Examples with JSparklinesArrayListBarChartTableCellRenderer no.uib.jsparklines.renderers.JSparklinesArrayListBarChartTableCellRenderer used on opensource projects

Example 1 with JSparklinesArrayListBarChartTableCellRenderer

use of no.uib.jsparklines.renderers.JSparklinesArrayListBarChartTableCellRenderer in project peptide-shaker by compomics.

the class ProteinTableModel method setProteinTableProperties.

/**
 * Set up the properties of the protein table.
 *
 * @param proteinTable the protein table
 * @param sparklineColor the sparkline color to use
 * @param sparklineColorNotValidated the sparkline color for not validated
 * stuffs
 * @param parentClass the parent class used to get icons
 * @param sparklineColorNotFound the sparkline color for not found stuffs
 * @param sparklineColorDoubtful the sparkline color for doubtful
 * @param scoreAndConfidenceDecimalFormat the decimal format for score and
 * confidence
 * @param maxProteinKeyLength the longest protein key to display
 */
public static void setProteinTableProperties(JTable proteinTable, Color sparklineColor, Color sparklineColorNotValidated, Color sparklineColorNotFound, Color sparklineColorDoubtful, DecimalFormat scoreAndConfidenceDecimalFormat, Class parentClass, Integer maxProteinKeyLength) {
    // @TODO: find a better location for this method?
    // the index column
    proteinTable.getColumn(" ").setMaxWidth(50);
    proteinTable.getColumn(" ").setMinWidth(50);
    proteinTable.getColumn("Chr").setMaxWidth(50);
    proteinTable.getColumn("Chr").setMinWidth(50);
    try {
        proteinTable.getColumn("Confidence").setMaxWidth(90);
        proteinTable.getColumn("Confidence").setMinWidth(90);
    } catch (IllegalArgumentException w) {
        proteinTable.getColumn("Score").setMaxWidth(90);
        proteinTable.getColumn("Score").setMinWidth(90);
    }
    // the validated column
    proteinTable.getColumn("").setMaxWidth(30);
    proteinTable.getColumn("").setMinWidth(30);
    // the selected columns
    proteinTable.getColumn("  ").setMaxWidth(30);
    proteinTable.getColumn("  ").setMinWidth(30);
    // the protein inference column
    proteinTable.getColumn("PI").setMaxWidth(37);
    proteinTable.getColumn("PI").setMinWidth(37);
    // set up the protein inference color map
    HashMap<Integer, Color> proteinInferenceColorMap = new HashMap<>();
    proteinInferenceColorMap.put(PSParameter.NOT_GROUP, sparklineColor);
    proteinInferenceColorMap.put(PSParameter.RELATED, Color.YELLOW);
    proteinInferenceColorMap.put(PSParameter.RELATED_AND_UNRELATED, Color.ORANGE);
    proteinInferenceColorMap.put(PSParameter.UNRELATED, Color.RED);
    // set up the protein inference tooltip map
    HashMap<Integer, String> proteinInferenceTooltipMap = new HashMap<>();
    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;
    ArrayList<Color> sparklineColors = new ArrayList<>(4);
    sparklineColors.add(sparklineColor);
    sparklineColors.add(sparklineColorDoubtful);
    sparklineColors.add(nonValidatedColor);
    sparklineColors.add(sparklineColorNotFound);
    JSparklinesArrayListBarChartTableCellRenderer coverageCellRendered = new JSparklinesArrayListBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, sparklineColors, JSparklinesArrayListBarChartTableCellRenderer.ValueDisplayType.sumExceptLastNumber);
    coverageCellRendered.showNumberAndChart(true, TableProperties.getLabelWidth(), new DecimalFormat("0.00"));
    proteinTable.getColumn("Coverage").setCellRenderer(coverageCellRendered);
    JSparklinesArrayListBarChartTableCellRenderer peptidesCellRenderer = new JSparklinesArrayListBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, sparklineColors, JSparklinesArrayListBarChartTableCellRenderer.ValueDisplayType.sumOfNumbers);
    peptidesCellRenderer.showNumberAndChart(true, TableProperties.getLabelWidth(), new DecimalFormat("0"));
    proteinTable.getColumn("#Peptides").setCellRenderer(peptidesCellRenderer);
    JSparklinesArrayListBarChartTableCellRenderer spectraCellRenderer = new JSparklinesArrayListBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, sparklineColors, JSparklinesArrayListBarChartTableCellRenderer.ValueDisplayType.sumOfNumbers);
    spectraCellRenderer.showNumberAndChart(true, TableProperties.getLabelWidth(), new DecimalFormat("0"));
    proteinTable.getColumn("#Spectra").setCellRenderer(spectraCellRenderer);
    JSparklinesBarChartTableCellRenderer spectrumCountingCellRenderer = new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 10.0, sparklineColor);
    spectrumCountingCellRenderer.showNumberAndChart(true, TableProperties.getLabelWidth() + 20, new DecimalFormat("0.00E00"));
    proteinTable.getColumn("MS2 Quant.").setCellRenderer(spectrumCountingCellRenderer);
    JSparklinesBarChartTableCellRenderer mwCellRenderer = new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 10.0, sparklineColor);
    mwCellRenderer.showNumberAndChart(true, TableProperties.getLabelWidth());
    proteinTable.getColumn("MW").setCellRenderer(mwCellRenderer);
    proteinTable.getColumn("Chr").setCellRenderer(new ChromosomeTableCellRenderer(Color.WHITE, Color.BLACK));
    try {
        proteinTable.getColumn("Confidence").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, sparklineColor));
        ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("Confidence").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() - 20, scoreAndConfidenceDecimalFormat);
    } catch (IllegalArgumentException e) {
        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));
    // set the preferred size of the accession column
    if (maxProteinKeyLength != null) {
        Integer width = getPreferredAccessionColumnWidth(proteinTable, proteinTable.getColumn("Accession").getModelIndex(), 6, maxProteinKeyLength);
        if (width != null) {
            proteinTable.getColumn("Accession").setMinWidth(width);
            proteinTable.getColumn("Accession").setMaxWidth(width);
        } else {
            proteinTable.getColumn("Accession").setMinWidth(15);
            proteinTable.getColumn("Accession").setMaxWidth(Integer.MAX_VALUE);
        }
    }
}

