Example usage for javax.swing JTextPane setText

List of usage examples for javax.swing JTextPane setText

Introduction

In this page you can find the example usage for javax.swing JTextPane setText.

Prototype

@BeanProperty(bound = false, description = "the text of this component")
public void setText(String t) 

Source Link

Document

Sets the text of this TextComponent to the specified content, which is expected to be in the format of the content type of this editor.

Usage

From source file:lu.lippmann.cdb.ext.hydviga.ui.GapFillingFrame.java

/**
 * Constructor.//from  w  w w . j  ava  2s. c o  m
 */
public GapFillingFrame(final AbstractTabView atv, final Instances dataSet, final Attribute attr,
        final int dateIdx, final int valuesBeforeAndAfter, final int position, final int gapsize,
        final StationsDataProvider gcp, final boolean inBatchMode) {
    super();

    setTitle("Gap filling for " + attr.name() + " ("
            + dataSet.attribute(dateIdx).formatDate(dataSet.instance(position).value(dateIdx)) + " -> "
            + dataSet.attribute(dateIdx).formatDate(dataSet.instance(position + gapsize).value(dateIdx)) + ")");
    LogoHelper.setLogo(this);

    this.atv = atv;

    this.dataSet = dataSet;
    this.attr = attr;
    this.dateIdx = dateIdx;
    this.valuesBeforeAndAfter = valuesBeforeAndAfter;
    this.position = position;
    this.gapsize = gapsize;

    this.gcp = gcp;

    final Instances testds = WekaDataProcessingUtil.buildFilteredDataSet(dataSet, 0,
            dataSet.numAttributes() - 1, Math.max(0, position - valuesBeforeAndAfter),
            Math.min(position + gapsize + valuesBeforeAndAfter, dataSet.numInstances() - 1));

    this.attrNames = WekaTimeSeriesUtil.getNamesOfAttributesWithoutGap(testds);

    this.isGapSimulated = (this.attrNames.contains(attr.name()));
    this.originaldataSet = new Instances(dataSet);
    if (this.isGapSimulated) {
        setTitle(getTitle() + " [SIMULATED GAP]");
        /*final JXLabel fictiveGapLabel=new JXLabel("                                                                        FICTIVE GAP");
        fictiveGapLabel.setForeground(Color.RED);
        fictiveGapLabel.setFont(new Font(fictiveGapLabel.getFont().getName(), Font.PLAIN,fictiveGapLabel.getFont().getSize()*2));
        final JXPanel fictiveGapPanel=new JXPanel();
        fictiveGapPanel.setLayout(new BorderLayout());
        fictiveGapPanel.add(fictiveGapLabel,BorderLayout.CENTER);
        getContentPane().add(fictiveGapPanel,BorderLayout.NORTH);*/
        this.attrNames.remove(attr.name());
        this.originalDataBeforeGapSimulation = dataSet.attributeToDoubleArray(attr.index());
        for (int i = position; i < position + gapsize; i++)
            dataSet.instance(i).setMissing(attr);
    }

    final Object[] attrNamesObj = this.attrNames.toArray();

    this.centerPanel = new JXPanel();
    this.centerPanel.setLayout(new BorderLayout());
    getContentPane().add(this.centerPanel, BorderLayout.CENTER);

    //final JXPanel algoPanel=new JXPanel();
    //getContentPane().add(algoPanel,BorderLayout.NORTH);
    final JXPanel filterPanel = new JXPanel();
    //filterPanel.setLayout(new BoxLayout(filterPanel, BoxLayout.Y_AXIS));      
    filterPanel.setLayout(new GridBagLayout());
    final GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.weightx = 1;
    gbc.weighty = 1;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.insets = new Insets(10, 10, 10, 10);
    getContentPane().add(filterPanel, BorderLayout.WEST);

    final JXComboBox algoCombo = new JXComboBox(Algo.values());
    algoCombo.setBorder(new TitledBorder("Algorithm"));
    filterPanel.add(algoCombo, gbc);
    gbc.gridy++;

    final JXLabel infoLabel = new JXLabel("Usable = with no missing values on the period");
    //infoLabel.setBorder(new TitledBorder(""));
    filterPanel.add(infoLabel, gbc);
    gbc.gridy++;

    final JList<Object> timeSeriesList = new JList<Object>(attrNamesObj);
    timeSeriesList.setBorder(new TitledBorder("Usable time series"));
    timeSeriesList.setSelectionMode(DefaultListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
    final JScrollPane jcpMap = new JScrollPane(timeSeriesList);
    jcpMap.setPreferredSize(new Dimension(225, 150));
    jcpMap.setMinimumSize(new Dimension(225, 150));
    filterPanel.add(jcpMap, gbc);
    gbc.gridy++;

