/**
* Sets up transcriptComboBox (pulldown list) with transcript and its parent gene's other
* transcripts, with transcript selected
*/
private void setupTranscriptComboBox(AnnotatedFeatureI annot) {
// could also check for gene change before doing a removeAll
if (transcriptComboBox.getSelectedItem() == annot) return;
// adding and removing items causes item events to fire so need to remove
// listener here - is there any other way to supress firing?
transcriptComboBox.removeItemListener(transItemListener);
transcriptComboBox.removeAllItems();
if (annot == null) {
transcriptComboBox.addItem("<no feature selected>");
return;
}
// 1 LEVEL ANNOT
if (annot.isAnnotTop()) {
transcriptComboBox.addItem(annot);
return;
}
// TRANSCRIPT
SeqFeatureI gene = annot.getRefFeature();
Vector transcripts = gene.getFeatures();
for (int i = 0; i < transcripts.size(); i++)
transcriptComboBox.addItem(transcripts.elementAt(i));
transcriptComboBox.setSelectedItem(annot); // transcript
transcriptComboBox.addItemListener(transItemListener);
}
/**
* AssemblyFeature is the only GAI at the moment that has no relation to // a transcript. Dont
* think they can end up in ede (??). // Would be nice to have an interface that was solely for
* the exon // trans gene heirarchy? Should we actively make sure AssemblyFeatures dont // get
* into ede? (filter in AnnotationMenu?) returns null if no transcript can be found.
*/
private AnnotatedFeatureI getTransOrOneLevelAnn(AnnotatedFeatureI af) {
if (af != null) {
if (af.isTranscript()) return af;
if (af.isExon()) return af.getRefFeature().getAnnotatedFeature();
if (af.isAnnotTop()) {
if (af.hasKids()) return af.getFeatureAt(0).getAnnotatedFeature(); // transcript
else // 1 level annot
return af;
}
}
return null;
}
private void initGui(AnnotatedFeatureI annot) {
translationViewer = new TranslationViewer(editorPanel);
translationViewer.setBackground(Color.black);
transcriptComboBox = new JComboBox();
lengthLabel = new JLabel("Translation length: <no feature selected>");
lengthLabel.setForeground(Color.black);
findButton = new JButton("Find sequence...");
clearFindsButton = new JButton("Clear search hits");
// Disable until we actually get search results
clearFindsButton.setEnabled(false);
goToButton = new JButton("GoTo...");
showIntronBox = new JCheckBox("Show introns in translation viewer", true);
showIntronBox.setBackground(Color.white);
followSelectionCheckBox = new JCheckBox("Follow external selection", false);
followSelectionCheckBox.setBackground(Color.white);
upstream_button = new JButton();
downstream_button = new JButton();
colorSwatch = new JPanel();
setSize(824, 500);
JScrollPane pane = new JScrollPane(editorPanel);
pane.setHorizontalScrollBarPolicy(
JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED); // RAY: SET SCROLL POLICY HERE! WAS
// HORIZONTAL_SCROLLBAR_NEVER
// pane.setColumnHeaderView(new BaseFineEditorRowHeader(editorPanel)); // RAY: setRowHeader need
// to create column header
pane.setColumnHeaderView(new BaseFineEditorHorizontalColHeader(editorPanel));
viewport = pane.getViewport();
colorSwatch.setPreferredSize(new Dimension(10, 10));
getContentPane().setBackground(Color.white);
getContentPane().setLayout(new BorderLayout());
getContentPane().add(colorSwatch, "North");
getContentPane().add(pane, "Center");
Box transcriptListBox = new Box(BoxLayout.X_AXIS);
JLabel tranLabel;
// 1 LEVEL ANNOT
if (annot.isAnnotTop()) tranLabel = new JLabel("Annotation: ");
else // 3-level
tranLabel = new JLabel("Transcript: ");
tranLabel.setForeground(Color.black);
transcriptListBox.add(Box.createHorizontalStrut(5));
transcriptListBox.add(tranLabel);
transcriptListBox.setBackground(Color.white);
transcriptComboBox.setMaximumSize(new Dimension(300, 30));
transcriptListBox.add(transcriptComboBox);
transcriptListBox.add(Box.createHorizontalGlue());
transcriptListBox.add(Box.createHorizontalStrut(5));
transcriptListBox.add(lengthLabel);
transcriptListBox.add(Box.createHorizontalGlue());
Box checkboxesTop = new Box(BoxLayout.X_AXIS);
checkboxesTop.setBackground(Color.white);
checkboxesTop.add(Box.createHorizontalStrut(5));
checkboxesTop.add(findButton);
checkboxesTop.add(Box.createHorizontalStrut(10));
checkboxesTop.add(clearFindsButton);
checkboxesTop.add(Box.createHorizontalStrut(15));
checkboxesTop.add(goToButton);
checkboxesTop.add(Box.createHorizontalGlue());
Box checkboxesBottom = new Box(BoxLayout.X_AXIS);
checkboxesBottom.add(showIntronBox);
checkboxesBottom.add(Box.createHorizontalGlue());
checkboxesBottom.add(Box.createHorizontalStrut(10));
checkboxesBottom.add(followSelectionCheckBox);
Box checkboxes = new Box(BoxLayout.Y_AXIS);
checkboxes.add(checkboxesTop);
checkboxes.add(checkboxesBottom);
Box labelPanel = new Box(BoxLayout.Y_AXIS);
labelPanel.setBackground(Color.white);
labelPanel.add(transcriptListBox);
labelPanel.add(Box.createVerticalStrut(5));
labelPanel.add(checkboxes);
Box navPanel = new Box(BoxLayout.Y_AXIS);
navPanel.setBackground(Color.white);
navPanel.add(upstream_button);
navPanel.add(Box.createVerticalStrut(10));
navPanel.add(downstream_button);
navPanel.add(Box.createVerticalGlue());
Box textBoxes = new Box(BoxLayout.X_AXIS);
textBoxes.setBackground(Color.white);
textBoxes.add(labelPanel);
textBoxes.add(navPanel);
Box detailPanel = new Box(BoxLayout.Y_AXIS);
detailPanel.setBackground(Color.white);
detailPanel.add(translationViewer);
detailPanel.add(textBoxes);
getContentPane().add(detailPanel, "South");
validateTree();
scrollListener = new FineEditorScrollListener();
viewport.addChangeListener(scrollListener);
transcriptComboBox.addKeyListener(
new KeyAdapter() {
public void keyPressed(KeyEvent e) {
if (e.getKeyCode() == KeyEvent.VK_U && (e.getModifiers() & KeyEvent.CTRL_MASK) != 0) {
CurationManager.getActiveCurationState().getTransactionManager().undo(this);
}
}
});
}
