Examples of JSparklinesIntegerColorTableCellRenderer

Examples of no.uib.jsparklines.renderers.JSparklinesIntegerColorTableCellRenderer

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
        idSoftwareTooltipMap.put(AGREEMENT_WITH_MODS, "ID Software Agree");
        idSoftwareTooltipMap.put(AGREEMENT, "ID Software Agree - PTM Certainty Issues");
        idSoftwareTooltipMap.put(CONFLICT, "ID Software Disagree");
        idSoftwareTooltipMap.put(PARTIALLY_MISSING, "First Hit(s) Missing");

        peptideShakerJTable.getColumn("ID").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(java.awt.Color.lightGray, softwareAgreementColorMap, idSoftwareTooltipMap));
        peptideShakerJTable.getColumn("Protein(s)").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        peptideShakerJTable.getColumn("Confidence").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100d, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) peptideShakerJTable.getColumn("Confidence").getCellRenderer()).showNumberAndChart(
                true, TableProperties.getLabelWidth() - 20, peptideShakerGUI.getScoreAndConfidenceDecimalFormat());

        searchResultsTable.getColumn("SE").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(java.awt.Color.lightGray, Advocate.getAdvocateColorMap(), Advocate.getAdvocateToolTipMap()));

        searchResultsTable.getColumn("Confidence").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100d, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) searchResultsTable.getColumn("Confidence").getCellRenderer()).showNumberAndChart(
                true, TableProperties.getLabelWidth() - 20, peptideShakerGUI.getScoreAndConfidenceDecimalFormat());
        searchResultsTable.getColumn("Charge").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 10d, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) searchResultsTable.getColumn("Charge").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() - 30);

        // set up the psm color map
        HashMap<Integer, java.awt.Color> idSoftwareSpectrumLevelColorMap = new HashMap<Integer, java.awt.Color>();
        idSoftwareSpectrumLevelColorMap.put(AGREEMENT_WITH_MODS, peptideShakerGUI.getSparklineColor()); // id softwares agree with PTM certainty
        idSoftwareSpectrumLevelColorMap.put(AGREEMENT, java.awt.Color.CYAN); // id softwares agree on peptide but not ptm certainty
        idSoftwareSpectrumLevelColorMap.put(CONFLICT, java.awt.Color.YELLOW); // id softwares don't agree
        idSoftwareSpectrumLevelColorMap.put(PARTIALLY_MISSING, java.awt.Color.ORANGE); // some id softwares id'ed some didn't
        idSoftwareSpectrumLevelColorMap.put(NO_ID, java.awt.Color.lightGray); // no psm

        // set up the psm tooltip map
        HashMap<Integer, String> idSoftwareSpectrumLevelTooltipMap = new HashMap<Integer, String>();
        idSoftwareSpectrumLevelTooltipMap.put(AGREEMENT_WITH_MODS, "ID Software Agree");
        idSoftwareSpectrumLevelTooltipMap.put(AGREEMENT, "ID Software Agree - PTM Certainty Issues");
        idSoftwareSpectrumLevelTooltipMap.put(CONFLICT, "ID Software Disagree");
        idSoftwareSpectrumLevelTooltipMap.put(PARTIALLY_MISSING, "ID Software(s) Missing");
        idSoftwareSpectrumLevelTooltipMap.put(NO_ID, "(No PSM)");

        spectrumTable.getColumn("ID").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(java.awt.Color.lightGray, idSoftwareSpectrumLevelColorMap, idSoftwareSpectrumLevelTooltipMap));
        spectrumTable.getColumn("m/z").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100d, peptideShakerGUI.getSparklineColor()));
        spectrumTable.getColumn("Charge").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 4d, peptideShakerGUI.getSparklineColor()));
        spectrumTable.getColumn("Int").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 1000d, peptideShakerGUI.getSparklineColor()));
        spectrumTable.getColumn("RT").setCellRenderer(new JSparklinesIntervalChartTableCellRenderer(PlotOrientation.HORIZONTAL, 0d,
                1000d, 10d, peptideShakerGUI.getSparklineColor(), peptideShakerGUI.getSparklineColor()));
View Full Code Here

Examples of no.uib.jsparklines.renderers.JSparklinesIntegerColorTableCellRenderer

