Package eu.isas.peptideshaker.myparameters

Examples of eu.isas.peptideshaker.myparameters.PSPtmScores

1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
     */
    public String getConfidentPtmSitesNumber(String proteinKey)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);

        StringBuilder result = new StringBuilder();
        boolean firstPtm = true;
        ArrayList<String> ptms = psPtmScores.getConfidentlyLocalizedPtms();
        Collections.sort(ptms);

        for (String ptm : ptms) {
            if (firstPtm) {
                firstPtm = false;
            } else {
                result.append("; ");
            }
            result.append(ptm);
            result.append("(");
            result.append(psPtmScores.getConfidentSitesForPtm(ptm).size());
            result.append(")");
        }

        return result.toString();
    }
View Full Code Here
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
     */
    public String getConfidentPtmSitesNumber(String proteinKey, ArrayList<String> targetedPtms)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);

        ArrayList<Integer> sites = new ArrayList<Integer>();
        for (String ptm : targetedPtms) {
            for (Integer site : psPtmScores.getConfidentSitesForPtm(ptm)) {
                if (!sites.contains(site)) {
                    sites.add(site);
                }
            }
        }
View Full Code Here
1600
1601
1602
1603
1604
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
1615
1616
1617
1618
1619
1620
    public String getAmbiguousPtmSites(String proteinKey)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        String sequence = sequenceFactory.getProtein(proteinMatch.getMainMatch()).getSequence();
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);
        StringBuilder result = new StringBuilder();
        ArrayList<String> ptms = psPtmScores.getAmbiguouslyLocalizedPtms();
        Collections.sort(ptms);
        for (String ptmName : ptms) {
            if (result.length() > 0) {
                result.append(", ");
            }
            result.append(ptmName).append(" (");
            HashMap<Integer, ArrayList<Integer>> sites = psPtmScores.getAmbiguousModificationsSites(ptmName);
            ArrayList<Integer> representativeSites = new ArrayList<Integer>(sites.keySet());
            Collections.sort(representativeSites);
            boolean firstRepresentativeSite = true;
            for (int representativeSite : representativeSites) {
                if (firstRepresentativeSite) {
View Full Code Here
1665
1666
1667
1668
1669
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
    public String getAmbiguousPtmSites(String proteinKey, ArrayList<String> targetedPtms)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        String sequence = sequenceFactory.getProtein(proteinMatch.getMainMatch()).getSequence();
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);
        HashMap<Integer, ArrayList<String>> reportPerSite = new HashMap<Integer, ArrayList<String>>();

        for (String ptmName : targetedPtms) {

            HashMap<Integer, ArrayList<Integer>> sites = psPtmScores.getAmbiguousModificationsSites(ptmName);
            ArrayList<Integer> representativeSites = new ArrayList<Integer>(sites.keySet());
            Collections.sort(representativeSites);

            for (int representativeSite : representativeSites) {
View Full Code Here
1749
1750
1751
1752
1753
1754
1755
1756
1757
1758
1759
1760
1761
1762
1763
1764
1765
1766
1767
1768
     */
    public String getAmbiguousPtmSiteNumber(String proteinKey)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);
        StringBuilder result = new StringBuilder();
        ArrayList<String> ptms = psPtmScores.getAmbiguouslyLocalizedPtms();
        Collections.sort(ptms);

        for (String ptmName : ptms) {
            if (result.length() > 0) {
                result.append(", ");
            }
            result.append(ptmName).append(" (").append(psPtmScores.getAmbiguousModificationsSites(ptmName).size()).append(")");
        }

        return result.toString();
    }
View Full Code Here
1786
1787
1788
1789
1790
1791
1792
1793
1794
1795
1796
1797
1798
1799
1800
1801
     */
    public String getAmbiguousPtmSiteNumber(String proteinKey, ArrayList<String> targetedPtms)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);
        ArrayList<Integer> sites = new ArrayList<Integer>();

        for (String ptmName : targetedPtms) {
            HashMap<Integer, ArrayList<Integer>> ptmAmbiguousSites = psPtmScores.getAmbiguousModificationsSites(ptmName);
            for (int site : ptmAmbiguousSites.keySet()) {
                if (!sites.contains(site)) {
                    sites.add(site);
                }
            }
View Full Code Here
1817
1818
1819
1820
1821
1822
1823
1824
1825
1826
1827
1828
1829
1830
1831
1832
1833
1834
1835
1836
     */
    public String getModifiedSequence(String proteinKey) throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException {

        ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
        String sequence = sequenceFactory.getProtein(proteinMatch.getMainMatch()).getSequence();
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);
        StringBuilder result = new StringBuilder();

        for (int aa = 0; aa < sequence.length(); aa++) {
            result.append(sequence.charAt(aa));
            if (!psPtmScores.getConfidentModificationsAt(aa).isEmpty()) {
                boolean first = true;
                result.append("<");
                for (String ptm : psPtmScores.getConfidentModificationsAt(aa)) {
                    if (first) {
                        first = false;
                    } else {
                        result.append(", ");
                    }
View Full Code Here
4164
4165
4166
4167
4168
4169
4170
4171
4172
4173
4174
4175
4176
4177
4178
4179
4180
4181
4182
4183
4184
4185
4186
4187
4188
4189
4190
4191
4192
4193
4194
4195
4196
4197
4198
4199
4200
4201
4202
4203
4204
4205
4206
4207
4208
4209
4210
4211
4212
4213
4214
4215
4216
4217
4218
4219
4220
4221
4222
                ArrayList<Double> data = new ArrayList<Double>();
                data.add(new Double(1));
                JSparklinesDataSeries sparklineDataseriesPtm = new JSparklinesDataSeries(data, new Color(0, 0, 0, 0), null);
                sparkLineDataSeriesPtm.add(sparklineDataseriesPtm);

                PSPtmScores psPtmScores = new PSPtmScores();
                ProteinMatch proteinMatch = peptideShakerGUI.getIdentification().getProteinMatch(proteinKey);

                String sequence = sequenceFactory.getProtein(proteinMatch.getMainMatch()).getSequence();
                psPtmScores = (PSPtmScores) proteinMatch.getUrParam(psPtmScores);
                int unmodifiedCounter = 0;

                // get the fixed ptms
                HashMap<Integer, String> fixedPtms = new HashMap<Integer, String>(); // @TODO: note this this only supports one fixed ptm per residue

                Identification identification = peptideShakerGUI.getIdentification();
                identification.loadPeptideMatches(peptideKeys, null);
                DisplayPreferences displayPreferences = peptideShakerGUI.getDisplayPreferences();

                for (String peptideKey : peptideKeys) {
                    boolean modified = false;
                    for (String ptmName : displayPreferences.getDisplayedPtms()) {
                        if (Peptide.isModified(peptideKey, ptmName)) {
                            modified = true;
                            break;
                        }
                    }
                    if (modified) {
                        PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);
                        for (ModificationMatch modMatch : peptideMatch.getTheoreticPeptide().getModificationMatches()) {
                            if (!modMatch.isVariable()) {
                                String ptmName = modMatch.getTheoreticPtm();
                                if (displayPreferences.isDisplayedPTM(ptmName)) {
                                    ArrayList<Integer> indexes = sequenceFactory.getProtein(proteinAccession).getPeptideStart(Peptide.getSequence(peptideKey),
                                            peptideShakerGUI.getSequenceMatchingPreferences());
                                    for (Integer index : indexes) {
                                        fixedPtms.put(modMatch.getModificationSite() + index - 2, ptmName);
                                    }
                                }
                            }
                        }
                    }
                }

                for (int aa = 0; aa < sequence.length(); aa++) {

                    String ptmName = fixedPtms.get(aa);
                    for (String variablePTM : psPtmScores.getPtmsAtRepresentativeSite(aa)) {
                        if (displayPreferences.isDisplayedPTM(variablePTM)) {
                            ptmName = variablePTM;
                            break;
                        }
                    }
                    for (String variablePTM : psPtmScores.getConfidentModificationsAt(aa)) {
                        if (displayPreferences.isDisplayedPTM(variablePTM)) {
                            ptmName = variablePTM;
                            break;
                        }
                    }
View Full Code Here
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
            ClassNotFoundException, InterruptedException, MzMLUnmarshallerException {

