Beispiel #1
0
  public void updateThumbnail(HiC hic) {
    if (hic.getMatrix() != null) {

      //   MatrixZoomData zd0 = initialZoom == null ?
      // hic.getMatrix().getFirstZoomData(hic.getZoom().getUnit()) :
      //           hic.getMatrix().getZoomData(initialZoom);
      MatrixZoomData zd0 = hic.getMatrix().getFirstZoomData(hic.getZoom().getUnit());
      MatrixZoomData zdControl = null;
      if (hic.getControlMatrix() != null)
        zdControl = hic.getControlMatrix().getFirstZoomData(hic.getZoom().getUnit());
      Image thumbnail =
          heatmapPanel.getThumbnailImage(
              zd0,
              zdControl,
              thumbnailPanel.getWidth(),
              thumbnailPanel.getHeight(),
              hic.getDisplayOption());
      if (thumbnail != null) {
        thumbnailPanel.setImage(thumbnail);
        thumbnailPanel.repaint();
      }
    } else {
      thumbnailPanel.setImage(null);
    }
  }
Beispiel #2
0
  /**
   * Chromosome "0" is whole genome
   *
   * @param chromosomes list of chromosomes
   */
  void setChromosomes(List<Chromosome> chromosomes) {
    int[] chromosomeBoundaries = new int[chromosomes.size() - 1];
    long bound = 0;
    for (int i = 1; i < chromosomes.size(); i++) {
      Chromosome c = chromosomes.get(i);
      bound += (c.getLength() / 1000);
      chromosomeBoundaries[i - 1] = (int) bound;
    }
    heatmapPanel.setChromosomeBoundaries(chromosomeBoundaries);

    chrBox1.setModel(
        new DefaultComboBoxModel<Chromosome>(
            chromosomes.toArray(new Chromosome[chromosomes.size()])));
    chrBox2.setModel(
        new DefaultComboBoxModel<Chromosome>(
            chromosomes.toArray(new Chromosome[chromosomes.size()])));
  }
Beispiel #3
0
  public void initializeMainView(
      final SuperAdapter superAdapter,
      Container contentPane,
      Dimension bigPanelDim,
      Dimension panelDim) {
    contentPane.setLayout(new BorderLayout());

    final JPanel mainPanel = new JPanel();
    mainPanel.setLayout(new BorderLayout());
    contentPane.add(mainPanel, BorderLayout.CENTER);
    mainPanel.setBackground(Color.white);

    final JPanel toolbarPanel = new JPanel();
    toolbarPanel.setBorder(null);

    toolbarPanel.setLayout(new GridBagLayout());
    mainPanel.add(toolbarPanel, BorderLayout.NORTH);

    JPanel bigPanel = new JPanel();
    bigPanel.setLayout(new BorderLayout());
    bigPanel.setBackground(Color.white);

    bigPanel.setPreferredSize(new Dimension(bigPanelDim));
    bigPanel.setMaximumSize(new Dimension(bigPanelDim));
    bigPanel.setMinimumSize(new Dimension(bigPanelDim));

    JPanel bottomPanel = new JPanel();
    bottomPanel.setBackground(Color.white);

    JMenuBar menuBar = null;
    try {
      menuBar = superAdapter.createMenuBar();
    } catch (Exception e) {
      e.printStackTrace();
    }
    assert menuBar != null;
    contentPane.add(menuBar, BorderLayout.NORTH);

    GridBagConstraints toolbarConstraints = new GridBagConstraints();
    toolbarConstraints.anchor = GridBagConstraints.LINE_START;
    toolbarConstraints.fill = GridBagConstraints.HORIZONTAL;
    toolbarConstraints.gridx = 0;
    toolbarConstraints.gridy = 0;
    toolbarConstraints.weightx = 0.1;

    // --- Chromosome panel ---
    JPanel chrSelectionPanel = new JPanel();
    toolbarPanel.add(chrSelectionPanel, toolbarConstraints);

    chrSelectionPanel.setBorder(LineBorder.createGrayLineBorder());

    chrSelectionPanel.setLayout(new BorderLayout());

