public void setEnableForAllElements(SuperAdapter superAdapter, boolean status) {
chrBox1.setEnabled(status);
chrBox2.setEnabled(status);
refreshButton.setEnabled(status);
colorRangePanel.setElementsVisible(status, superAdapter);
setResolutionSliderVisible(status, superAdapter);
goPanel.setEnabled(status);
}
public void setSelectedChromosomesNoRefresh(
Chromosome xChrom, Chromosome yChrom, Context xContext, Context yContext) {
chrBox1.setSelectedIndex(yChrom.getIndex());
chrBox2.setSelectedIndex(xChrom.getIndex());
rulerPanelX.setContext(xContext, HiCRulerPanel.Orientation.HORIZONTAL);
rulerPanelY.setContext(yContext, HiCRulerPanel.Orientation.VERTICAL);
resolutionSlider.setEnabled(!xChrom.getName().equals(Globals.CHR_ALL));
}
public void setEnabledForNormalization(String[] normalizationOptions, boolean status) {
if (normalizationOptions.length == 1) {
normalizationComboBox.setEnabled(false);
} else {
normalizationComboBox.setModel(new DefaultComboBoxModel<String>(normalizationOptions));
normalizationComboBox.setSelectedIndex(0);
normalizationComboBox.setEnabled(status && !isWholeGenome());
}
}
public void setNormalizationDisplayState(HiC hic) {
// Test for new dataset ("All"), or change in chromosome
if (isWholeGenome()) { // for now only allow observed
hic.setDisplayOption(MatrixType.OBSERVED);
displayOptionComboBox.setSelectedIndex(0);
normalizationComboBox.setSelectedIndex(0);
} else if (isIntraChromosomal()) {
if (hic.getDisplayOption() == MatrixType.PEARSON) {
hic.setDisplayOption(MatrixType.OBSERVED);
displayOptionComboBox.setSelectedIndex(0);
}
}
normalizationComboBox.setEnabled(!isWholeGenome());
displayOptionComboBox.setEnabled(true);
}
/**
* 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()])));
}
public void setSelectedDisplayOption(MatrixType[] options, boolean control) {
if (control) {
MatrixType originalMatrixType = (MatrixType) displayOptionComboBox.getSelectedItem();
displayOptionComboBox.setModel(new DefaultComboBoxModel<MatrixType>(options));
int indx = 0;
for (int i = 0; i < displayOptionComboBox.getItemCount(); i++) {
if (originalMatrixType.equals(displayOptionComboBox.getItemAt(i))) {
indx = i;
break;
}
}
displayOptionComboBox.setSelectedIndex(indx);
} else {
displayOptionComboBox.setModel(new DefaultComboBoxModel<MatrixType>(options));
displayOptionComboBox.setSelectedIndex(0);
}
}
public void unsafeRefreshChromosomes(SuperAdapter superAdapter) {
if (chrBox1.getSelectedIndex() == 0 || chrBox2.getSelectedIndex() == 0) {
chrBox1.setSelectedIndex(0);
chrBox2.setSelectedIndex(0);
}
Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem();
Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem();
Chromosome chrX = chr1.getIndex() < chr2.getIndex() ? chr1 : chr2;
Chromosome chrY = chr1.getIndex() < chr2.getIndex() ? chr2 : chr1;
setNormalizationDisplayState(superAdapter.getHiC());
superAdapter.unsafeUpdateHiCChromosomes(chrX, chrY);
updateThumbnail(superAdapter.getHiC());
}
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);
}
public void setNormalizationEnabledForReload() {
// normalizationComboBox.setEnabled(true);
normalizationComboBox.setEnabled(!isWholeGenome());
}
public void setNormalizationBox(int indx) {
normalizationComboBox.setSelectedIndex(indx);
}
public void setDisplayBox(int indx) {
displayOptionComboBox.setSelectedIndex(indx);
}
private void chrBox2ActionPerformed(ActionEvent e) {
if (chrBox2.getSelectedIndex() == 0) {
chrBox1.setSelectedIndex(0);
}
}
private boolean isWholeGenome() {
Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem();
Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem();
return chr1.getName().equals("All") || chr2.getName().equals("All");
}
private boolean isIntraChromosomal() {
Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem();
Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem();
return chr1.getIndex() != chr2.getIndex();
}
/*
* Only accessed from within another unsafe method in Heatmap Panel class,
* which in turn is encapsulated (i.e. made safe)
*/
public void unsafeSetSelectedChromosomes(
SuperAdapter superAdapter, Chromosome xChrom, Chromosome yChrom) {
chrBox1.setSelectedIndex(yChrom.getIndex());
chrBox2.setSelectedIndex(xChrom.getIndex());
unsafeRefreshChromosomes(superAdapter);
}