341
342
343
344
345
346
347
348
349
350
351
        peptideInferenceTooltipMap.put(PSParameter.NOT_GROUP, "Unique to a single protein");
        peptideInferenceTooltipMap.put(PSParameter.RELATED, "Belongs to a group of related proteins");
        peptideInferenceTooltipMap.put(PSParameter.RELATED_AND_UNRELATED, "Belongs to a group of related and unrelated proteins");
        peptideInferenceTooltipMap.put(PSParameter.UNRELATED, "Belongs to unrelated proteins");

        peptideTable.getColumn("PI").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(peptideShakerGUI.getSparklineColor(), peptideInferenceColorMap, peptideInferenceTooltipMap));
        peptideTable.getColumn("Start").setCellRenderer(new JSparklinesIntervalChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100d, 100d, peptideShakerGUI.getSparklineColor()));
        peptideTable.getColumn("PDB").setCellRenderer(new TrueFalseIconRenderer(
                new ImageIcon(this.getClass().getResource("/icons/pdb.png")),
                null,
                "Mapped to PDB Structure", null));
View Full Code Here

Examples of no.uib.jsparklines.renderers.JSparklinesIntegerColorTableCellRenderer

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
385
386
387
388
389
390
391
392
        proteinInferenceTooltipMap.put(PSParameter.NOT_GROUP, "Unique to a single protein");
        proteinInferenceTooltipMap.put(PSParameter.RELATED, "Belongs to a group of related proteins");
        proteinInferenceTooltipMap.put(PSParameter.RELATED_AND_UNRELATED, "Belongs to a group of related and unrelated proteins");
        proteinInferenceTooltipMap.put(PSParameter.UNRELATED, "Belongs to unrelated proteins");

        peptidesTable.getColumn("PI").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(Color.lightGray, proteinInferenceColorMap, proteinInferenceTooltipMap));
        relatedPeptidesTable.getColumn("PI").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(Color.lightGray, proteinInferenceColorMap, proteinInferenceTooltipMap));
        peptidesTable.getColumn("   ").setCellRenderer(new TrueFalseIconRenderer(
                new ImageIcon(this.getClass().getResource("/icons/star_yellow.png")),
                new ImageIcon(this.getClass().getResource("/icons/star_grey.png")),
                new ImageIcon(this.getClass().getResource("/icons/star_grey.png")),
                "Starred", null, null));
        relatedPeptidesTable.getColumn("   ").setCellRenderer(new TrueFalseIconRenderer(
                new ImageIcon(this.getClass().getResource("/icons/star_yellow.png")),
                new ImageIcon(this.getClass().getResource("/icons/star_grey.png")),
                new ImageIcon(this.getClass().getResource("/icons/star_grey.png")),
                "Starred", null, null));

        // set up the PTM confidence color map
        HashMap<Integer, Color> ptmConfidenceColorMap = new HashMap<Integer, Color>();
        ptmConfidenceColorMap.put(PtmScoring.NOT_FOUND, Color.lightGray);
        ptmConfidenceColorMap.put(PtmScoring.RANDOM, Color.RED);
        ptmConfidenceColorMap.put(PtmScoring.DOUBTFUL, Color.ORANGE);
        ptmConfidenceColorMap.put(PtmScoring.CONFIDENT, Color.YELLOW);
        ptmConfidenceColorMap.put(PtmScoring.VERY_CONFIDENT, peptideShakerGUI.getSparklineColor());

        // set up the PTM confidence tooltip map
        ptmConfidenceTooltipMap = new HashMap<Integer, String>();
        ptmConfidenceTooltipMap.put(-1, "(No PTMs)");
        ptmConfidenceTooltipMap.put(PtmScoring.RANDOM, "Random Assignment");
        ptmConfidenceTooltipMap.put(PtmScoring.DOUBTFUL, "Doubtful Assignment");
        ptmConfidenceTooltipMap.put(PtmScoring.CONFIDENT, "Confident Assignment");
        ptmConfidenceTooltipMap.put(PtmScoring.VERY_CONFIDENT, "Very Confident Assignment");

