.getIndex()) {
                    writeCvTerm(new CvTerm("PSI-MS", "MS:1001172", "Mascot:expectation value", Double.toString(eValue)));
                } else if (tempAdvocate == Advocate.omssa.getIndex()) {
                    writeCvTerm(new CvTerm("PSI-MS", "MS:1001328", "OMSSA:evalue", Double.toString(eValue)));
                } else if (tempAdvocate == Advocate.xtandem.getIndex()) {
                    writeCvTerm(new CvTerm("PSI-MS", "MS:1001330", "X!Tandem:expect", Double.toString(eValue)));
                } else if (tempAdvocate == Advocate.comet.getIndex()) {
                    writeCvTerm(new CvTerm("PSI-MS", "MS:1002257", "Comet:expectation value", Double.toString(eValue)));
                } else {
                    writeUserParam(Advocate.getAdvocate(tempAdvocate).getName() + " e-value", "" + eValue);
                }
                
                // @TODO: add scores for MyriMatch!


                // @TODO: add generic e-value for user algorithms?
            }


            // add the additional search engine scores
            if (mascotScore != null) {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1001171", "Mascot:score", "" + mascotScore));
            }
            if (msAmandaScore != null) {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1002319", "Amanda:AmandaScore", "" + msAmandaScore));
            }


            // add other cv and user params
            writeCvTerm(new CvTerm("PSI-MS", "MS:1001117", "theoretical mass", String.valueOf(bestPeptideAssumption.getTheoreticMass()))); // @TODO: add more? MS:1001105 - peptide result details


            // @TODO: 
            // add validation level information
            //writeUserParam(psmParameter.getMatchValidationLevel().getIndex());
            tabCounter--;
            br.write(getCurrentTabSpace() + "</SpectrumIdentificationItem>" + System.getProperty("line.separator"));


            // add the spectrum title
            writeCvTerm(new CvTerm("PSI-MS", "MS:1000796", "spectrum title", spectrumTitleHtml));


            tabCounter--;
            br.write(getCurrentTabSpace() + "</SpectrumIdentificationResult>" + System.getProperty("line.separator"));
        }
    }

View Full Code Here

            if (algorithms != null && !algorithms.isEmpty()) {
                for (String algorithmName : algorithms.keySet()) {
                    Advocate advocate = Advocate.getAdvocate(algorithmName);
                    int advocateIndex = advocate.getIndex();
                    if (advocateIndex == Advocate.mascot.getIndex()) {
                        writeCvTerm(new CvTerm("PSI-MS", "MS:1001199", "Mascot DAT format", null));
                    } else if (advocateIndex == Advocate.xtandem.getIndex()) {
                        writeCvTerm(new CvTerm("PSI-MS", "MS:1001401", "xtandem xml file", null));
                    } else if (advocateIndex == Advocate.omssa.getIndex()) {
                        writeCvTerm(new CvTerm("PSI-MS", "MS:1001400", "OMSSA xml format", null));
                    } else if (advocateIndex == Advocate.msgf.getIndex()) {
                        writeCvTerm(new CvTerm("PSI-MS", "MS:1002073", "mzIdentML format", null));
                    } else if (advocateIndex == Advocate.msAmanda.getIndex()) {
                        writeCvTerm(new CvTerm("PSI-MS", "MS:1002459", "MS Amanda csv format", null));
                    } else if (advocateIndex == Advocate.comet.getIndex()) {
                        writeCvTerm(new CvTerm("PSI-MS", "MS:1001421", "pepXML format", null));
                    } else if (advocateIndex == Advocate.myriMatch.getIndex()) {
                        writeCvTerm(new CvTerm("PSI-MS", "MS:1000914", "tab delimited text format", null));
                    } else {
                        // @TODO: add support for the new advocates!!
                        writeUserParam("Unknown"); // @TODO: add cv term?
                        break;
                    }
                }
            } else {
                // A backward compatibility error occurred
                writeUserParam("Unknown"); // @TODO: add cv term?
            }


            tabCounter--;
            br.write(getCurrentTabSpace() + "</FileFormat>" + System.getProperty("line.separator"));
            tabCounter--;
            br.write(getCurrentTabSpace() + "</SourceFile>" + System.getProperty("line.separator"));
        }


