Package no.uib.jsparklines.extra

Examples of no.uib.jsparklines.extra.HtmlLinksRenderer

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        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()));
        ((JSparklinesBarChartTableCellRenderer) spectrumTable.getColumn("m/z").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
        ((JSparklinesBarChartTableCellRenderer) spectrumTable.getColumn("Charge").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() - 30);
        ((JSparklinesBarChartTableCellRenderer) spectrumTable.getColumn("Int").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
        ((JSparklinesIntervalChartTableCellRenderer) spectrumTable.getColumn("RT").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() + 5);
        ((JSparklinesIntervalChartTableCellRenderer) spectrumTable.getColumn("RT").getCellRenderer()).showReferenceLine(true, 0.02, java.awt.Color.BLACK);

        spectrumTable.getColumn("Confidence").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) spectrumTable.getColumn("Confidence").getCellRenderer()).showNumberAndChart(
                true, TableProperties.getLabelWidth() - 20, peptideShakerGUI.getScoreAndConfidenceDecimalFormat());
        spectrumTable.getColumn("  ").setCellRenderer(new JSparklinesIntegerIconTableCellRenderer(MatchValidationLevel.getIconMap(this.getClass()), MatchValidationLevel.getTooltipMap()));
        spectrumTable.getColumn("Protein(s)").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));

        // set up the table header tooltips
        idSoftwareTableToolTips = new ArrayList<String>();
        idSoftwareTableToolTips.add(null);
        idSoftwareTableToolTips.add("Identification Software");
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        if (onePercentRadioButton.isSelected()) {
            significanceLevel = 0.01;
        }

        // cell renderers
        goMappingsTable.getColumn("GO Accession").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        goMappingsTable.getColumn("Frequency All (%)").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, Color.RED));
        ((JSparklinesBarChartTableCellRenderer) goMappingsTable.getColumn("Frequency All (%)").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
        goMappingsTable.getColumn("Frequency Dataset (%)").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) goMappingsTable.getColumn("Frequency Dataset (%)").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
        goMappingsTable.getColumn("p-value").setCellRenderer(
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        } else {
            proteinTable.getColumn("Accession").setMinWidth(15);
            proteinTable.getColumn("Accession").setMaxWidth(Integer.MAX_VALUE);
        }

        proteinTable.getColumn("Accession").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));

        // use a gray color for no decoy searches
        Color nonValidatedColor = peptideShakerGUI.getSparklineColorNonValidated();
        if (!sequenceFactory.concatenatedTargetDecoy()) {
            nonValidatedColor = peptideShakerGUI.getUtilitiesUserPreferences().getSparklineColorNotFound();
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        pdbChainsJTable.getTableHeader().setReorderingAllowed(false);

        pdbChainsJTable.setAutoCreateRowSorter(true);
        pdbMatchesJTable.setAutoCreateRowSorter(true);

        pdbMatchesJTable.getColumn("PDB").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        pdbMatchesJTable.getColumn("Chains").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 10.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) pdbMatchesJTable.getColumn("Chains").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());

        pdbChainsJTable.getColumn("Coverage").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) pdbChainsJTable.getColumn("Coverage").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
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        JPanel filesCorner = new JPanel();
        filesCorner.setBackground(filesTable.getTableHeader().getBackground());
        filesTableScrollPane.setCorner(ScrollPaneConstants.UPPER_RIGHT_CORNER, filesCorner);

        projectsTable.getColumn("Accession").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        assaysTable.getColumn("Accession").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        filesTable.getColumn("Assay").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        filesTable.getColumn("Download").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));

        filesTable.getColumn("  ").setCellRenderer(new TrueFalseIconRenderer(
                new ImageIcon(this.getClass().getResource("/icons/accept.png")),
                null,
                "Reshakeable", null));
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        searchSettingsTable.getColumn("Download").setMaxWidth(90);
        searchSettingsTable.getColumn("Download").setMinWidth(90);
        searchSettingsTable.getColumn("Size").setMaxWidth(90);
        searchSettingsTable.getColumn("Size").setMinWidth(90);