    final JXPanel mapPanel = new JXPanel();
    mapPanel.setBorder(new TitledBorder(""));
    mapPanel.setLayout(new BorderLayout());
    mapPanel.add(gcp.getMapPanel(Arrays.asList(attr.name()), this.attrNames, true), BorderLayout.CENTER);
    filterPanel.add(mapPanel, gbc);
    gbc.gridy++;

    final JXLabel mssLabel = new JXLabel(
            "<html>Most similar usable serie: <i>[... computation ...]</i></html>");
    mssLabel.setBorder(new TitledBorder(""));
    filterPanel.add(mssLabel, gbc);
    gbc.gridy++;

    final JXLabel nsLabel = new JXLabel("<html>Nearest usable serie: <i>[... computation ...]</i></html>");
    nsLabel.setBorder(new TitledBorder(""));
    filterPanel.add(nsLabel, gbc);
    gbc.gridy++;

    final JXLabel ussLabel = new JXLabel("<html>Upstream serie: <i>[... computation ...]</i></html>");
    ussLabel.setBorder(new TitledBorder(""));
    filterPanel.add(ussLabel, gbc);
    gbc.gridy++;

    final JXLabel dssLabel = new JXLabel("<html>Downstream serie: <i>[... computation ...]</i></html>");
    dssLabel.setBorder(new TitledBorder(""));
    filterPanel.add(dssLabel, gbc);
    gbc.gridy++;

    final JCheckBox hideOtherSeriesCB = new JCheckBox("Hide the others series");
    hideOtherSeriesCB.setSelected(DEFAULT_HIDE_OTHER_SERIES_OPTION);
    filterPanel.add(hideOtherSeriesCB, gbc);
    gbc.gridy++;

    final JCheckBox showErrorCB = new JCheckBox("Show error on plot");
    filterPanel.add(showErrorCB, gbc);
    gbc.gridy++;

    final JCheckBox zoomCB = new JCheckBox("Auto-adjusted size");
    zoomCB.setSelected(DEFAULT_ZOOM_OPTION);
    filterPanel.add(zoomCB, gbc);
    gbc.gridy++;

    final JCheckBox multAxisCB = new JCheckBox("Multiple axis");
    filterPanel.add(multAxisCB, gbc);
    gbc.gridy++;

    final JCheckBox showEnvelopeCB = new JCheckBox("Show envelope (all algorithms, SLOW)");
    filterPanel.add(showEnvelopeCB, gbc);
    gbc.gridy++;

    final JXButton showModelButton = new JXButton("Show the model");
    filterPanel.add(showModelButton, gbc);
    gbc.gridy++;

    showModelButton.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(final ActionEvent e) {
            final JXFrame dialog = new JXFrame();
            dialog.setTitle("Model");
            LogoHelper.setLogo(dialog);
            dialog.getContentPane().removeAll();
            dialog.getContentPane().setLayout(new BorderLayout());
            final JTextPane modelTxtPane = new JTextPane();
            modelTxtPane.setText(gapFiller.getModel());
            modelTxtPane.setBackground(Color.WHITE);
            modelTxtPane.setEditable(false);
            final JScrollPane jsp = new JScrollPane(modelTxtPane, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
                    JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
            jsp.setSize(new Dimension(400 - 20, 400 - 20));
            dialog.getContentPane().add(jsp, BorderLayout.CENTER);
            dialog.setSize(new Dimension(400, 400));
            dialog.setLocationRelativeTo(centerPanel);
            dialog.pack();
            dialog.setVisible(true);
        }
    });

    algoCombo.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(final ActionEvent e) {
            try {
                refresh(Algo.valueOf(algoCombo.getSelectedItem().toString()),
                        timeSeriesList.getSelectedIndices(), hideOtherSeriesCB.isSelected(),
                        showErrorCB.isSelected(), zoomCB.isSelected(), showEnvelopeCB.isSelected(),
                        multAxisCB.isSelected());
                showModelButton.setEnabled(gapFiller.hasExplicitModel());
            } catch (final Exception e1) {
                e1.printStackTrace();
            }
        }
    });

    timeSeriesList.addListSelectionListener(new ListSelectionListener() {
        @Override
        public void valueChanged(final ListSelectionEvent e) {
            try {
                refresh(Algo.valueOf(algoCombo.getSelectedItem().toString()),
                        timeSeriesList.getSelectedIndices(), hideOtherSeriesCB.isSelected(),
                        showErrorCB.isSelected(), zoomCB.isSelected(), showEnvelopeCB.isSelected(),
                        multAxisCB.isSelected());
                mapPanel.removeAll();
                final List<String> currentlySelected = new ArrayList<String>();
                currentlySelected.add(attr.name());
                for (final Object sel : timeSeriesList.getSelectedValues())
                    currentlySelected.add(sel.toString());
                mapPanel.add(gcp.getMapPanel(currentlySelected, attrNames, true), BorderLayout.CENTER);
            } catch (final Exception e1) {
                e1.printStackTrace();
            }
        }
    });

