Examples of TargetDecoyMap

Examples of eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

238
239
240
241
242
243
244
245
246
247
248
249
250
251
        ArrayList<Integer> charges = new ArrayList(fileSpecificPsmsMaps.keySet());
        Collections.sort(charges);
        int ref = 0;
        for (Integer charge : charges) {
            ArrayList<String> nonSignificantFiles = new ArrayList<String>();
            TargetDecoyMap tempMap = new TargetDecoyMap();
            for (String file : fileSpecificPsmsMaps.get(charge).keySet()) {
                TargetDecoyMap targetDecoyMap = fileSpecificPsmsMaps.get(charge).get(file);
                if (targetDecoyMap.getnMax() < 100 || targetDecoyMap.getnTargetOnly() < 100) {
                    nonSignificantFiles.add(file);
                    tempMap.addAll(targetDecoyMap);
                }
            }
            if (nonSignificantFiles.isEmpty()) {
View Full Code Here

Examples of eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

425
426
427
428
429
430
431
432
433
434
                    result.add(fileSpecificPsmsMaps.get(charge).get(file));
                }
            }
        }
        for (int charge : getGroupedCharges()) {
            TargetDecoyMap map = psmsMaps.get(charge);
            result.add(map);
        }
        return result;
    }
View Full Code Here

Examples of eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
            for (int mapKey : psmPTMMap.getKeys(ptmMass).keySet()) {
                if (waitingHandler.isRunCanceled()) {
                    return;
                }
                waitingHandler.increaseSecondaryProgressCounter();
                TargetDecoyMap currentMap = psmPTMMap.getTargetDecoyMap(ptmMass, mapKey);
                TargetDecoyResults currentResults = currentMap.getTargetDecoyResults();
                currentResults.setInputType(1);
                currentResults.setUserInput(psmError);
                currentResults.setClassicalEstimators(true);
                currentResults.setClassicalValidation(true);
                currentResults.setFdrLimit(psmError);
                currentMap.getTargetDecoySeries().getFDRResults(currentResults);
            }
        }
    }
View Full Code Here

Examples of eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

1863
1864
1865
1866
1867
1868
1869
1870
1871
1872
1873
1874
1875
1876
1877
1878
1879
1880
                    dScoreSites.add(site);
                }
                ArrayList<Double> pScores = new ArrayList<Double>(scoreToSiteMap.keySet());
                Collections.sort(pScores, Collections.reverseOrder());
                int key = spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value;
                TargetDecoyMap currentMap = psmPTMMap.getTargetDecoyMap(ptmMass, key);
                if (currentMap == null) {
                    throw new IllegalArgumentException("No FLR map found for PTM of mass " + ptmMass + " in PSMs of charge " + key + ".");
                }
                int cpt = 0;
                double doubtfulThreshold;
                if (ptmScoringPreferences.isEstimateFlr()) {
                    doubtfulThreshold = -currentMap.getTargetDecoyResults().getScoreLimit();
                } else {
                    doubtfulThreshold = ptmScoringPreferences.getProbabilisticScoreThreshold();
                }
                double randomThreshold = 0;
                if (ptmScoringPreferences.getSelectedProbabilisticScore() == PtmScore.PhosphoRS) {
View Full Code Here

Examples of eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
            double aPSMFDR, double aPeptideFDR, double aProteinFDR, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences,
            AnnotationPreferences annotationPreferences, IdentificationFeaturesGenerator identificationFeaturesGenerator, InputMap inputMap) {

        waitingHandler.setWaitingText("Finding FDR thresholds. Please Wait...");

        TargetDecoyMap currentMap = proteinMap.getTargetDecoyMap();
        TargetDecoyResults currentResults = currentMap.getTargetDecoyResults();
        currentResults.setInputType(1);
        currentResults.setUserInput(aProteinFDR);
        currentResults.setClassicalEstimators(true);
        currentResults.setClassicalValidation(true);
        currentResults.setFdrLimit(aProteinFDR);
        currentMap.getTargetDecoySeries().getFDRResults(currentResults);

