Package no.uib.jsparklines.renderers

Examples of no.uib.jsparklines.renderers.JSparklinesIntegerIconTableCellRenderer

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        spectrumTableJScrollPane.setCorner(ScrollPaneConstants.UPPER_RIGHT_CORNER, spectrumCorner);
        JPanel idResultsCorner = new JPanel();
        idResultsCorner.setBackground(searchResultsTable.getTableHeader().getBackground());
        idResultsTableJScrollPane.setCorner(ScrollPaneConstants.UPPER_RIGHT_CORNER, idResultsCorner);

        peptideShakerJTable.getColumn("  ").setCellRenderer(new JSparklinesIntegerIconTableCellRenderer(MatchValidationLevel.getIconMap(this.getClass()), MatchValidationLevel.getTooltipMap()));
        searchResultsTable.getColumn("  ").setCellRenderer(new JSparklinesIntegerIconTableCellRenderer(MatchValidationLevel.getIconMap(this.getClass()), MatchValidationLevel.getTooltipMap()));

        peptideShakerJTable.getTableHeader().setReorderingAllowed(false);
        spectrumTable.getTableHeader().setReorderingAllowed(false);
        searchResultsTable.getTableHeader().setReorderingAllowed(false);

        spectrumTable.setAutoCreateRowSorter(true);

        // make sure that the user is made aware that the tool is doing something during sorting of the spectrum table
        spectrumTable.getRowSorter().addRowSorterListener(new RowSorterListener() {
            @Override
            public void sorterChanged(RowSorterEvent e) {

                if (e.getType() == RowSorterEvent.Type.SORT_ORDER_CHANGED) {
                    peptideShakerGUI.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
                    spectrumTable.getTableHeader().setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));

                    // change the peptide shaker icon to a "waiting version"
                    peptideShakerGUI.setIconImage(Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")));

                } else if (e.getType() == RowSorterEvent.Type.SORTED) {
                    peptideShakerGUI.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
                    spectrumTable.getTableHeader().setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));

                    // change the peptide shaker icon to a "waiting version"
                    peptideShakerGUI.setIconImage(Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")));
                }
            }
        });

        peptideShakerJTable.getColumn(" ").setMinWidth(30);
        peptideShakerJTable.getColumn(" ").setMaxWidth(30);
        peptideShakerJTable.getColumn("  ").setMinWidth(30);
        peptideShakerJTable.getColumn("  ").setMaxWidth(30);
        spectrumTable.getColumn(" ").setMinWidth(50);
        spectrumTable.getColumn(" ").setMaxWidth(50);
        spectrumTable.getColumn("  ").setMinWidth(30);
        spectrumTable.getColumn("  ").setMaxWidth(30);
        spectrumTable.getColumn("Confidence").setMaxWidth(90);
        spectrumTable.getColumn("Confidence").setMinWidth(90);

        searchResultsTable.getColumn(" ").setMinWidth(30);
        searchResultsTable.getColumn(" ").setMaxWidth(30);
        searchResultsTable.getColumn("SE").setMinWidth(37);
        searchResultsTable.getColumn("SE").setMaxWidth(37);
        searchResultsTable.getColumn("Rnk").setMinWidth(37);
        searchResultsTable.getColumn("Rnk").setMaxWidth(37);
        searchResultsTable.getColumn("  ").setMinWidth(30);
        searchResultsTable.getColumn("  ").setMaxWidth(30);

        peptideShakerJTable.getColumn("ID").setMaxWidth(37);
        peptideShakerJTable.getColumn("ID").setMinWidth(37);
        spectrumTable.getColumn("ID").setMaxWidth(37);
        spectrumTable.getColumn("ID").setMinWidth(37);

        peptideShakerJTable.getColumn("Confidence").setMaxWidth(90);
        peptideShakerJTable.getColumn("Confidence").setMinWidth(90);
        searchResultsTable.getColumn("Confidence").setMaxWidth(90);
        searchResultsTable.getColumn("Confidence").setMinWidth(90);
        searchResultsTable.getColumn("Charge").setMaxWidth(90);
        searchResultsTable.getColumn("Charge").setMinWidth(90);

        // set up the psm color map
        HashMap<Integer, java.awt.Color> softwareAgreementColorMap = new HashMap<Integer, java.awt.Color>();
        softwareAgreementColorMap.put(AGREEMENT_WITH_MODS, peptideShakerGUI.getSparklineColor()); // id softwares agree with PTM certainty
        softwareAgreementColorMap.put(AGREEMENT, java.awt.Color.CYAN); // id softwares agree on peptide but not ptm certainty
        softwareAgreementColorMap.put(CONFLICT, java.awt.Color.YELLOW); // id softwares don't agree
        softwareAgreementColorMap.put(PARTIALLY_MISSING, java.awt.Color.ORANGE); // some id softwares id'ed some didn't

