Package com.compomics.util.experiment.identification

Examples of com.compomics.util.experiment.identification.PeptideAssumption


                                    break;
                                }

                                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(psmKey);
                                psParameter = (PSParameter) identification.getSpectrumMatchParameter(psmKey, psParameter);
                                PeptideAssumption bestAssumption = spectrumMatch.getBestPeptideAssumption();

                                writer.write(++psmCounter + SEPARATOR);

                                String proteinAccessions = "";
                                String proteinDescriptions = "";

                                for (String protein : bestAssumption.getPeptide().getParentProteins(peptideShakerGUI.getSequenceMatchingPreferences())) {
                                    if (!proteinAccessions.equals("")) {
                                        proteinAccessions += ", ";
                                        proteinDescriptions += "; ";
                                    }
                                    proteinAccessions += protein;
                                    proteinDescriptions += sequenceFactory.getHeader(protein).getSimpleProteinDescription();
                                }
                                writer.write(proteinAccessions + SEPARATOR);
                                writer.write(proteinDescriptions + SEPARATOR);
                                String sequence = bestAssumption.getPeptide().getSequence();
                                writer.write(sequence + SEPARATOR);
                                HashMap<String, ArrayList<Integer>> modMap = new HashMap<String, ArrayList<Integer>>();
                                for (ModificationMatch modificationMatch : bestAssumption.getPeptide().getModificationMatches()) {
                                    if (modificationMatch.isVariable()) {
                                        if (!modMap.containsKey(modificationMatch.getTheoreticPtm())) {
                                            modMap.put(modificationMatch.getTheoreticPtm(), new ArrayList<Integer>());
                                        }
                                        modMap.get(modificationMatch.getTheoreticPtm()).add(modificationMatch.getModificationSite());
                                    }
                                }
                                boolean first = true, first2;
                                ArrayList<String> mods = new ArrayList<String>(modMap.keySet());
                                Collections.sort(mods);
                                for (String mod : mods) {
                                    if (first) {
                                        first = false;
                                    } else {
                                        writer.write(", ");
                                    }
                                    first2 = true;
                                    writer.write(mod + "(");
                                    for (int aa : modMap.get(mod)) {
                                        if (first2) {
                                            first2 = false;
                                        } else {
                                            writer.write(", ");
                                        }
                                        writer.write(aa + "");
                                    }
                                    writer.write(")");
                                }
                                writer.write(SEPARATOR);
                                int nPhospho = 0;
                                ArrayList<String> modList = new ArrayList<String>();
                                for (ModificationMatch modificationMatch : bestAssumption.getPeptide().getModificationMatches()) {
                                    if (modificationMatch.isVariable()) {
                                        String ptmName = modificationMatch.getTheoreticPtm();
                                        if (ptmName.contains("phospho")) {
                                            nPhospho++;
                                        }
                                        PTM refPtm = ptmFactory.getPTM(ptmName);
                                        for (String equivalentPtm : ptmProfile.getSimilarNotFixedModifications(refPtm.getMass())) {
                                            if (!modList.contains(equivalentPtm)) {
                                                modList.add(equivalentPtm);
                                            }
                                        }
                                    }
                                }

                                Collections.sort(modList);
                                PSPtmScores ptmScores = new PSPtmScores();
                                first = true;
                                StringBuilder dLocalizations = new StringBuilder();
                                StringBuilder probabilisticLocalizations = new StringBuilder();
                                String mdLocation = "";
                                String mdScore = "";
                                String[] split = sequence.split("[STY]");
                                int nSites = split.length - 1;
                                ArrayList<String> phosphoNames = new ArrayList<String>();

                                for (String mod : modList) {
                                    if (mod.contains("phospho")) {
                                        phosphoNames.add(mod);
                                        if (spectrumMatch.getUrParam(ptmScores) != null) {
                                            ptmScores = (PSPtmScores) spectrumMatch.getUrParam(new PSPtmScores());
                                            if (ptmScores != null && ptmScores.getPtmScoring(mod) != null) {
                                                PtmScoring ptmScoring = ptmScores.getPtmScoring(mod);
                                                ArrayList<Integer> sites = new ArrayList<Integer>(ptmScoring.getProbabilisticSites());
                                                Collections.sort(sites);
                                                for (Integer site : sites) {
                                                    if (probabilisticLocalizations.length() > 0) {
                                                        probabilisticLocalizations.append(", ");
                                                    }
                                                    probabilisticLocalizations.append(site.toString()).append(": ").append(ptmScoring.getProbabilisticScore(site));
                                                }
                                                sites = new ArrayList<Integer>(ptmScoring.getDSites());
                                                Collections.sort(sites);
                                                for (Integer site : sites) {
                                                    if (dLocalizations.length() > 0) {
                                                        dLocalizations.append(", ");
                                                    }
                                                    dLocalizations.append(site.toString()).append(": ").append(ptmScoring.getDeltaScore(site));
                                                }
                                            }
                                        }
                                    }
                                }
                                if (algorithms.size() == 1 && algorithms.get(0) == Advocate.mascot.getIndex()) {
                                    if (!phosphoNames.isEmpty() && spectrumMatch.hasAssumption(Advocate.mascot.getIndex())) {
                                        PeptideAssumption mascotAssumption = null;
                                        double bestScore = 0;
                                        for (ArrayList<SpectrumIdentificationAssumption> peptideAssumptionList : spectrumMatch.getAllAssumptions(Advocate.mascot.getIndex()).values()) {
                                            for (SpectrumIdentificationAssumption assumption : peptideAssumptionList) {
                                                PeptideAssumption peptideAssumption = (PeptideAssumption) assumption;
                                                MascotScore mascotScore = new MascotScore();
                                                mascotScore = (MascotScore) peptideAssumption.getUrParam(mascotScore);
                                                if (mascotScore.getScore() > bestScore) {
                                                    mascotAssumption = peptideAssumption;
                                                    bestScore = mascotScore.getScore();
                                                }
                                            }
View Full Code Here