    JPanel chrLabelPanel = new JPanel();
    JLabel chrLabel = new JLabel("Chromosomes");
    chrLabel.setHorizontalAlignment(SwingConstants.CENTER);
    chrLabelPanel.setBackground(HiCGlobals.backgroundColor);
    chrLabelPanel.setLayout(new BorderLayout());
    chrLabelPanel.add(chrLabel, BorderLayout.CENTER);
    chrSelectionPanel.add(chrLabelPanel, BorderLayout.PAGE_START);

    JPanel chrButtonPanel = new JPanel();
    chrButtonPanel.setBackground(new Color(238, 238, 238));
    chrButtonPanel.setLayout(new BoxLayout(chrButtonPanel, BoxLayout.X_AXIS));

    // ---- chrBox1 ----
    chrBox1 = new JComboBox<Chromosome>();
    chrBox1.setModel(
        new DefaultComboBoxModel<Chromosome>(new Chromosome[] {new Chromosome(0, "All", 0)}));
    chrBox1.addActionListener(
        new ActionListener() {
          public void actionPerformed(ActionEvent e) {
            chrBox1ActionPerformed(e);
          }
        });
    chrBox1.setPreferredSize(new Dimension(95, 70));
    chrButtonPanel.add(chrBox1);

    // ---- chrBox2 ----
    chrBox2 = new JComboBox<Chromosome>();
    chrBox2.setModel(
        new DefaultComboBoxModel<Chromosome>(new Chromosome[] {new Chromosome(0, "All", 0)}));
    chrBox2.addActionListener(
        new ActionListener() {
          public void actionPerformed(ActionEvent e) {
            chrBox2ActionPerformed(e);
          }
        });
    chrBox2.setPreferredSize(new Dimension(95, 70));
    chrButtonPanel.add(chrBox2);

    // ---- refreshButton ----
    refreshButton = new JideButton();
    refreshButton.setIcon(
        new ImageIcon(getClass().getResource("/toolbarButtonGraphics/general/Refresh24.gif")));
    refreshButton.addActionListener(
        new ActionListener() {
          public void actionPerformed(ActionEvent e) {
            superAdapter.safeRefreshButtonActionPerformed();
          }
        });
    refreshButton.setPreferredSize(new Dimension(24, 24));
    chrButtonPanel.add(refreshButton);

    chrBox1.setEnabled(false);
    chrBox2.setEnabled(false);
    refreshButton.setEnabled(false);
    chrSelectionPanel.add(chrButtonPanel, BorderLayout.CENTER);

    chrSelectionPanel.setMinimumSize(new Dimension(200, 70));
    chrSelectionPanel.setPreferredSize(new Dimension(210, 70));

    // ======== Display Option Panel ========
    JPanel displayOptionPanel = new JPanel();
    displayOptionPanel.setBackground(new Color(238, 238, 238));
    displayOptionPanel.setBorder(LineBorder.createGrayLineBorder());
    displayOptionPanel.setLayout(new BorderLayout());
    JPanel displayOptionLabelPanel = new JPanel();
    displayOptionLabelPanel.setBackground(HiCGlobals.backgroundColor);
    displayOptionLabelPanel.setLayout(new BorderLayout());

    JLabel displayOptionLabel = new JLabel("Show");
    displayOptionLabel.setHorizontalAlignment(SwingConstants.CENTER);
    displayOptionLabelPanel.add(displayOptionLabel, BorderLayout.CENTER);
    displayOptionPanel.add(displayOptionLabelPanel, BorderLayout.PAGE_START);
    JPanel displayOptionButtonPanel = new JPanel();
    displayOptionButtonPanel.setBorder(new EmptyBorder(0, 10, 0, 10));
    displayOptionButtonPanel.setLayout(new GridLayout(1, 0, 20, 0));
    displayOptionComboBox = new JComboBox<MatrixType>();
    displayOptionComboBox.setModel(
        new DefaultComboBoxModel<MatrixType>(new MatrixType[] {MatrixType.OBSERVED}));
    displayOptionComboBox.addActionListener(
        new ActionListener() {
          public void actionPerformed(ActionEvent e) {
            superAdapter.safeDisplayOptionComboBoxActionPerformed();
            normalizationComboBox.setEnabled(!isWholeGenome());
          }
        });
    displayOptionButtonPanel.add(displayOptionComboBox);
    displayOptionPanel.add(displayOptionButtonPanel, BorderLayout.CENTER);
    displayOptionPanel.setMinimumSize(new Dimension(140, 70));
    displayOptionPanel.setPreferredSize(new Dimension(140, 70));
    displayOptionPanel.setMaximumSize(new Dimension(140, 70));