        peptidesTable.getColumn("PTM").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(Color.lightGray, ptmConfidenceColorMap, ptmConfidenceTooltipMap));
        relatedPeptidesTable.getColumn("PTM").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(Color.lightGray, ptmConfidenceColorMap, ptmConfidenceTooltipMap));
        selectedPsmsTable.getColumn("PTM").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(Color.lightGray, ptmConfidenceColorMap, ptmConfidenceTooltipMap));
        relatedPsmsTable.getColumn("PTM").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(Color.lightGray, ptmConfidenceColorMap, ptmConfidenceTooltipMap));

        peptidesTable.getColumn("Peptide").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) peptidesTable.getColumn("Peptide").getCellRenderer()).showNumberAndChart(
                true, TableProperties.getLabelWidth() - 20, peptideShakerGUI.getScoreAndConfidenceDecimalFormat());
        peptidesTable.getColumn("  ").setCellRenderer(new JSparklinesIntegerIconTableCellRenderer(MatchValidationLevel.getIconMap(this.getClass()), MatchValidationLevel.getTooltipMap()));
View Full Code Here

Examples of no.uib.jsparklines.renderers.JSparklinesIntegerColorTableCellRenderer

410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
        proteinInferenceTooltipMap.put(PSParameter.RELATED, "Related Proteins");
        proteinInferenceTooltipMap.put(PSParameter.RELATED_AND_UNRELATED, "Related and Unrelated Proteins");
        proteinInferenceTooltipMap.put(PSParameter.UNRELATED, "Unrelated Proteins");

        //proteinTable.getColumn("Accession").setCellRenderer(new HtmlLinksRenderer(peptideShakerGUI.getSelectedRowHtmlTagFontColor(), peptideShakerGUI.getNotSelectedRowHtmlTagFontColor()));
        proteinTable.getColumn("PI").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(peptideShakerGUI.getSparklineColor(), proteinInferenceColorMap, proteinInferenceTooltipMap));
        proteinTable.getColumn("#Peptides").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 10.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("#Peptides").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
        proteinTable.getColumn("#Spectra").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 10.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("#Spectra").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
        proteinTable.getColumn("MS2 Quant.").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 10.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("MS2 Quant.").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
        proteinTable.getColumn("Confidence").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("Confidence").getCellRenderer()).showNumberAndChart(
                true, TableProperties.getLabelWidth() - 20, peptideShakerGUI.getScoreAndConfidenceDecimalFormat());
        proteinTable.getColumn("Score").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("Score").getCellRenderer()).showNumberAndChart(
                true, TableProperties.getLabelWidth() - 20, peptideShakerGUI.getScoreAndConfidenceDecimalFormat());
        proteinTable.getColumn("Coverage").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("Coverage").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
        ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("Coverage").getCellRenderer()).setMinimumChartValue(5d);
        proteinTable.getColumn("S").setCellRenderer(new TrueFalseIconRenderer(
                new ImageIcon(this.getClass().getResource("/icons/star_yellow.png")),
                new ImageIcon(this.getClass().getResource("/icons/star_grey.png")),
                new ImageIcon(this.getClass().getResource("/icons/star_grey.png")),
                "Starred", null, null));
        proteinTable.getColumn("H").setCellRenderer(new NimbusCheckBoxRenderer());

        ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("#Peptides").getCellRenderer()).setMaxValue(peptideShakerGUI.getMetrics().getMaxNPeptides());
        ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("#Spectra").getCellRenderer()).setMaxValue(peptideShakerGUI.getMetrics().getMaxNSpectra());
        ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("MS2 Quant.").getCellRenderer()).setMaxValue(peptideShakerGUI.getMetrics().getMaxSpectrumCounting());

        // set up the peptide inference color map
        HashMap<Integer, Color> peptideInferenceColorMap = new HashMap<Integer, Color>();
        peptideInferenceColorMap.put(PSParameter.NOT_GROUP, peptideShakerGUI.getSparklineColor());
        peptideInferenceColorMap.put(PSParameter.RELATED, Color.YELLOW);
        peptideInferenceColorMap.put(PSParameter.RELATED_AND_UNRELATED, Color.ORANGE);
        peptideInferenceColorMap.put(PSParameter.UNRELATED, Color.RED);