        // set up the psm tooltip map
        HashMap<Integer, String> idSoftwareTooltipMap = new HashMap<Integer, String>();
        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()));
        ((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);
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            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("  ").setCellRenderer(new JSparklinesIntegerIconTableCellRenderer(MatchValidationLevel.getIconMap(this.getClass()), MatchValidationLevel.getTooltipMap()));

        sparklineColors = new ArrayList<Color>();
        sparklineColors.add(peptideShakerGUI.getSparklineColor());
        sparklineColors.add(peptideShakerGUI.getUtilitiesUserPreferences().getSparklineColorDoubtful());
        sparklineColors.add(nonValidatedColor);
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        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));
        peptideTable.getColumn("").setCellRenderer(new JSparklinesIntegerIconTableCellRenderer(MatchValidationLevel.getIconMap(this.getClass()), MatchValidationLevel.getTooltipMap()));
        peptideTable.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));
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        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()));

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

        selectedPsmsTable.getColumn("Charge").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 10.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) selectedPsmsTable.getColumn("Charge").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() - 30);
        selectedPsmsTable.getColumn("  ").setCellRenderer(new JSparklinesIntegerIconTableCellRenderer(MatchValidationLevel.getIconMap(this.getClass()), MatchValidationLevel.getTooltipMap()));
        selectedPsmsTable.getColumn("RT").setCellRenderer(new JSparklinesIntervalChartTableCellRenderer(PlotOrientation.HORIZONTAL, 0d,
                1000d, 10d, peptideShakerGUI.getSparklineColor(), peptideShakerGUI.getSparklineColor()));
        ((JSparklinesIntervalChartTableCellRenderer) selectedPsmsTable.getColumn("RT").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() + 5);
        ((JSparklinesIntervalChartTableCellRenderer) selectedPsmsTable.getColumn("RT").getCellRenderer()).showReferenceLine(true, 0.02, java.awt.Color.BLACK);
        selectedPsmsTable.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));

        relatedPsmsTable.getColumn("Charge").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 10.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) relatedPsmsTable.getColumn("Charge").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() - 30);
        relatedPsmsTable.getColumn("  ").setCellRenderer(new JSparklinesIntegerIconTableCellRenderer(MatchValidationLevel.getIconMap(this.getClass()), MatchValidationLevel.getTooltipMap()));
        relatedPsmsTable.getColumn("RT").setCellRenderer(new JSparklinesIntervalChartTableCellRenderer(PlotOrientation.HORIZONTAL, 0d,
                1000d, 10d, peptideShakerGUI.getSparklineColor(), peptideShakerGUI.getSparklineColor()));
        ((JSparklinesIntervalChartTableCellRenderer) relatedPsmsTable.getColumn("RT").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() + 5);
        ((JSparklinesIntervalChartTableCellRenderer) relatedPsmsTable.getColumn("RT").getCellRenderer()).showReferenceLine(true, 0.02, java.awt.Color.BLACK);
        relatedPsmsTable.getColumn("   ").setCellRenderer(new TrueFalseIconRenderer(
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        }

        proteinTable.getColumn("Coverage").setCellRenderer(new JSparklinesTwoValueBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0,
                peptideShakerGUI.getSparklineColor(), peptideShakerGUI.getUtilitiesUserPreferences().getSparklineColorNotFound(), true));
        ((JSparklinesTwoValueBarChartTableCellRenderer) proteinTable.getColumn("Coverage").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth(), new DecimalFormat("0.00"));
        proteinTable.getColumn("").setCellRenderer(new JSparklinesIntegerIconTableCellRenderer(MatchValidationLevel.getIconMap(this.getClass()), MatchValidationLevel.getTooltipMap()));
        proteinTable.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));
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                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);
        ((JSparklinesBarChartTableCellRenderer) relatedHitsTable.getColumn("Confidence").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() + 5);
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            proteinTable.getColumn("Score").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, sparklineColor));
            ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("Score").getCellRenderer()).showNumberAndChart(
                    true, TableProperties.getLabelWidth() - 20, scoreAndConfidenceDecimalFormat);
        }

        proteinTable.getColumn("").setCellRenderer(new JSparklinesIntegerIconTableCellRenderer(MatchValidationLevel.getIconMap(parentClass), MatchValidationLevel.getTooltipMap()));
        proteinTable.getColumn("  ").setCellRenderer(new TrueFalseIconRenderer(
                new ImageIcon(parentClass.getResource("/icons/star_yellow.png")),
                new ImageIcon(parentClass.getResource("/icons/star_grey.png")),
                new ImageIcon(parentClass.getResource("/icons/star_grey.png")),
                "Starred", null, null));
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Related Classes of no.uib.jsparklines.renderers.JSparklinesIntegerIconTableCellRenderer

  • eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceDialog
  • 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.PtmPanel
  • eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel
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