    toolbarConstraints.gridx = 1;
    toolbarConstraints.weightx = 0.1;
    toolbarPanel.add(displayOptionPanel, toolbarConstraints);
    displayOptionComboBox.setEnabled(false);

    // ======== Normalization Panel ========
    JPanel normalizationPanel = new JPanel();
    normalizationPanel.setBackground(new Color(238, 238, 238));
    normalizationPanel.setBorder(LineBorder.createGrayLineBorder());
    normalizationPanel.setLayout(new BorderLayout());

    JPanel normalizationLabelPanel = new JPanel();
    normalizationLabelPanel.setBackground(HiCGlobals.backgroundColor);
    normalizationLabelPanel.setLayout(new BorderLayout());

    JLabel normalizationLabel = new JLabel("Normalization");
    normalizationLabel.setHorizontalAlignment(SwingConstants.CENTER);
    normalizationLabelPanel.add(normalizationLabel, BorderLayout.CENTER);
    normalizationPanel.add(normalizationLabelPanel, BorderLayout.PAGE_START);

    JPanel normalizationButtonPanel = new JPanel();
    normalizationButtonPanel.setBorder(new EmptyBorder(0, 10, 0, 10));
    normalizationButtonPanel.setLayout(new GridLayout(1, 0, 20, 0));
    normalizationComboBox = new JComboBox<String>();
    normalizationComboBox.setModel(
        new DefaultComboBoxModel<String>(new String[] {NormalizationType.NONE.getLabel()}));
    normalizationComboBox.addActionListener(
        new ActionListener() {
          public void actionPerformed(ActionEvent e) {
            superAdapter.safeNormalizationComboBoxActionPerformed(e);
          }
        });
    normalizationButtonPanel.add(normalizationComboBox);
    normalizationPanel.add(normalizationButtonPanel, BorderLayout.CENTER);
    normalizationPanel.setPreferredSize(new Dimension(180, 70));
    normalizationPanel.setMinimumSize(new Dimension(140, 70));

    toolbarConstraints.gridx = 2;
    toolbarConstraints.weightx = 0.1;
    toolbarPanel.add(normalizationPanel, toolbarConstraints);
    normalizationComboBox.setEnabled(false);

    // ======== Resolution Panel ========
    hiCPanel = new JPanel();
    hiCPanel.setBackground(Color.white);
    hiCPanel.setLayout(new HiCLayout());
    bigPanel.add(hiCPanel, BorderLayout.CENTER);

    JPanel wrapGapPanel = new JPanel();
    wrapGapPanel.setBackground(Color.white);
    wrapGapPanel.setMaximumSize(new Dimension(5, 5));
    wrapGapPanel.setMinimumSize(new Dimension(5, 5));
    wrapGapPanel.setPreferredSize(new Dimension(5, 5));
    wrapGapPanel.setBorder(LineBorder.createBlackLineBorder());
    bigPanel.add(wrapGapPanel, BorderLayout.EAST);

    // splitPanel.insertPane(hiCPanel, 0);
    // splitPanel.setBackground(Color.white);

