Package eu.isas.peptideshaker.validation

Examples of eu.isas.peptideshaker.validation.MatchesValidator

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                    try {
                        PSMaps pSMaps = new PSMaps();
                        pSMaps = (PSMaps) peptideShakerGUI.getIdentification().getUrParam(pSMaps);

                        MatchesValidator matchesValidator = new MatchesValidator(pSMaps.getPsmSpecificMap(), pSMaps.getPeptideSpecificMap(), pSMaps.getProteinMap());
                        matchesValidator.validateIdentifications(peptideShakerGUI.getIdentification(), peptideShakerGUI.getMetrics(), pSMaps.getInputMap(), progressDialog, peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getAnnotationPreferences(), peptideShakerGUI.getSequenceMatchingPreferences());

                        progressDialog.setPrimaryProgressCounterIndeterminate(true);

                        if (!progressDialog.isRunCanceled()) {
                            // update the other tabs
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        this.sample = sample;
        this.replicateNumber = replicateNumber;
        PsmSpecificMap psmMap = new PsmSpecificMap();
        PeptideSpecificMap peptideMap = new PeptideSpecificMap();
        ProteinMap proteinMap = new ProteinMap();
        matchesValidator = new MatchesValidator(psmMap, peptideMap, proteinMap);
        PsmPTMMap psmPTMMap = new PsmPTMMap();
        ptmScorer = new PtmScorer(psmPTMMap);
    }
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     */
    public PeptideShaker(MsExperiment experiment, Sample sample, int replicateNumber, PSMaps psMaps) {
        this.experiment = experiment;
        this.sample = sample;
        this.replicateNumber = replicateNumber;
        matchesValidator = new MatchesValidator(psMaps.getPsmSpecificMap(), psMaps.getPeptideSpecificMap(), psMaps.getProteinMap());
        ptmScorer = new PtmScorer(psMaps.getPsmPTMMap());
    }
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Related Classes of eu.isas.peptideshaker.validation.MatchesValidator

  • com.compomics.util.experiment.biology.Peptide
  • com.compomics.util.experiment.identification.matches.PeptideMatch
  • com.compomics.util.experiment.identification.matches.ProteinMatch
  • com.compomics.util.experiment.identification.matches.SpectrumMatch
  • com.compomics.util.experiment.identification.PeptideAssumption
  • com.compomics.util.experiment.identification.SequenceFactory
  • com.compomics.util.experiment.identification.spectrum_annotators.PeptideSpectrumAnnotator
  • com.compomics.util.experiment.identification.TagAssumption
  • com.compomics.util.experiment.massspectrometry.Precursor
  • com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
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