List of validateIdentifications() Examples

Examples of validateIdentifications()

eu.isas.peptideshaker.validation.MatchesValidator.validateIdentifications()

Validates the identification matches comprised in an identification object based on the target/decoy strategy and quality control metrics based on given FDR thresholds. @param identification the identification class containing the matches tovalidate @param metrics if provided, metrics on fractions will be saved whileiterating the matches @param waitingHandler the handler displaying feedback to the user @param aPSMFDR Accepted FDR at Peptide-Spectrum-Match level (e.g. '1.0'for 1% FDR) @param aPeptideFDR Accepted FDR at Peptide level (e.g. '1.0' for 1% FDR) @param aProteinFDR Accepted FDR at Protein level (e.g. '1.0' for 1% FDR) @param searchParameters the identification parameters used for thisproject @param sequenceMatchingPreferences the sequence matching preferences @param annotationPreferences the spectrum annotation preferences @param identificationFeaturesGenerator the identification featuresgenerator providing information about the matches @param inputMap the input target/decoy map

                    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

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.

Examples of validateIdentifications()

Examples of eu.isas.peptideshaker.validation.MatchesValidator.validateIdentifications()