    // ---- rulerPanel2 ----
    JPanel topPanel = new JPanel();
    topPanel.setBackground(Color.green);
    topPanel.setLayout(new BorderLayout());
    hiCPanel.add(topPanel, BorderLayout.NORTH);
    trackLabelPanel = new TrackLabelPanel(superAdapter.getHiC());
    trackLabelPanel.setBackground(Color.white);
    hiCPanel.add(trackLabelPanel, HiCLayout.NORTH_WEST);

    trackPanelX = new TrackPanel(superAdapter, superAdapter.getHiC(), TrackPanel.Orientation.X);
    trackPanelX.setMaximumSize(new Dimension(4000, 50));
    trackPanelX.setPreferredSize(new Dimension(1, 50));
    trackPanelX.setMinimumSize(new Dimension(1, 50));
    trackPanelX.setVisible(false);
    topPanel.add(trackPanelX, BorderLayout.NORTH);

    rulerPanelX = new HiCRulerPanel(superAdapter.getHiC());
    rulerPanelX.setMaximumSize(new Dimension(4000, 50));
    rulerPanelX.setMinimumSize(new Dimension(1, 50));
    rulerPanelX.setPreferredSize(new Dimension(1, 50));
    rulerPanelX.setBorder(null);
    topPanel.add(rulerPanelX, BorderLayout.SOUTH);

    // ---- rulerPanel1 ----
    JPanel leftPanel = new JPanel();
    leftPanel.setBackground(Color.white);
    leftPanel.setLayout(new BorderLayout());
    hiCPanel.add(leftPanel, BorderLayout.WEST);

    trackPanelY = new TrackPanel(superAdapter, superAdapter.getHiC(), TrackPanel.Orientation.Y);
    trackPanelY.setMaximumSize(new Dimension(50, 4000));
    trackPanelY.setPreferredSize(new Dimension(50, 1));
    trackPanelY.setMinimumSize(new Dimension(50, 1));
    trackPanelY.setVisible(false);
    leftPanel.add(trackPanelY, BorderLayout.WEST);

    rulerPanelY = new HiCRulerPanel(superAdapter.getHiC());
    rulerPanelY.setMaximumSize(new Dimension(50, 4000));
    rulerPanelY.setPreferredSize(new Dimension(50, 800));
    rulerPanelY.setBorder(null);
    rulerPanelY.setMinimumSize(new Dimension(50, 1));
    leftPanel.add(rulerPanelY, BorderLayout.EAST);

    // ---- heatmapPanel ----
    // Dimension screenDimension = Toolkit.getDefaultToolkit().getScreenSize();
    // int panelSize = screenDimension.height - 210;

    int panelWidth = (int) panelDim.getWidth();
    int panelHeight = (int) panelDim.getHeight();
    System.err.println("Window W: " + panelWidth + " H" + panelHeight);

    JPanel wrapHeatmapPanel = new JPanel(new BorderLayout());
    wrapHeatmapPanel.setMaximumSize(new Dimension(panelDim));
    wrapHeatmapPanel.setMinimumSize(new Dimension(panelDim));
    wrapHeatmapPanel.setPreferredSize(new Dimension(panelDim));
    wrapHeatmapPanel.setBackground(Color.BLUE);
    wrapHeatmapPanel.setVisible(true);

    heatmapPanel = new HeatmapPanel(superAdapter);
    heatmapPanel.setMaximumSize(new Dimension(panelWidth - 5, panelHeight - 5));
    heatmapPanel.setMinimumSize(new Dimension(panelWidth - 5, panelHeight - 5));
    heatmapPanel.setPreferredSize(new Dimension(panelWidth - 5, panelHeight - 5));
    heatmapPanel.setBackground(Color.white);

    wrapHeatmapPanel.add(heatmapPanel, BorderLayout.CENTER);

    // hiCPanel.setMaximumSize(new Dimension(panelWidth, panelHeight));
    // hiCPanel.setMinimumSize(new Dimension(panelWidth, panelHeight));
    // hiCPanel.setPreferredSize(new Dimension(panelWidth, panelHeight));

    hiCPanel.add(wrapHeatmapPanel, BorderLayout.CENTER);

    // ======== Resolution Slider Panel ========

    // Resolution  panel
    resolutionSlider = new ResolutionControl(superAdapter);
    resolutionSlider.setPreferredSize(new Dimension(200, 70));
    resolutionSlider.setMinimumSize(new Dimension(150, 70));

    toolbarConstraints.gridx = 3;
    toolbarConstraints.weightx = 0.1;
    toolbarPanel.add(resolutionSlider, toolbarConstraints);