Example 2 with JSparklinesArrayListBarChartTableCellRenderer

use of no.uib.jsparklines.renderers.JSparklinesArrayListBarChartTableCellRenderer in project peptide-shaker by compomics.

the class GOEAPanel method setProteinGoTableProperties.

/**
 * Set the properties of the GO protein table.
 */
private void setProteinGoTableProperties() {
    proteinTable.getColumn(" ").setMaxWidth(60);
    proteinTable.getColumn(" ").setMinWidth(60);
    proteinTable.getColumn("  ").setMaxWidth(30);
    proteinTable.getColumn("  ").setMinWidth(30);
    try {
        proteinTable.getColumn("Confidence").setMaxWidth(90);
        proteinTable.getColumn("Confidence").setMinWidth(90);
    } catch (IllegalArgumentException w) {
        proteinTable.getColumn("Score").setMaxWidth(90);
        proteinTable.getColumn("Score").setMinWidth(90);
    }
    // set the preferred size of the accession column
    Integer width = ProteinTableModel.getPreferredAccessionColumnWidth(proteinTable, proteinTable.getColumn("Accession").getModelIndex(), 6, peptideShakerGUI.getMetrics().getMaxProteinAccessionLength());
    if (width != null) {
        proteinTable.getColumn("Accession").setMinWidth(width);
        proteinTable.getColumn("Accession").setMaxWidth(width);
    } 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 (!peptideShakerGUI.getIdentificationParameters().getFastaParameters().isTargetDecoy()) {
        nonValidatedColor = peptideShakerGUI.getUtilitiesUserParameters().getSparklineColorNotFound();
    }
    ArrayList<Color> sparklineColors = new ArrayList<>();
    sparklineColors.add(peptideShakerGUI.getSparklineColor());
    sparklineColors.add(peptideShakerGUI.getUtilitiesUserParameters().getSparklineColorDoubtful());
    sparklineColors.add(nonValidatedColor);
    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()));
    ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("MS2 Quant.").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth(), new DecimalFormat("0.00E00"));
    try {
        proteinTable.getColumn("Confidence").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) proteinTable.getColumn("Confidence").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() - 20, peptideShakerGUI.getScoreAndConfidenceDecimalFormat());
    } catch (IllegalArgumentException e) {
        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<>();
    sparklineColors.add(peptideShakerGUI.getSparklineColor());
    sparklineColors.add(peptideShakerGUI.getUtilitiesUserParameters().getSparklineColorDoubtful());
    sparklineColors.add(nonValidatedColor);
    sparklineColors.add(peptideShakerGUI.getUtilitiesUserParameters().getSparklineColorNotFound());
    JSparklinesArrayListBarChartTableCellRenderer coverageCellRendered = new JSparklinesArrayListBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, 100.0, sparklineColors, JSparklinesArrayListBarChartTableCellRenderer.ValueDisplayType.sumExceptLastNumber);
    coverageCellRendered.showNumberAndChart(true, TableProperties.getLabelWidth(), new DecimalFormat("0.00"));
    proteinTable.getColumn("Coverage").setCellRenderer(coverageCellRendered);
    // make sure that the user is made aware that the tool is doing something during sorting of the protein table
    proteinTable.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));
                proteinTable.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));
                proteinTable.getTableHeader().setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
                // change the peptide shaker icon back to the normal version
                peptideShakerGUI.setIconImage(Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")));
            }
        }
    });
}