        spectrumTable.getColumn("Assay").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        searchSettingsTable.getColumn("Assay").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        spectrumTable.getColumn("Download").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        searchSettingsTable.getColumn("Download").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));

        spectrumTable.getColumn("  ").setCellRenderer(new NimbusCheckBoxRenderer());
        searchSettingsTable.getColumn("  ").setCellRenderer(new NimbusCheckBoxRenderer());

        // correct the color for the upper right corner
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        ArrayList<Color> sparklineColors = new ArrayList<Color>();
        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"));
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        proteinsJScrollPane.getViewport().setOpaque(false);
        otherProteinsJScrollPane.getViewport().setOpaque(false);

        // set up the table properties
        otherProteinJTable.getTableHeader().setReorderingAllowed(false);
        otherProteinJTable.getColumn("Accession").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));

        retainedProteinJTable.getTableHeader().setReorderingAllowed(false);
        retainedProteinJTable.getColumn("Accession").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));

        // insert the values
        sequenceLabel.setText(peptideShakerGUI.getDisplayFeaturesGenerator().getTaggedPeptideSequence(peptideMatch, true, true, true));

        // set the modification tooltip
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        relatedHitsTable.getColumn("Score").setMinWidth(90);

        // change the cell renderer to fix a problem in Nimbus and alternating row colors
        proteinMatchTable.getColumn("  ").setCellRenderer(new NimbusCheckBoxRenderer());

        proteinMatchTable.getColumn("Accession").setCellRenderer(new HtmlLinksRenderer(
                TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        proteinMatchTable.getColumn("Chr").setCellRenderer(new ChromosomeTableCellRenderer());
        proteinMatchTable.getColumn("Enz").setCellRenderer(new TrueFalseIconRenderer(
                new ImageIcon(this.getClass().getResource("/icons/selected_green.png")),
                null,
                "Enzymatic", "Not Enzymatic"));

        uniqueHitsTable.getColumn("Protein(s)").setCellRenderer(new HtmlLinksRenderer(
                TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        uniqueHitsTable.getColumn(" ").setCellRenderer(new JSparklinesIntegerIconTableCellRenderer(MatchValidationLevel.getIconMap(this.getClass()), MatchValidationLevel.getTooltipMap()));
        uniqueHitsTable.getColumn("Score").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        uniqueHitsTable.getColumn("Confidence").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) uniqueHitsTable.getColumn("Score").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() + 5);
        ((JSparklinesBarChartTableCellRenderer) uniqueHitsTable.getColumn("Confidence").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() + 5);

        relatedHitsTable.getColumn("Protein(s)").setCellRenderer(new HtmlLinksRenderer(
                TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));
        relatedHitsTable.getColumn(" ").setCellRenderer(new JSparklinesIntegerIconTableCellRenderer(MatchValidationLevel.getIconMap(this.getClass()), MatchValidationLevel.getTooltipMap()));
        relatedHitsTable.getColumn("Score").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        relatedHitsTable.getColumn("Confidence").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) relatedHitsTable.getColumn("Score").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() + 5);
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        proteinInferenceTooltipMap.put(PSParameter.NOT_GROUP, "Single Protein");
        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()) {
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Related Classes of no.uib.jsparklines.extra.HtmlLinksRenderer

  • eu.isas.peptideshaker.gui.pride.PrideReshakeGUI
  • eu.isas.peptideshaker.gui.pride.PrideReshakeSetupDialog
  • eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceDialog
  • eu.isas.peptideshaker.gui.protein_inference.ProteinInferencePeptideLevelDialog
  • eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel
  • eu.isas.peptideshaker.gui.tabpanels.GOEAPanel
  • eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel
  • eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel
  • eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel
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