        // set up the peptide inference tooltip map
        HashMap<Integer, String> peptideInferenceTooltipMap = new HashMap<Integer, String>();
        peptideInferenceTooltipMap.put(PSParameter.NOT_GROUP, "Unique to a single protein");
        peptideInferenceTooltipMap.put(PSParameter.RELATED, "Belongs to a group of related proteins");
        peptideInferenceTooltipMap.put(PSParameter.RELATED_AND_UNRELATED, "Belongs to a group of related and unrelated proteins");
        peptideInferenceTooltipMap.put(PSParameter.UNRELATED, "Belongs to unrelated proteins");

        peptideTable.getColumn("PI").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(peptideShakerGUI.getSparklineColor(), peptideInferenceColorMap, peptideInferenceTooltipMap));
        peptideTable.getColumn("Confidence").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        peptideTable.getColumn("#Spectra").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) peptideTable.getColumn("Confidence").getCellRenderer()).showNumberAndChart(
                true, TableProperties.getLabelWidth() - 20, peptideShakerGUI.getScoreAndConfidenceDecimalFormat());
        peptideTable.getColumn("Score").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
View Full Code Here

Examples of no.uib.jsparklines.renderers.JSparklinesIntegerColorTableCellRenderer

255
256
257
258
259
260
261
262
263
264
265
        sparklineColors.add(peptideShakerGUI.getSparklineColor());
        sparklineColors.add(peptideShakerGUI.getUtilitiesUserPreferences().getSparklineColorDoubtful());
        sparklineColors.add(nonValidatedColor);

        proteinTable.getColumn("Accession").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        proteinTable.getColumn("PI").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(peptideShakerGUI.getSparklineColor(), proteinInferenceColorMap, proteinInferenceTooltipMap));
        proteinTable.getColumn("#Peptides").setCellRenderer(new JSparklinesArrayListBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, sparklineColors, JSparklinesArrayListBarChartTableCellRenderer.ValueDisplayType.sumOfNumbers));
        ((JSparklinesArrayListBarChartTableCellRenderer) proteinTable.getColumn("#Peptides").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth(), new DecimalFormat("0"));
        proteinTable.getColumn("#Spectra").setCellRenderer(new JSparklinesArrayListBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, sparklineColors, JSparklinesArrayListBarChartTableCellRenderer.ValueDisplayType.sumOfNumbers));
        ((JSparklinesArrayListBarChartTableCellRenderer) proteinTable.getColumn("#Spectra").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth(), new DecimalFormat("0"));
        proteinTable.getColumn("MS2 Quant.").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 10.0, peptideShakerGUI.getSparklineColor()));
View Full Code Here

Examples of no.uib.jsparklines.renderers.JSparklinesIntegerColorTableCellRenderer

192
193
194
195
196
197
198
199
        ptmConfidenceTooltipMap.put(PtmScoring.CONFIDENT, "Confident Assignment");
        ptmConfidenceTooltipMap.put(PtmScoring.VERY_CONFIDENT, "Very Confident Assignment");

        for (int i = 1; i < ptmsTable.getColumnCount(); i++) {
            ptmsTable.getColumn(ptmsTable.getColumnName(i)).setCellRenderer(
                    new JSparklinesIntegerColorTableCellRenderer(peptideShakerGUI.getSparklineColor(), ptmConfidenceColorMap, ptmConfidenceTooltipMap));
        }
    }
View Full Code Here

Examples of no.uib.jsparklines.renderers.JSparklinesIntegerColorTableCellRenderer

611
612
613
614
615
616
617
618
619
620
621
        proteinInferenceTooltipMap.put(PSParameter.RELATED, "Related Proteins");
        proteinInferenceTooltipMap.put(PSParameter.RELATED_AND_UNRELATED, "Related and Unrelated Proteins");
        proteinInferenceTooltipMap.put(PSParameter.UNRELATED, "Unrelated Proteins");

        proteinTable.getColumn("Accession").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        proteinTable.getColumn("PI").setCellRenderer(new JSparklinesIntegerColorTableCellRenderer(sparklineColor, proteinInferenceColorMap, proteinInferenceTooltipMap));

        // use a gray color for no decoy searches
        Color nonValidatedColor = sparklineColorNotValidated;
        if (!SequenceFactory.getInstance().isClosed() && !SequenceFactory.getInstance().concatenatedTargetDecoy()) {
            nonValidatedColor = sparklineColorNotFound;
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.