                                        Collections.sort(eValues);
                                        rank = 1;
                                        for (double eValue : eValues) {
                                            for (SpectrumIdentificationAssumption assumption : spectrumMatch.getAllAssumptions(se).get(eValue)) {
                                                if (assumption instanceof PeptideAssumption) {
                                                    PeptideAssumption peptideAssumption = (PeptideAssumption) assumption;
                                                    writer.write(Advocate.getAdvocate(se).getName() + SEPARATOR);
                                                    writer.write(rank + SEPARATOR);
                                                    if (accession || proteinDescription) {

                                                        String proteinAccessions = "";
                                                        String proteinDescriptions = "";

                                                        boolean first = true;
                                                        for (String protein : peptideAssumption.getPeptide().getParentProteins(peptideShakerGUI.getSequenceMatchingPreferences())) {
                                                            if (first) {
                                                                first = false;
                                                            } else {
                                                                if (accession) {
                                                                    proteinAccessions += ", ";
                                                                }
                                                                if (proteinDescription) {
                                                                    proteinDescriptions += "; ";
                                                                }
                                                            }
                                                            if (accession) {
                                                                proteinAccessions += protein;
                                                            }
                                                            if (proteinDescription) {
                                                                proteinDescriptions += sequenceFactory.getHeader(protein).getSimpleProteinDescription();
                                                            }
                                                        }
                                                        if (accession) {
                                                            writer.write(proteinAccessions + SEPARATOR);
                                                        }
                                                        if (proteinDescription) {
                                                            writer.write(proteinDescriptions + SEPARATOR);
                                                        }
                                                    }
                                                    if (sequence) {
                                                        writer.write(peptideAssumption.getPeptide().getSequence() + SEPARATOR);
                                                    }
                                                    if (modifications) {
                                                        boolean first = true;
                                                        for (ModificationMatch modificationMatch : peptideAssumption.getPeptide().getModificationMatches()) {
                                                            if (modificationMatch.isVariable()) {
                                                                if (first) {
                                                                    first = false;
                                                                } else {
                                                                    writer.write(", ");
                                                                }
                                                                String modName = modificationMatch.getTheoreticPtm();
                                                                writer.write(modName + "(" + modificationMatch.getModificationSite() + ")");
                                                            }
                                                        }
                                                        writer.write(SEPARATOR);
                                                    }
                                                    if (file) {
                                                        writer.write(Spectrum.getSpectrumFile(spectrumMatch.getKey()) + SEPARATOR);
                                                    }
                                                    if (title) {
                                                        writer.write(Spectrum.getSpectrumTitle(spectrumMatch.getKey()) + SEPARATOR);
                                                    }
                                                    if (precursor) {
                                                        Precursor prec = spectrumFactory.getPrecursor(spectrumMatch.getKey());
                                                        writer.write(prec.getMz() + SEPARATOR);
                                                        writer.write(peptideAssumption.getIdentificationCharge().value + SEPARATOR);
                                                        writer.write(prec.getRt() + SEPARATOR);
                                                        writer.write(peptideAssumption.getPeptide().getMass() + SEPARATOR);
                                                        writer.write(peptideAssumption.getDeltaMass(prec.getMz(),
                                                                peptideShakerGUI.getSearchParameters().isPrecursorAccuracyTypePpm()) + SEPARATOR);
                                                        writer.write(peptideAssumption.getIsotopeNumber(prec.getMz()) + SEPARATOR);
                                                    }
                                                    if (scores) {
                                                        for (Integer advocateIndex : peptideShakerGUI.getProjectDetails().getIdentificationAlgorithms()) {
                                                            if (se == advocateIndex) {
                                                                writer.write("" + eValue);
                                                            }
                                                            writer.write(SEPARATOR);
                                                        }
                                                    }
                                                    if (confidence) {
                                                        psParameter = (PSParameter) peptideAssumption.getUrParam(psParameter);
                                                        writer.write(psParameter.getSearchEngineConfidence() + SEPARATOR);
                                                    }
                                                    if (peptideAssumption.getPeptide().isSameSequenceAndModificationStatus(spectrumMatch.getBestPeptideAssumption().getPeptide(), peptideShakerGUI.getSequenceMatchingPreferences())) {
                                                        writer.write(1 + SEPARATOR);
                                                    } else {
                                                        writer.write(0 + SEPARATOR);
                                                    }
                                                    if (peptideAssumption.getPeptide().isDecoy(peptideShakerGUI.getSequenceMatchingPreferences())) {
                                                        writer.write(1 + SEPARATOR);
                                                    } else {
                                                        writer.write(0 + SEPARATOR);
                                                    }
                                                    writer.write(System.getProperty("line.separator"));
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Related Classes of com.compomics.util.experiment.identification.PeptideAssumption

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