    hideOtherSeriesCB.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(final ActionEvent e) {
            try {
                refresh(Algo.valueOf(algoCombo.getSelectedItem().toString()),
                        timeSeriesList.getSelectedIndices(), hideOtherSeriesCB.isSelected(),
                        showErrorCB.isSelected(), zoomCB.isSelected(), showEnvelopeCB.isSelected(),
                        multAxisCB.isSelected());
            } catch (final Exception e1) {
                e1.printStackTrace();
            }
        }
    });

    showErrorCB.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(final ActionEvent e) {
            try {
                refresh(Algo.valueOf(algoCombo.getSelectedItem().toString()),
                        timeSeriesList.getSelectedIndices(), hideOtherSeriesCB.isSelected(),
                        showErrorCB.isSelected(), zoomCB.isSelected(), showEnvelopeCB.isSelected(),
                        multAxisCB.isSelected());
            } catch (Exception e1) {
                e1.printStackTrace();
            }
        }
    });

    zoomCB.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(final ActionEvent e) {
            try {
                refresh(Algo.valueOf(algoCombo.getSelectedItem().toString()),
                        timeSeriesList.getSelectedIndices(), hideOtherSeriesCB.isSelected(),
                        showErrorCB.isSelected(), zoomCB.isSelected(), showEnvelopeCB.isSelected(),
                        multAxisCB.isSelected());
            } catch (Exception e1) {
                e1.printStackTrace();
            }
        }
    });

    showEnvelopeCB.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(final ActionEvent e) {
            try {
                refresh(Algo.valueOf(algoCombo.getSelectedItem().toString()),
                        timeSeriesList.getSelectedIndices(), hideOtherSeriesCB.isSelected(),
                        showErrorCB.isSelected(), zoomCB.isSelected(), showEnvelopeCB.isSelected(),
                        multAxisCB.isSelected());
            } catch (Exception e1) {
                e1.printStackTrace();
            }
        }
    });

    multAxisCB.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(final ActionEvent e) {
            try {
                refresh(Algo.valueOf(algoCombo.getSelectedItem().toString()),
                        timeSeriesList.getSelectedIndices(), hideOtherSeriesCB.isSelected(),
                        showErrorCB.isSelected(), zoomCB.isSelected(), showEnvelopeCB.isSelected(),
                        multAxisCB.isSelected());
            } catch (Exception e1) {
                e1.printStackTrace();
            }
        }
    });

    this.inBatchMode = inBatchMode;

    if (!inBatchMode) {
        try {
            refresh(Algo.valueOf(algoCombo.getSelectedItem().toString()), new int[0],
                    DEFAULT_HIDE_OTHER_SERIES_OPTION, false, DEFAULT_ZOOM_OPTION, false, false);
            showModelButton.setEnabled(gapFiller.hasExplicitModel());
        } catch (Exception e1) {
            e1.printStackTrace();
        }
    }

    if (!inBatchMode) {
        /* automatically select computed series */
        new AbstractSimpleAsync<Void>(true) {
            @Override
            public Void execute() throws Exception {
                mostSimilar = WekaTimeSeriesSimilarityUtil.findMostSimilarTimeSerie(testds, attr, attrNames,
                        false);
                mssLabel.setText("<html>Most similar usable serie: <b>" + mostSimilar + "</b></html>");

                nearest = gcp.findNearestStation(attr.name(), attrNames);
                nsLabel.setText("<html>Nearest usable serie: <b>" + nearest + "</b></html>");

                upstream = gcp.findUpstreamStation(attr.name(), attrNames);
                if (upstream != null) {
                    ussLabel.setText("<html>Upstream usable serie: <b>" + upstream + "</b></html>");
                } else {
                    ussLabel.setText("<html>Upstream usable serie: <b>N/A</b></html>");
                }

                downstream = gcp.findDownstreamStation(attr.name(), attrNames);
                if (downstream != null) {
                    dssLabel.setText("<html>Downstream usable serie: <b>" + downstream + "</b></html>");
                } else {
                    dssLabel.setText("<html>Downstream usable serie: <b>N/A</b></html>");
                }

                timeSeriesList.setSelectedIndices(
                        new int[] { attrNames.indexOf(mostSimilar), attrNames.indexOf(nearest),
                                attrNames.indexOf(upstream), attrNames.indexOf(downstream) });

                return null;
            }

            @Override
            public void onSuccess(final Void result) {
            }

            @Override
            public void onFailure(final Throwable caught) {
                caught.printStackTrace();
            }
        }.start();
    } else {
        try {
            mostSimilar = WekaTimeSeriesSimilarityUtil.findMostSimilarTimeSerie(testds, attr, attrNames, false);
        } catch (Exception e1) {
            e1.printStackTrace();
        }
        nearest = gcp.findNearestStation(attr.name(), attrNames);
        upstream = gcp.findUpstreamStation(attr.name(), attrNames);
        downstream = gcp.findDownstreamStation(attr.name(), attrNames);
    }
}

