Package no.uib.jsparklines.extra

Examples of no.uib.jsparklines.extra.NimbusCheckBoxRenderer

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        hiddenPeptidesScrollPane.getViewport().setOpaque(false);
        starredPsmsScrollPane.getViewport().setOpaque(false);
        hiddenPsmsScrollPane.getViewport().setOpaque(false);

        // cell renderer
        starredProteinsTable.getColumn(" ").setCellRenderer(new NimbusCheckBoxRenderer());
        hiddenProteinsTable.getColumn(" ").setCellRenderer(new NimbusCheckBoxRenderer());
        starredPeptidesTable.getColumn(" ").setCellRenderer(new NimbusCheckBoxRenderer());
        hiddenPeptidesTable.getColumn(" ").setCellRenderer(new NimbusCheckBoxRenderer());
        starredPsmTable.getColumn(" ").setCellRenderer(new NimbusCheckBoxRenderer());
        hiddenPsmTable.getColumn(" ").setCellRenderer(new NimbusCheckBoxRenderer());
    }
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        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()));
        ((JSparklinesBarChartTableCellRenderer) peptideTable.getColumn("Score").getCellRenderer()).showNumberAndChart(
                true, TableProperties.getLabelWidth() - 20, peptideShakerGUI.getScoreAndConfidenceDecimalFormat());
        ((JSparklinesBarChartTableCellRenderer) peptideTable.getColumn("#Spectra").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() + 5);
        peptideTable.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));
        peptideTable.getColumn("H").setCellRenderer(new NimbusCheckBoxRenderer());

        ((JSparklinesBarChartTableCellRenderer) peptideTable.getColumn("#Spectra").getCellRenderer()).setMaxValue(peptideShakerGUI.getMetrics().getMaxNSpectra()); // @TODO: this is not the correct max value

        psmTable.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));
        psmTable.getColumn("H").setCellRenderer(new NimbusCheckBoxRenderer());
        psmTable.getColumn("m/z").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, SpectrumFactory.getInstance().getMaxMz(), peptideShakerGUI.getSparklineColor()));
        psmTable.getColumn("Charge").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL,
                (double) ((PSMaps) peptideShakerGUI.getIdentification().getUrParam(new PSMaps())).getPsmSpecificMap().getMaxCharge(), peptideShakerGUI.getSparklineColor()));
        psmTable.getColumn("RT").setCellRenderer(new JSparklinesIntervalChartTableCellRenderer(PlotOrientation.HORIZONTAL, SpectrumFactory.getInstance().getMinRT(),
                SpectrumFactory.getInstance().getMaxRT(), SpectrumFactory.getInstance().getMaxRT() / 50, peptideShakerGUI.getSparklineColor(), peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) psmTable.getColumn("m/z").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
        ((JSparklinesBarChartTableCellRenderer) psmTable.getColumn("Charge").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
        ((JSparklinesIntervalChartTableCellRenderer) psmTable.getColumn("RT").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() + 5);
        ((JSparklinesIntervalChartTableCellRenderer) psmTable.getColumn("RT").getCellRenderer()).showReferenceLine(true, 0.02, java.awt.Color.BLACK);
        psmTable.getColumn("Mass Error").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL,
                peptideShakerGUI.getSearchParameters().getPrecursorAccuracy(), peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) psmTable.getColumn("Mass Error").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() + 5);
        ((JSparklinesBarChartTableCellRenderer) psmTable.getColumn("Mass Error").getCellRenderer()).setMaxValue(
                peptideShakerGUI.getSearchParameters().getPrecursorAccuracy());
        psmTable.getColumn("Confidence").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) psmTable.getColumn("Confidence").getCellRenderer()).showNumberAndChart(
                true, TableProperties.getLabelWidth() - 20, peptideShakerGUI.getScoreAndConfidenceDecimalFormat());

        spectrumFilesTable.getColumn(" ").setCellRenderer(new NimbusCheckBoxRenderer());
        modificationTable.getColumn(" ").setCellRenderer(new NimbusCheckBoxRenderer());
        modificationTable.getColumn("  ").setCellRenderer(new JSparklinesColorTableCellRenderer());
    }
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        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
        JPanel spectrumCorner = new JPanel();
        spectrumCorner.setBackground(spectrumTable.getTableHeader().getBackground());
        spectrumTableScrollPane.setCorner(ScrollPaneConstants.UPPER_RIGHT_CORNER, spectrumCorner);
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        neutralLossesTable.getColumn(" ").setMaxWidth(50);
        neutralLossesTable.getColumn(" ").setMinWidth(50);
        neutralLossesTable.getColumn("  ").setMaxWidth(30);
        neutralLossesTable.getColumn("  ").setMinWidth(30);

        chargesTable.getColumn("  ").setCellRenderer(new NimbusCheckBoxRenderer());
        neutralLossesTable.getColumn("  ").setCellRenderer(new NimbusCheckBoxRenderer());

        chargesTable.getColumn("  ").setCellRenderer(new TrueFalseIconRenderer(
                new ImageIcon(this.getClass().getResource("/icons/selected_green.png")),
                null,
                "Selected", null));
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        // cell renderers
        ptmSiteTable.getColumn("").setCellRenderer(new AlignedTableCellRenderer(SwingConstants.CENTER, Color.LIGHT_GRAY));

        for (int i = 1; i < ptmSiteTable.getColumnCount(); i++) {
            ptmSiteTable.getColumn(ptmSiteTable.getColumnName(i)).setCellRenderer(new NimbusCheckBoxRenderer());
        }

        ptmsTable.getColumn("").setCellRenderer(new AlignedTableCellRenderer(SwingConstants.CENTER, Color.LIGHT_GRAY));

        ptmSiteTable.getColumn("").setMinWidth(35);
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        modificationTable.getColumn(" ").setMaxWidth(50);
        modificationTable.getColumn(" ").setMinWidth(50);
        modificationTable.getColumn("  ").setMaxWidth(30);
        modificationTable.getColumn("  ").setMinWidth(30);
       
        modificationTable.getColumn("  ").setCellRenderer(new NimbusCheckBoxRenderer());
    }
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        relatedHitsTable.getColumn("Confidence").setMinWidth(90);
        relatedHitsTable.getColumn("Score").setMaxWidth(90);
        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(
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Related Classes of no.uib.jsparklines.extra.NimbusCheckBoxRenderer

  • eu.isas.peptideshaker.gui.exportdialogs.PtmSelectionDialog
  • eu.isas.peptideshaker.gui.FiltersDialog
  • eu.isas.peptideshaker.gui.FindDialog
  • eu.isas.peptideshaker.gui.preferencesdialogs.AnnotationPreferencesDialog
  • eu.isas.peptideshaker.gui.pride.PrideReshakeSetupDialog
  • eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceDialog
  • eu.isas.peptideshaker.gui.PtmSiteInferenceDialog
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