        ArrayList<TargetDecoyMap> psmMaps = psmMap.getTargetDecoyMaps(),
                inputMaps = inputMap.getTargetDecoyMaps();

        int max = peptideMap.getKeys().size() + psmMaps.size() + inputMap.getNalgorithms();
        waitingHandler.setSecondaryProgressCounterIndeterminate(false);
        waitingHandler.setMaxSecondaryProgressCounter(max);

        for (String mapKey : peptideMap.getKeys()) {
            if (waitingHandler.isRunCanceled()) {
                return;
            }
            waitingHandler.increaseSecondaryProgressCounter();
            currentMap = peptideMap.getTargetDecoyMap(mapKey);
            currentResults = currentMap.getTargetDecoyResults();
            currentResults.setInputType(1);
            currentResults.setUserInput(aPeptideFDR);
            currentResults.setClassicalEstimators(true);
            currentResults.setClassicalValidation(true);
            currentResults.setFdrLimit(aPeptideFDR);
            currentMap.getTargetDecoySeries().getFDRResults(currentResults);
        }

        for (TargetDecoyMap targetDecoyMap : psmMaps) {
            if (waitingHandler.isRunCanceled()) {
                return;
View Full Code Here

Examples of eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

501
502
503
504
505
506
507
508
509
510
511
512
513
514
            NonSymmetricalNormalDistribution lengthDistribution = NonSymmetricalNormalDistribution.getRobustNonSymmetricalNormalDistribution(validatedPeptideLengths);
            metrics.setPeptideLengthDistribution(lengthDistribution);
        }

        // validate the proteins
        TargetDecoyMap targetDecoyMap = proteinMap.getTargetDecoyMap();
        TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
        double proteinThreshold = targetDecoyResults.getScoreLimit();
        double proteinConfidentThreshold = targetDecoyResults.getConfidenceLimit() + targetDecoyMap.getResolution();
        if (proteinConfidentThreshold > 100) {
            proteinConfidentThreshold = 100;
        }
        boolean noValidated = proteinMap.getTargetDecoyMap().getTargetDecoyResults().noValidated();
View Full Code Here

Examples of eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

638
639
640
641
642
643
644
645
646
647
648
649
650
651
     */
    public static void updateProteinMatchValidationLevel(Identification identification, IdentificationFeaturesGenerator identificationFeaturesGenerator,
            SearchParameters searchParameters, AnnotationPreferences annotationPreferences, ProteinMap proteinMap, String proteinKey)
            throws SQLException, IOException, ClassNotFoundException, InterruptedException, MzMLUnmarshallerException {

        TargetDecoyMap targetDecoyMap = proteinMap.getTargetDecoyMap();
        TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
        double proteinThreshold = targetDecoyResults.getScoreLimit();
        double proteinConfidentThreshold = targetDecoyResults.getConfidenceLimit() + targetDecoyMap.getResolution();

        if (proteinConfidentThreshold > 100) {
            proteinConfidentThreshold = 100;
        }

View Full Code Here

Examples of eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
        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) {
                confidenceThreshold = 100;
            }
            boolean noValidated = peptideMap.getTargetDecoyMap(peptideMap.getCorrectedKey(psParameter.getSpecificMapKey())).getTargetDecoyResults().noValidated();
            if (!noValidated && psParameter.getPeptideProbabilityScore() <= peptideThreshold) {
                String reasonDoubtful = null;
                boolean filterPassed = true;
                for (PeptideFilter filter : peptideMap.getDoubtfulMatchesFilters()) {
                    boolean validation = filter.isValidated(peptideKey, identification, identificationFeaturesGenerator);
                    psParameter.setQcResult(filter.getName(), validation);
                    if (!validation) {
                        filterPassed = false;
                        if (reasonDoubtful == null) {
                            reasonDoubtful = "";
                        } else {
                            reasonDoubtful += ", ";
                        }
                        reasonDoubtful += filter.getDescription();
                    }
                }
                boolean confidenceThresholdPassed = psParameter.getPeptideConfidence() >= confidenceThreshold; //@TODO: not sure whether we should include all 100% confidence hits by default?
                if (!confidenceThresholdPassed) {
                    if (reasonDoubtful == null) {
                        reasonDoubtful = "";
                    } else {
                        reasonDoubtful += ", ";
                    }
                    reasonDoubtful += "Low confidence";
                }
                boolean enoughHits = targetDecoyMap.getnTargetOnly() > 100;
                if (!enoughHits) {
                    if (reasonDoubtful == null) {
                        reasonDoubtful = "";
                    } else {
                        reasonDoubtful += ", ";
View Full Code Here

Examples of eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
        if (sequenceFactory.concatenatedTargetDecoy()) {

