Examples of concatenatedTargetDecoy()

Examples of com.compomics.util.experiment.identification.SequenceFactory.concatenatedTargetDecoy()

113
114
115
116
117
118
119
120
121
122
123
       
        SequenceFactory sequenceFactory = SequenceFactory.getInstance();
       
        String text = "";
       
        if (sequenceFactory.concatenatedTargetDecoy()) {
            text += "Protein identification was conducted against a concatenated target/decoy [PMID 20013364] version of the ";
        } else {
            text += "Protein identification was conducted against a version of the ";
        }
       
View Full Code Here

Examples of com.compomics.util.experiment.identification.SequenceFactory.concatenatedTargetDecoy()

688
689
690
691
692
693
694
695
696
697
698
        psParameter = (PSParameter) identification.getProteinMatchParameter(proteinKey, psParameter);
        psParameter.resetQcResults();

        if (!psParameter.isManualValidation()) {

            if (sequenceFactory.concatenatedTargetDecoy()) {

                if (!noValidated && psParameter.getProteinProbabilityScore() <= scoreThreshold) {
                    String reasonDoubtful = null;
                    boolean filterPassed = true;
                    for (ProteinFilter filter : doubtfulMatchFilters) {
View Full Code Here

Examples of com.compomics.util.experiment.identification.SequenceFactory.concatenatedTargetDecoy()

777
778
779
780
781
782
783
784
785
786
787
        SequenceFactory sequenceFactory = SequenceFactory.getInstance();
        PSParameter psParameter = new PSParameter();
        psParameter = (PSParameter) identification.getPeptideMatchParameter(peptideKey, psParameter);
        psParameter.resetQcResults();

        if (sequenceFactory.concatenatedTargetDecoy()) {
            TargetDecoyMap targetDecoyMap = peptideMap.getTargetDecoyMap(peptideMap.getCorrectedKey(psParameter.getSpecificMapKey()));
            TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
            double peptideThreshold = targetDecoyResults.getScoreLimit();
            double confidenceThreshold = targetDecoyResults.getConfidenceLimit() + targetDecoyMap.getResolution();
            if (confidenceThreshold > 100) {
View Full Code Here

Examples of com.compomics.util.experiment.identification.SequenceFactory.concatenatedTargetDecoy()

875
876
877
878
879
880
881
882
883
884
885
        SequenceFactory sequenceFactory = SequenceFactory.getInstance();
        PSParameter psParameter = new PSParameter();
        psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);
        psParameter.resetQcResults();

        if (sequenceFactory.concatenatedTargetDecoy()) {

            Integer charge = new Integer(psParameter.getSpecificMapKey());
            String fileName = Spectrum.getSpectrumFile(spectrumKey);
            TargetDecoyMap targetDecoyMap = psmMap.getTargetDecoyMap(charge, fileName);
            double psmThreshold = 0;
View Full Code Here

Examples of com.compomics.util.experiment.identification.SequenceFactory.concatenatedTargetDecoy()

1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
        SequenceFactory sequenceFactory = SequenceFactory.getInstance();
        PSParameter psParameter = new PSParameter();
        psParameter = (PSParameter) tagAssumption.getUrParam(psParameter);

        if (sequenceFactory.concatenatedTargetDecoy()) {

            TargetDecoyMap targetDecoyMap = inputMap.getTargetDecoyMap(tagAssumption.getAdvocate());
            TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
            double seThreshold = targetDecoyResults.getScoreLimit();
            double confidenceThreshold = targetDecoyResults.getConfidenceLimit() + targetDecoyMap.getResolution();
View Full Code Here

Examples of com.compomics.util.experiment.identification.SequenceFactory.concatenatedTargetDecoy()

1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
        SequenceFactory sequenceFactory = SequenceFactory.getInstance();
        PSParameter psParameter = new PSParameter();
        psParameter = (PSParameter) peptideAssumption.getUrParam(psParameter);
        psParameter.resetQcResults();

        if (sequenceFactory.concatenatedTargetDecoy()) {

            TargetDecoyMap targetDecoyMap = inputMap.getTargetDecoyMap(peptideAssumption.getAdvocate());
            TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
            double seThreshold = targetDecoyResults.getScoreLimit();
            double confidenceThreshold = targetDecoyResults.getConfidenceLimit() + targetDecoyMap.getResolution();
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. All rights reserved.
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.