    // ======== Color Range Panel ========
    colorRangePanel = new JColorRangePanel(superAdapter, heatmapPanel, preDefMapColor);

    toolbarConstraints.gridx = 4;
    toolbarConstraints.weightx = 0.5;
    toolbarPanel.add(colorRangePanel, toolbarConstraints);

    goPanel = new GoToPanel(superAdapter);
    toolbarConstraints.gridx = 5;
    toolbarConstraints.weightx = 0.25;
    toolbarPanel.add(goPanel, toolbarConstraints);
    // not sure this is working
    // toolbarPanel.setPreferredSize(new Dimension(panelHeight,100));
    toolbarPanel.setEnabled(false);

    // ======== Right side panel ========

    JPanel rightSidePanel = new JPanel(new BorderLayout()); // (new BorderLayout());
    rightSidePanel.setBackground(Color.white);
    rightSidePanel.setPreferredSize(new Dimension(210, 1000));
    rightSidePanel.setMaximumSize(new Dimension(10000, 10000));

    // ======== Bird's view mini map ========

    JPanel thumbPanel = new JPanel();
    thumbPanel.setLayout(new BorderLayout());

    // ---- thumbnailPanel ----
    thumbnailPanel = new ThumbnailPanel(superAdapter);
    thumbnailPanel.setBackground(Color.white);
    thumbnailPanel.setMaximumSize(new Dimension(210, 210));
    thumbnailPanel.setMinimumSize(new Dimension(210, 210));
    thumbnailPanel.setPreferredSize(new Dimension(210, 210));

    //        JPanel gapPanel = new JPanel();
    //        gapPanel.setMaximumSize(new Dimension(1, 1));
    //        rightSidePanel.add(gapPanel,BorderLayout.WEST);
    thumbPanel.add(thumbnailPanel, BorderLayout.CENTER);
    thumbPanel.setBackground(Color.white);
    rightSidePanel.add(thumbPanel, BorderLayout.NORTH);

    // ========= mouse hover text ======
    JPanel tooltipPanel = new JPanel(new BorderLayout());
    tooltipPanel.setBackground(Color.white);
    tooltipPanel.setPreferredSize(new Dimension(210, 490));
    mouseHoverTextPanel = new JEditorPane();
    mouseHoverTextPanel.setEditable(false);
    mouseHoverTextPanel.setContentType("text/html");
    mouseHoverTextPanel.setFont(new Font("sans-serif", 0, 20));
    mouseHoverTextPanel.setBackground(Color.white);
    mouseHoverTextPanel.setBorder(null);
    int mouseTextY = rightSidePanel.getBounds().y + rightSidePanel.getBounds().height;

    // *Dimension prefSize = new Dimension(210, 490);
    Dimension prefSize = new Dimension(210, 390);
    mouseHoverTextPanel.setPreferredSize(prefSize);

    JScrollPane tooltipScroller = new JScrollPane(mouseHoverTextPanel);
    tooltipScroller.setBackground(Color.white);
    tooltipScroller.setBorder(null);

    tooltipPanel.setPreferredSize(new Dimension(210, 500));
    tooltipPanel.add(tooltipScroller);
    tooltipPanel.setBounds(new Rectangle(new Point(0, mouseTextY), prefSize));
    tooltipPanel.setBackground(Color.white);
    tooltipPanel.setBorder(null);

    rightSidePanel.add(tooltipPanel, BorderLayout.CENTER);

    // compute preferred size
    Dimension preferredSize = new Dimension();
    for (int i = 0; i < rightSidePanel.getComponentCount(); i++) {
      Rectangle bounds = rightSidePanel.getComponent(i).getBounds();
      preferredSize.width = Math.max(bounds.x + bounds.width, preferredSize.width);
      preferredSize.height = Math.max(bounds.y + bounds.height, preferredSize.height);
    }
    Insets insets = rightSidePanel.getInsets();
    preferredSize.width += insets.right + 20;
    preferredSize.height += insets.bottom;
    rightSidePanel.setMinimumSize(preferredSize);
    rightSidePanel.setPreferredSize(preferredSize);
    mainPanel.add(bigPanel, BorderLayout.CENTER);
    mainPanel.add(rightSidePanel, BorderLayout.EAST);
  }