From source file:edu.snu.leader.discrete.simulator.SimulatorLauncherGUI.java

JTextPane createErrorPane(String errorMessage, Component component, final JTabbedPane tabbedPane,
        final int tabIndex) {
    final JTextPane errorPane = new JTextPane();

    errorPane.setEditable(false);//w  w w  .j  a v a  2s .  c  om
    errorPane.setText(errorMessage);
    errorPane.addFocusListener(new FocusAdapter() {
        @Override
        public void focusGained(FocusEvent arg0) {
            errorPane.setBackground(Color.YELLOW);
            tabbedPane.setSelectedIndex(tabIndex);
        }

        @Override
        public void focusLost(FocusEvent arg0) {
            errorPane.setBackground(Color.WHITE);
        }
    });

    component.requestFocusInWindow();

    return errorPane;
}

From source file:juicebox.windowui.QCDialog.java

public QCDialog(MainWindow mainWindow, HiC hic, String title) {
    super(mainWindow);

    Dataset dataset = hic.getDataset();//from ww w  .ja  va 2  s .  c o m

    String text = dataset.getStatistics();
    String textDescription = null;
    String textStatistics = null;
    String graphs = dataset.getGraphs();
    JTextPane description = null;
    JTabbedPane tabbedPane = new JTabbedPane();
    HTMLEditorKit kit = new HTMLEditorKit();

    StyleSheet styleSheet = kit.getStyleSheet();
    styleSheet.addRule("table { border-collapse: collapse;}");
    styleSheet.addRule("body {font-family: Sans-Serif; font-size: 12;}");
    styleSheet.addRule("td { padding: 2px; }");
    styleSheet.addRule(
            "th {border-bottom: 1px solid #000; text-align: left; background-color: #D8D8D8; font-weight: normal;}");

    if (text != null) {
        int split = text.indexOf("</table>") + 8;
        textDescription = text.substring(0, split);
        textStatistics = text.substring(split);
        description = new JTextPane();
        description.setEditable(false);
        description.setContentType("text/html");
        description.setEditorKit(kit);
        description.setText(textDescription);
        tabbedPane.addTab("About Library", description);

        JTextPane textPane = new JTextPane();
        textPane.setEditable(false);
        textPane.setContentType("text/html");

        textPane.setEditorKit(kit);
        textPane.setText(textStatistics);
        JScrollPane pane = new JScrollPane(textPane);
        tabbedPane.addTab("Statistics", pane);
    }
    boolean success = true;
    if (graphs != null) {

        long[] A = new long[2000];
        long sumA = 0;
        long[] mapq1 = new long[201];
        long[] mapq2 = new long[201];
        long[] mapq3 = new long[201];
        long[] intraCount = new long[100];
        final XYSeries intra = new XYSeries("Intra Count");
        final XYSeries leftRead = new XYSeries("Left");
        final XYSeries rightRead = new XYSeries("Right");
        final XYSeries innerRead = new XYSeries("Inner");
        final XYSeries outerRead = new XYSeries("Outer");
        final XYSeries allMapq = new XYSeries("All MapQ");
        final XYSeries intraMapq = new XYSeries("Intra MapQ");
        final XYSeries interMapq = new XYSeries("Inter MapQ");

        Scanner scanner = new Scanner(graphs);
        try {
            while (!scanner.next().equals("["))
                ;

            for (int idx = 0; idx < 2000; idx++) {
                A[idx] = scanner.nextLong();
                sumA += A[idx];
            }

            while (!scanner.next().equals("["))
                ;
            for (int idx = 0; idx < 201; idx++) {
                mapq1[idx] = scanner.nextInt();
                mapq2[idx] = scanner.nextInt();
                mapq3[idx] = scanner.nextInt();