        // add the database
        br.write(getCurrentTabSpace() + "<SearchDatabase numDatabaseSequences=\"" + sequenceFactory.getNSequences()
                + "\" location=\"" + searchParameters.getFastaFile().getAbsolutePath() + "\" "
                + "id=\"" + "SearchDB_1\">" + System.getProperty("line.separator"));
        tabCounter++;
        br.write(getCurrentTabSpace() + "<FileFormat>" + System.getProperty("line.separator"));
        tabCounter++;
        writeCvTerm(new CvTerm("PSI-MS", "MS:1001348", "FASTA format", null));
        tabCounter--;
        br.write(getCurrentTabSpace() + "</FileFormat>" + System.getProperty("line.separator"));
        br.write(getCurrentTabSpace() + "<DatabaseName>" + System.getProperty("line.separator"));
        tabCounter++;
        writeUserParam(searchParameters.getFastaFile().getName());
        tabCounter--;
        br.write(getCurrentTabSpace() + "</DatabaseName>" + System.getProperty("line.separator"));
        writeCvTerm(new CvTerm("PSI-MS", "MS:1001073", "database type amino acid", null));
        tabCounter--;
        br.write(getCurrentTabSpace() + "</SearchDatabase>" + System.getProperty("line.separator"));


        // add the spectra location
        for (String mgfFileName : spectrumFactory.getMgfFileNames()) {
            File mgfFile = projectDetails.getSpectrumFile(mgfFileName);


            br.write(getCurrentTabSpace() + "<SpectraData location=\"" + mgfFile.getAbsolutePath() + "\" id=\"" + mgfFileName
                    + "\" name=\"" + mgfFile.getName() + "\">" + System.getProperty("line.separator"));
            tabCounter++;


            br.write(getCurrentTabSpace() + "<FileFormat>" + System.getProperty("line.separator"));
            tabCounter++;
            writeCvTerm(new CvTerm("PSI-MS", "MS:1001062", "Mascot MGF file", null));
            tabCounter--;
            br.write(getCurrentTabSpace() + "</FileFormat>" + System.getProperty("line.separator"));


            br.write(getCurrentTabSpace() + "<SpectrumIDFormat>" + System.getProperty("line.separator"));
            tabCounter++;
            writeCvTerm(new CvTerm("PSI-MS", "MS:1000774", "multiple peak list nativeID format", null));
            tabCounter--;
            br.write(getCurrentTabSpace() + "</SpectrumIDFormat>" + System.getProperty("line.separator"));


            tabCounter--;
            br.write(getCurrentTabSpace() + "</SpectraData>" + System.getProperty("line.separator"));

View Full Code Here

                            modifiedSequence += sequence.charAt(aa);
                            for (ModificationMatch modificationMatch : peptide.getModificationMatches()) {
                                if (modificationMatch.getModificationSite() == aa + 1) {
                                    String ptmName = modificationMatch.getTheoreticPtm();
                                    PTM ptm = ptmFactory.getPTM(ptmName);
                                    CvTerm cvTerm = null;
                                    if (ptmToPrideMap != null) {
                                        try {
                                            cvTerm = ptmToPrideMap.getCVTerm(ptmName);
                                            if (cvTerm == null) {
                                                cvTerm = PtmToPrideMap.getDefaultCVTerm(ptmName);
                                            }
                                        } catch (Exception e) {
                                        }
                                    }
                                    if (cvTerm != null) {
                                        modifiedSequence += "[" + cvTerm.getName() + "]";
                                    } else {
                                        modifiedSequence += "[" + ptm.getShortName() + "]";
                                    }
                                }
                            }

View Full Code Here

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eu.isas.peptideshaker.export.MzIdentMLExport

eu.isas.peptideshaker.export.PrideXmlExport

eu.isas.peptideshaker.followup.SwathExport

eu.isas.peptideshaker.gui.pride.annotationdialogs.NewInstrumentDialog

eu.isas.peptideshaker.gui.pride.annotationdialogs.NewProtocolDialog

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