Package no.uib.jsparklines.renderers

Examples of no.uib.jsparklines.renderers.JSparklinesIntegerColorTableCellRenderer

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        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
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        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
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        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
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        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()));
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        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()));
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        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));
        }
    }
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        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;
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Related Classes of no.uib.jsparklines.renderers.JSparklinesIntegerColorTableCellRenderer

  • eu.isas.peptideshaker.gui.FindDialog
  • eu.isas.peptideshaker.gui.PtmSiteInferenceDialog
  • eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel
  • eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel
  • eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel
  • eu.isas.peptideshaker.gui.tabpanels.PtmPanel
  • eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel
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