            }

            for (int idx = 199; idx >= 0; idx--) {
                mapq1[idx] = mapq1[idx] + mapq1[idx + 1];
                mapq2[idx] = mapq2[idx] + mapq2[idx + 1];
                mapq3[idx] = mapq3[idx] + mapq3[idx + 1];
                allMapq.add(idx, mapq1[idx]);
                intraMapq.add(idx, mapq2[idx]);
                interMapq.add(idx, mapq3[idx]);
            }
            while (!scanner.next().equals("["))
                ;
            for (int idx = 0; idx < 100; idx++) {
                int tmp = scanner.nextInt();
                if (tmp != 0)
                    innerRead.add(logXAxis[idx], tmp);
                intraCount[idx] = tmp;
                tmp = scanner.nextInt();
                if (tmp != 0)
                    outerRead.add(logXAxis[idx], tmp);
                intraCount[idx] += tmp;
                tmp = scanner.nextInt();
                if (tmp != 0)
                    rightRead.add(logXAxis[idx], tmp);
                intraCount[idx] += tmp;
                tmp = scanner.nextInt();
                if (tmp != 0)
                    leftRead.add(logXAxis[idx], tmp);
                intraCount[idx] += tmp;
                if (idx > 0)
                    intraCount[idx] += intraCount[idx - 1];
                if (intraCount[idx] != 0)
                    intra.add(logXAxis[idx], intraCount[idx]);
            }
        } catch (NoSuchElementException exception) {
            JOptionPane.showMessageDialog(getParent(), "Graphing file improperly formatted", "Error",
                    JOptionPane.ERROR_MESSAGE);
            success = false;
        }

        if (success) {
            final XYSeriesCollection readTypeCollection = new XYSeriesCollection();
            readTypeCollection.addSeries(innerRead);
            readTypeCollection.addSeries(outerRead);
            readTypeCollection.addSeries(leftRead);
            readTypeCollection.addSeries(rightRead);

            final JFreeChart readTypeChart = ChartFactory.createXYLineChart("Types of reads vs distance", // chart title
                    "Distance (log)", // domain axis label
                    "Binned Reads (log)", // range axis label
                    readTypeCollection, // data
                    PlotOrientation.VERTICAL, true, // include legend
                    true, false);

            final XYPlot readTypePlot = readTypeChart.getXYPlot();

            readTypePlot.setDomainAxis(new LogarithmicAxis("Distance (log)"));
            readTypePlot.setRangeAxis(new LogarithmicAxis("Binned Reads (log)"));
            readTypePlot.setBackgroundPaint(Color.white);
            readTypePlot.setRangeGridlinePaint(Color.lightGray);
            readTypePlot.setDomainGridlinePaint(Color.lightGray);
            readTypeChart.setBackgroundPaint(Color.white);
            readTypePlot.setOutlinePaint(Color.black);
            final ChartPanel chartPanel = new ChartPanel(readTypeChart);

            final XYSeriesCollection reCollection = new XYSeriesCollection();
            final XYSeries reDistance = new XYSeries("Distance");

            for (int i = 0; i < A.length; i++) {
                if (A[i] != 0)
                    reDistance.add(i, A[i] / (float) sumA);
            }
            reCollection.addSeries(reDistance);

            final JFreeChart reChart = ChartFactory.createXYLineChart(
                    "Distance from closest restriction enzyme site", // chart title
                    "Distance (bp)", // domain axis label
                    "Fraction of Reads (log)", // range axis label
                    reCollection, // data
                    PlotOrientation.VERTICAL, true, // include legend
                    true, false);

            final XYPlot rePlot = reChart.getXYPlot();
            rePlot.setDomainAxis(new NumberAxis("Distance (bp)"));
            rePlot.setRangeAxis(new LogarithmicAxis("Fraction of Reads (log)"));
            rePlot.setBackgroundPaint(Color.white);
            rePlot.setRangeGridlinePaint(Color.lightGray);
            rePlot.setDomainGridlinePaint(Color.lightGray);
            reChart.setBackgroundPaint(Color.white);
            rePlot.setOutlinePaint(Color.black);
            final ChartPanel chartPanel2 = new ChartPanel(reChart);

            final XYSeriesCollection intraCollection = new XYSeriesCollection();

            intraCollection.addSeries(intra);

            final JFreeChart intraChart = ChartFactory.createXYLineChart("Intra reads vs distance", // chart title
                    "Distance (log)", // domain axis label
                    "Cumulative Sum of Binned Reads (log)", // range axis label
                    intraCollection, // data
                    PlotOrientation.VERTICAL, true, // include legend
                    true, false);

            final XYPlot intraPlot = intraChart.getXYPlot();
            intraPlot.setDomainAxis(new LogarithmicAxis("Distance (log)"));
            intraPlot.setRangeAxis(new NumberAxis("Cumulative Sum of Binned Reads (log)"));
            intraPlot.setBackgroundPaint(Color.white);
            intraPlot.setRangeGridlinePaint(Color.lightGray);
            intraPlot.setDomainGridlinePaint(Color.lightGray);
            intraChart.setBackgroundPaint(Color.white);
            intraPlot.setOutlinePaint(Color.black);
            final ChartPanel chartPanel3 = new ChartPanel(intraChart);