        switch (psmFeature) {
            case probabilistic_score:
                if (spectrumMatch.getBestPeptideAssumption() != null) {
                    PSPtmScores ptmScores = new PSPtmScores();
                    ptmScores = (PSPtmScores) spectrumMatch.getUrParam(ptmScores);
                    if (ptmScores != null) {
                        StringBuilder result = new StringBuilder();
                        ArrayList<String> modList = new ArrayList<String>(ptmScores.getScoredPTMs());
                        Collections.sort(modList);
                        for (String mod : modList) {
                            PtmScoring ptmScoring = ptmScores.getPtmScoring(mod);
                            ArrayList<Integer> sites = new ArrayList<Integer>(ptmScoring.getProbabilisticSites());
                            if (!sites.isEmpty()) {
                                Collections.sort(sites);
                                if (result.length() > 0) {
                                    result.append(", ");
                                }
                                result.append(mod).append(" (");
                                boolean firstSite = true;
                                for (int site : sites) {
                                    if (firstSite) {
                                        firstSite = false;
                                    } else {
                                        result.append(", ");
                                    }
                                    result.append(site).append(": ").append(ptmScoring.getProbabilisticScore(site));
                                }
                                result.append(")");
                            }
                        }
                        return result.toString();
                    }
                }
                return "";
            case d_score:
                if (spectrumMatch.getBestPeptideAssumption() != null) {
                    StringBuilder result = new StringBuilder();
                    PSPtmScores ptmScores = new PSPtmScores();
                    ptmScores = (PSPtmScores) spectrumMatch.getUrParam(ptmScores);
                    if (ptmScores != null) {
                        ArrayList<String> modList = new ArrayList<String>(ptmScores.getScoredPTMs());
                        Collections.sort(modList);
                        for (String mod : modList) {
                            PtmScoring ptmScoring = ptmScores.getPtmScoring(mod);
                            ArrayList<Integer> sites = new ArrayList<Integer>(ptmScoring.getDSites());
                            if (!sites.isEmpty()) {
                                Collections.sort(sites);
                                if (result.length() > 0) {
                                    result.append(", ");
                                }
                                result.append(mod).append(" (");
                                boolean firstSite = true;
                                for (int site : sites) {
                                    if (firstSite) {
                                        firstSite = false;
                                    } else {
                                        result.append(", ");
                                    }
                                    result.append(site).append(": ").append(ptmScoring.getDeltaScore(site));
                                }
                                result.append(")");
                            }
                        }
                    }
                    return result.toString();
                }
                return "";
            case localization_confidence:
                if (spectrumMatch.getBestPeptideAssumption() != null) {
                    PSPtmScores ptmScores = new PSPtmScores();
                    ptmScores = (PSPtmScores) spectrumMatch.getUrParam(ptmScores);
                    if (ptmScores != null) {
                        StringBuilder result = new StringBuilder();
                        ArrayList<String> modList = ptmScores.getScoredPTMs();
                        Collections.sort(modList);
                        for (String mod : modList) {

                            PTM ptm = PTMFactory.getInstance().getPTM(mod);

                            if (ptm.getType() == PTM.MODAA) {

                                if (result.length() > 0) {
                                    result.append(", ");
                                }
                                result.append(mod);

                                result.append(" (");
                                PtmScoring ptmScoring = ptmScores.getPtmScoring(mod);
                                boolean firstSite = true;

                                ArrayList<Integer> sites = ptmScoring.getOrderedPtmLocations();
                                if (sites.isEmpty()) {
                                    result.append("Not Scored");
View Full Code Here
90
91
92
93
94
95
96
97
98
99
100
        double ptmMass = ptm.getMass();

        try {
            peptideMatch = peptideShakerGUI.getIdentification().getPeptideMatch(peptideKey);
            Peptide peptide = peptideMatch.getTheoreticPeptide();
            peptidePtmScore = (PSPtmScores) peptideMatch.getUrParam(new PSPtmScores());
            if (peptidePtmScore != null) {

                mainSelection = new boolean[peptide.getSequence().length()];
                for (String ptmName : peptidePtmScore.getConfidentlyLocalizedPtms()) {
                    PTM tempPTM = ptmFactory.getPTM(ptmName);
View Full Code Here
TOP

Related Classes of eu.isas.peptideshaker.myparameters.PSPtmScores

  • com.compomics.util.experiment.biology.PTM
  • com.compomics.util.experiment.biology.PTMFactory
  • eu.isas.peptideshaker.export.MzIdentMLExport
  • eu.isas.peptideshaker.export.OutputGenerator
  • eu.isas.peptideshaker.export.PrideXmlExport
  • eu.isas.peptideshaker.export.sections.PsPeptideSection
  • eu.isas.peptideshaker.export.sections.PsPsmSection
  • eu.isas.peptideshaker.gui.PtmSiteInferenceDialog
  • eu.isas.peptideshaker.gui.PtmSiteInferenceDialog$PtmTable
  • eu.isas.peptideshaker.gui.tabpanels.OverviewPanel
    • Copyright © 2018 www.massapicom. 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.