            Integer charge = new Integer(psParameter.getSpecificMapKey());
            String fileName = Spectrum.getSpectrumFile(spectrumKey);
            TargetDecoyMap targetDecoyMap = psmMap.getTargetDecoyMap(charge, fileName);
            double psmThreshold = 0;
            double confidenceThreshold = 100;
            boolean noValidated = true;

            if (targetDecoyMap != null) {
                TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
                psmThreshold = targetDecoyResults.getScoreLimit();
                confidenceThreshold = targetDecoyResults.getConfidenceLimit() + targetDecoyMap.getResolution();
                if (confidenceThreshold > 100) {
                    confidenceThreshold = 100;
                }
                noValidated = targetDecoyResults.noValidated();
            }

            if (!noValidated && psParameter.getPsmProbabilityScore() <= psmThreshold) {

                String spectrumFile = Spectrum.getSpectrumFile(spectrumKey);
                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                if (spectrumMatch.getBestPeptideAssumption() != null) {
                    // update the annotation preferences for the new psm, mainly the charge
                    annotationPreferences.setCurrentSettings(spectrumMatch.getBestPeptideAssumption(), true, sequenceMatchingPreferences);
                } else if (spectrumMatch.getBestTagAssumption() != null) {
                    charge = spectrumMatch.getBestTagAssumption().getIdentificationCharge().value;
                } else {
                    throw new IllegalArgumentException("No best tag or peptide found for spectrum " + spectrumKey);
                }

                String reasonDoubtful = null;
                boolean filterPassed = true;

                for (PsmFilter filter : psmMap.getDoubtfulMatchesFilters(charge, spectrumFile)) {
                    boolean validated = filter.isValidated(spectrumKey, identification, searchParameters, annotationPreferences, peptideSpectrumAnnotator);
                    psParameter.setQcResult(filter.getName(), validated);
                    if (!validated) {
                        if (filter.getName().toLowerCase().contains("deviation")) {
                            filter.isValidated(spectrumKey, identification, searchParameters, annotationPreferences, peptideSpectrumAnnotator);
                        } else if (filter.getName().toLowerCase().contains("coverage")) {
                            filter.isValidated(spectrumKey, identification, searchParameters, annotationPreferences, peptideSpectrumAnnotator);
                        }
                        filterPassed = false;
                        if (reasonDoubtful == null) {
                            reasonDoubtful = "";
                        } else {
                            reasonDoubtful += ", ";
                        }
                        reasonDoubtful += filter.getDescription();
                    }
                }

                boolean confidenceThresholdPassed = psParameter.getPsmConfidence() >= confidenceThreshold; //@TODO: not sure whether we should include all 100% confidence hits by default?

                if (!confidenceThresholdPassed) {
                    if (reasonDoubtful == null) {
                        reasonDoubtful = "";
                    } else {
                        reasonDoubtful += ", ";
                    }
                    reasonDoubtful += "Low confidence";
                }

                boolean enoughHits = targetDecoyMap.getnTargetOnly() > 100;

                if (!enoughHits) {
                    if (reasonDoubtful == null) {
                        reasonDoubtful = "";
                    } else {
View Full Code Here

Examples of eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
        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();

            if (confidenceThreshold > 100) {
                confidenceThreshold = 100;
            }

            boolean noValidated = targetDecoyResults.noValidated();

            if (!noValidated && tagAssumption.getScore() <= seThreshold) { //@TODO: include ascending/descending scores

                String reasonDoubtful = null;
                boolean filterPassed = true;

                //TODO: implement tag quality filters
//                for (AssumptionFilter filter : inputMap.getDoubtfulMatchesFilters()) {
//                    boolean validated = filter.isValidated(spectrumKey, peptideAssumption, searchParameters, annotationPreferences);
//                    psParameter.setQcResult(filter.getName(), validated);
//                    if (!validated) {
//                        filterPassed = false;
//                        if (reasonDoubtful == null) {
//                            reasonDoubtful = "";
//                        } else {
//                            reasonDoubtful += ", ";
//                        }
//                        reasonDoubtful += filter.getDescription();
//                    }
//                }
                boolean confidenceThresholdPassed = psParameter.getSearchEngineConfidence() >= confidenceThreshold; //@TODO: not sure whether we should include all 100% confidence hits by default?

                if (!confidenceThresholdPassed) {
                    if (reasonDoubtful == null) {
                        reasonDoubtful = "";
                    } else {
                        reasonDoubtful += ", ";
                    }
                    reasonDoubtful += "Low confidence";
                }

                boolean enoughHits = targetDecoyMap.getnTargetOnly() > 100;

                if (!enoughHits) {
                    if (reasonDoubtful == null) {
                        reasonDoubtful = "";
                    } else {
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.