            final XYSeriesCollection mapqCollection = new XYSeriesCollection();
            mapqCollection.addSeries(allMapq);
            mapqCollection.addSeries(intraMapq);
            mapqCollection.addSeries(interMapq);

            final JFreeChart mapqChart = ChartFactory.createXYLineChart("MapQ Threshold Count", // chart title
                    "MapQ threshold", // domain axis label
                    "Count", // range axis label
                    mapqCollection, // data
                    PlotOrientation.VERTICAL, true, // include legend
                    true, // include tooltips
                    false);

            final XYPlot mapqPlot = mapqChart.getXYPlot();
            mapqPlot.setBackgroundPaint(Color.white);
            mapqPlot.setRangeGridlinePaint(Color.lightGray);
            mapqPlot.setDomainGridlinePaint(Color.lightGray);
            mapqChart.setBackgroundPaint(Color.white);
            mapqPlot.setOutlinePaint(Color.black);
            final ChartPanel chartPanel4 = new ChartPanel(mapqChart);

            tabbedPane.addTab("Pair Type", chartPanel);
            tabbedPane.addTab("Restriction", chartPanel2);
            tabbedPane.addTab("Intra vs Distance", chartPanel3);
            tabbedPane.addTab("MapQ", chartPanel4);
        }
    }

    final ExpectedValueFunction df = hic.getDataset().getExpectedValues(hic.getZoom(),
            hic.getNormalizationType());
    if (df != null) {
        double[] expected = df.getExpectedValues();
        final XYSeriesCollection collection = new XYSeriesCollection();
        final XYSeries expectedValues = new XYSeries("Expected");
        for (int i = 0; i < expected.length; i++) {
            if (expected[i] > 0)
                expectedValues.add(i + 1, expected[i]);
        }
        collection.addSeries(expectedValues);
        String title1 = "Expected at " + hic.getZoom() + " norm " + hic.getNormalizationType();
        final JFreeChart readTypeChart = ChartFactory.createXYLineChart(title1, // chart title
                "Distance between reads (log)", // domain axis label
                "Genome-wide expected (log)", // range axis label
                collection, // data
                PlotOrientation.VERTICAL, false, // include legend
                true, false);
        final XYPlot readTypePlot = readTypeChart.getXYPlot();

        readTypePlot.setDomainAxis(new LogarithmicAxis("Distance between reads (log)"));
        readTypePlot.setRangeAxis(new LogarithmicAxis("Genome-wide expected (log)"));
        readTypePlot.setBackgroundPaint(Color.white);
        readTypePlot.setRangeGridlinePaint(Color.lightGray);
        readTypePlot.setDomainGridlinePaint(Color.lightGray);
        readTypeChart.setBackgroundPaint(Color.white);
        readTypePlot.setOutlinePaint(Color.black);
        final ChartPanel chartPanel5 = new ChartPanel(readTypeChart);

        tabbedPane.addTab("Expected", chartPanel5);
    }

    if (text == null && graphs == null) {
        JOptionPane.showMessageDialog(this, "Sorry, no metrics are available for this dataset", "Error",
                JOptionPane.ERROR_MESSAGE);
        setVisible(false);
        dispose();

    } else {
        getContentPane().add(tabbedPane);
        pack();
        setModal(false);
        setLocation(100, 100);
        setTitle(title);
        setVisible(true);
    }
}

From source file:com.vgi.mafscaling.LogView.java

private void createUsageTab() {
    JTextPane usageTextArea = new JTextPane();
    usageTextArea.setMargin(new Insets(10, 10, 10, 10));
    usageTextArea.setContentType("text/html");
    usageTextArea.setText(usage());
    usageTextArea.setEditable(false);//from  ww  w .j  a  v  a  2  s.  co  m
    usageTextArea.setCaretPosition(0);

    JScrollPane textScrollPane = new JScrollPane(usageTextArea);
    textScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
    textScrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);

    add(textScrollPane, "<html><div style='text-align: center;'>U<br>s<br>a<br>g<br>e</div></html>");
}

From source file:main.UIController.java

/******** FROM GREGORIAN **********/

public void updateDayComboGregorian() {
    UI window = this.getUi();

    JTextField year = window.getYear();
    JComboBox month = window.getMonth();
    JComboBox day = window.getDay();
    JButton convert = window.getToImladris();
    JTextPane result = window.getResImladris();
    String value = year.getText();
    if (!value.isEmpty()) {
        try {/* w w w .j ava2s  . co m*/
            int yearNum = Integer.parseInt(value);
            if (yearNum > 0 && yearNum <= GregorianInfo.MAX_SUPPORTED_YEAR) {
                int monthNum = month.getSelectedIndex() + 1;
                int daySel = 0;
                if (day.isEnabled()) {
                    daySel = day.getSelectedIndex() + 1;
                }
                ArrayList<Integer> days = GregorianInfo.getInstance().getDaysArray(yearNum, monthNum);
                day.setModel(new DefaultComboBoxModel(days.toArray()));
                if (daySel > 0 && daySel <= days.size()) {
                    day.setSelectedIndex(daySel - 1);
                }
                day.setEnabled(true);
                convert.setEnabled(true);
                result.setText("");
            } else {
                day.setEnabled(false);
                convert.setEnabled(false);
                day.setModel(new DefaultComboBoxModel());
                result.setText("");
            }
        } catch (NumberFormatException e) {
            day.setEnabled(false);
            convert.setEnabled(false);
            day.setModel(new DefaultComboBoxModel());
            result.setText("");
        }
    } else {
        day.setEnabled(false);
        convert.setEnabled(false);
        day.setModel(new DefaultComboBoxModel());
        result.setText("");
    }
}

From source file:org.biojava.bio.view.MotifAnalyzer.java

private JScrollPane getOutputTextPane(String text) {
    JScrollPane jScrollPane = new JScrollPane();
    JTextPane outputPane = new JTextPane();
    outputPane.setEditable(false);//from  ww  w  .  j a  v a  2  s  . c om
    outputPane.setText(text);
    jScrollPane.setViewportView(outputPane);

    return jScrollPane;
}

From source file:main.UIController.java

public void convertToGregorian() {
    UI window = this.getUi();

    String errorNoLoa = "Please insert a loa.";
    String errorLoaNotNumeric = "Please insert the loa as a numeric value.";
    String errorYearNotValid = "Please insert a valid loa (from 1 to 144).";
    String errorDayNotRead = "Sorry, the day could not be read.";

    JComboBox yen = window.getYen();
    JTextField loa = window.getLoa();
    JComboBox period = window.getPeriod();
    JComboBox day = window.getDayOfLoa();
    JCheckBox beforeMidnight = window.getBeforeMidnight();
    JTextPane result = window.getResGregorian();
    int yenNum = yen.getSelectedIndex() + 1;
    String value = loa.getText();
    if (!value.isEmpty()) {
        try {// www  .  j  a  va2 s .co  m
            int loaNum = Integer.parseInt(value);
            if (loaNum > 0 && loaNum <= 144) {
                int periodNum = period.getSelectedIndex() + 1;
                ImladrisCalendar cal = new ImladrisCalendar();
                boolean success = false;
                if (periodNum == ImladrisCalendar.YESTARE || periodNum == ImladrisCalendar.METTARE) {
                    success = true;
                    cal = new ImladrisCalendar(cal.intToRoman(yenNum), loaNum, periodNum);
                } else {
                    int dayNum = 0;
                    if (day.isEnabled()) {
                        success = true;
                        dayNum = day.getSelectedIndex() + 1;
                        cal = new ImladrisCalendar(cal.intToRoman(yenNum), loaNum, periodNum, dayNum);
                    } else {
                        result.setText(errorDayNotRead);
                    }
                }
                if (success) {
                    GregorianCalendar gcal = cal.getGregorian();
                    if (beforeMidnight.isSelected()) {
                        gcal.add(GregorianCalendar.DAY_OF_YEAR, -1);
                    }
                    String gstr = this.gregorianToString(gcal);
                    result.setText(gstr);
                }
            } else {
                result.setText(errorYearNotValid);
            }
        } catch (NumberFormatException e) {
            result.setText(errorLoaNotNumeric);
        }
    } else {
        result.setText(errorNoLoa);
    }
}

From source file:main.UIController.java

@SuppressWarnings("deprecation")
public void convertToImladris() {
    UI window = this.getUi();

    String errorEmptyYear = "Please insert a year.";
    String errorYearNotNumeric = "Please insert the year as a numeric value.";
    String errorYearNotValid = "Please insert a valid year (from 1 to "
            + Integer.toString(GregorianInfo.MAX_SUPPORTED_YEAR) + ").";
    String errorDayNotRead = "Sorry, the day could not be read.";

    JTextField year = window.getYear();
    JComboBox month = window.getMonth();
    JComboBox day = window.getDay();
    JCheckBox afterSunset = window.getAfterSunset();
    JTextPane result = window.getResImladris();
    String value = year.getText();
    if (!value.isEmpty()) {
        try {/*w w  w  .j a  va2 s. c  o  m*/
            int yearNum = Integer.parseInt(value);
            if (yearNum > 0 && yearNum <= GregorianInfo.MAX_SUPPORTED_YEAR) {
                int monthNum = month.getSelectedIndex() + 1;
                int dayNum = 0;
                if (day.isEnabled()) {
                    dayNum = day.getSelectedIndex() + 1;
                    ImladrisCalendar cal;
                    if (afterSunset.isSelected()) {
                        GregorianCalendar gcal = new GregorianCalendar(yearNum, monthNum, dayNum);
                        Time time = this.calculateSunsetForActualLocation(gcal, true);
                        cal = new ImladrisCalendar(time, yearNum, monthNum, dayNum, time.getHours(),
                                time.getMinutes(), time.getSeconds());
                    } else {
                        cal = new ImladrisCalendar(yearNum, monthNum, dayNum);
                    }
                    result.setText(cal.toString());
                } else {
                    result.setText(errorDayNotRead);
                }
            } else {
                result.setText(errorYearNotValid);
            }
        } catch (NumberFormatException e) {
            result.setText(errorYearNotNumeric);
        }
    } else {
        result.setText(errorEmptyYear);
    }
}

From source file:es.ubu.XRayDetector.interfaz.PanelAplicacion.java

/**
 * Gets the application log./*  www .  ja v a  2  s. c om*/
 * 
 * @param panelLog The panel of the log.
 * @return The application log.
 */
private JTextPane getTxtLog(JPanel panelLog) {
    JTextPane textPaneLog = new JTextPane();
    textPaneLog.setBounds(4, 4, 209, 195);
    textPaneLog.setEditable(false);
    panelLog.add(textPaneLog);
    textPaneLog.setContentType("text/html");
    kit = new HTMLEditorKit();
    doc = new HTMLDocument();
    panelLog_1.setLayout(null);
    textPaneLog.setEditorKit(kit);
    textPaneLog.setDocument(doc);

    textPaneLog.setText("<!DOCTYPE html>" + "<html>" + "<head>" + "<style>" + "p.normal {font-weight:normal;}"
            + "p.error {font-weight:bold; color:red}" + "p.exito {font-weight:bold; color:green}"
            + "p.stop {font-weight:bold; color:blue}" + "</style>" + "</head>" + "<body>");
    JScrollPane scroll = new JScrollPane(textPaneLog);
    scroll.setBounds(10, 16, 242, 254);
    scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED);
    panelLog.add(scroll);
    return textPaneLog;
}

From source file:edu.ku.brc.specify.tasks.SystemSetupTask.java

/**
 * /*from   ww w. j av a  2s  .com*/
 */
private void synonymCleanup() {
    JTextPane tp = new JTextPane();
    JScrollPane js = new JScrollPane();
    js.getViewport().add(tp);

    String text = "";
    try {
        String template = "synonym_cleanup_%s.html";
        String fileName = String.format(template, Locale.getDefault().getLanguage());
        File file = XMLHelper.getConfigDir(fileName);
        if (!file.exists()) {
            fileName = String.format(template, "en");
            file = XMLHelper.getConfigDir(fileName);
        }
        text = FileUtils.readFileToString(file);

    } catch (Exception ex) {
        ex.printStackTrace();
    }

    JPanel p = new JPanel(new BorderLayout());
    p.setBorder(BorderFactory.createEmptyBorder(8, 8, 8, 8));
    p.add(js, BorderLayout.CENTER);

    tp.setContentType("text/html");
    tp.setText(text);
    tp.setCaretPosition(0);
    tp.setFont(new Font(Font.SANS_SERIF, Font.PLAIN, 18));

    CustomDialog dlg = new CustomDialog((Frame) getTopWindow(), getI18nRS("SYN_CLEANUP"), true,
            CustomDialog.OKCANCELAPPLY, p);
    dlg.setOkLabel(getI18nRS("SYN_CLEANUP"));
    dlg.setCancelLabel(getI18nRS("Report"));
    dlg.setApplyLabel(getResourceString("CANCEL"));
    dlg.setCloseOnApplyClk(true);
    dlg.createUI();
    dlg.setSize(600, 450);
    UIHelper.centerAndShow(dlg);
    if (dlg.getBtnPressed() == CustomDialog.OK_BTN || dlg.getBtnPressed() == CustomDialog.CANCEL_BTN) {
        boolean doCleanup = dlg.getBtnPressed() == CustomDialog.OK_BTN;
        SynonymCleanup synonymCleanup = new SynonymCleanup(doCleanup);
        synonymCleanup.execute(); // start the background task
    }
}