/** Both fires off selection event and displays annot */
private void selectAnnot(AnnotatedFeatureI annot) {
displayAnnot(getTransOrOneLevelAnn(annot));
translationViewer.repaint();
BaseFocusEvent evt = new BaseFocusEvent(this, annot.getStart(), annot);
getController().handleBaseFocusEvent(evt);
getSelectionManager().select(annot, this); // sends off selection
}
private BaseFineEditor(
AnnotatedFeatureI editMe,
GuiCurationState curationState,
SeqFeatureI geneHolder,
Set<SeqFeatureI> selectedResults) {
super((editMe.isForwardStrand() ? "Forward" : "Reverse") + " Strand Exon Editor");
this.curationState = curationState;
curationState.getController().addListener(this);
curationState.getController().addListener(new BaseEditorDataListener());
szap = curationState.getSZAP();
transformer = szap.getScaleView().getTransform();
int seqStart = curationState.getCurationSet().getLow();
int seqEnd = curationState.getCurationSet().getHigh();
CurationSet s = curationState.getCurationSet();
// FeatureSetI annFeatSet=((DrawableFeatureSet)view.getDrawableSet()).getFeatureSet();
// REFACTOR BaseEditorPanel - (what allows for selection and modification of the annotations?)
// create BaseViewPanel -> have BaseEditorPanel extend it
// take the header outside of the editorPanel (is it really inside right now?)
// create a new panel using BaseViewPanel
/*
* The viewable components of the new BaseFineEditor (should this be renamed?):
*
* 1) The Genomic Strand
* 2) The Annotations (will these always be a copy of the genomic strand?)
* q1) Can annotations also be nucliotides? - A: Yes. Create a separate view for those.
* q2) Does it make sense to view both the forward and reverse strand at once?
* q3) How do we know what to load - A: highlight the region we want to look at?
* q4) Will we expect users to be able to view many annotations at once?
* q4) How will the user know which annotation they are looking at? - A: Display the name when hovering over?
* 3) The Results
* q1) See above questions.
* 4) Result Score information
* 5) An overview - Right now this is at the transcript (gene model?) level
* q1) What should be contained in this view?
*
*
*/
// I think that right now every base in the ede is a copy of the genomic, will that always be
// the case?
// is there ever sequence associated with an annotation.
editorPanel =
new BaseEditorPanel(
curationState, this, !editMe.isForwardStrand(), seqStart, seqEnd, geneHolder);
addResults(selectedResults);
initGui(editMe); // cant do til after editorPanel made
// cant do this til after initGui (editorPanel needs to know size)
editorPanel.displayAnnot(editMe);
attachListeners();
showEditRegion();
displayAnnot(getTransOrOneLevelAnn(editMe));
translationViewer.repaint();
setVisible(true);
// Might just be linux, but bofe gets iconified on close
if (getState() == Frame.ICONIFIED) setState(Frame.NORMAL);
}
private BaseFineEditor(
AnnotatedFeatureI editMe, GuiCurationState curationState, SeqFeatureI geneHolder) {
super((editMe.isForwardStrand() ? "Forward" : "Reverse") + " Strand Exon Editor");
this.curationState = curationState;
curationState.getController().addListener(this);
curationState.getController().addListener(new BaseEditorDataListener());
szap = curationState.getSZAP();
transformer = szap.getScaleView().getTransform();
int seqStart = curationState.getCurationSet().getLow();
int seqEnd = curationState.getCurationSet().getHigh();
// FeatureSetI annFeatSet=((DrawableFeatureSet)view.getDrawableSet()).getFeatureSet();
editorPanel =
new BaseEditorPanel(
curationState, this, !editMe.isForwardStrand(), seqStart, seqEnd, geneHolder);
initGui(editMe); // cant do til after editorPanel made
// cant do this til after initGui (editorPanel needs to know size)
editorPanel.displayAnnot(editMe);
attachListeners();
showEditRegion();
displayAnnot(getTransOrOneLevelAnn(editMe));
translationViewer.repaint();
setVisible(true);
// Might just be linux, but bofe gets iconified on close
if (getState() == Frame.ICONIFIED) setState(Frame.NORMAL);
}
/**
* Handle the selection event (feature was selected in another window--select it here) This is
* also where selections from BaseFineEditor come in which are really internal selections. Only
* handle external selection if followSelection is checked
*/
public boolean handleFeatureSelectionEvent(FeatureSelectionEvent evt) {
if (!canHandleSelection(evt, this)) return false;
// now we do something, canHanSel filters for GenAnnIs
AnnotatedFeatureI gai = (AnnotatedFeatureI) evt.getFeatures().getFeature(0);
displayAnnot(getTransOrOneLevelAnn(gai));
translationViewer.repaint();
return true;
}
/**
* Display AnnotatedFeatureI feature. Exon, Transcript, and Gene are all GenericAnnotationI. No
* selection event is fired. (selectAnnot fires and displays)
*/
private void displayAnnot(AnnotatedFeatureI annot) {
currentAnnot = annot;
if (currentAnnot == null) {
transcriptComboBox.removeAllItems();
transcriptComboBox.addItem("<no feature selected>");
lengthLabel.setText("Translation length: <no feature selected>");
upstream_button.setLabel("");
downstream_button.setLabel("");
translationViewer.setTranscript(null, editorPanel.getSelectedTier()); // ??
return;
}
// else {
setupTranscriptComboBox(currentAnnot);
SeqFeatureI topAnnot = currentAnnot;
if (topAnnot.isTranscript()) topAnnot = currentAnnot.getRefFeature();
if (topAnnot.isProteinCodingGene()) {
String translation = currentAnnot.translate();
if (translation == null) {
lengthLabel.setText("Translation length: <no start selected>");
} else {
lengthLabel.setText("Translation length: " + currentAnnot.translate().length());
}
} else {
lengthLabel.setText(topAnnot.getFeatureType() + " annotation");
}
FeatureSetI holder = (FeatureSetI) topAnnot.getRefFeature();
neighbor_up = null;
neighbor_down = null;
if (holder != null) {
int index = holder.getFeatureIndex(topAnnot);
// get next neighbor up that has whole sequence
for (int i = index - 1; i >= 0 && neighbor_up == null; i--) {
FeatureSetI gene_sib = (FeatureSetI) holder.getFeatureAt(i);
if (gene_sib.getFeatureAt(0) instanceof Transcript) {
Transcript trans = (Transcript) gene_sib.getFeatureAt(0);
if (trans.haveWholeSequence()) // szap.getCurationSet()))
neighbor_up = trans;
}
}
// get next neighbor down that has whole sequence
for (int i = index + 1; i < holder.size() && neighbor_down == null; i++) {
FeatureSetI gene_sib = (FeatureSetI) holder.getFeatureAt(i);
if (gene_sib.getFeatureAt(0) instanceof Transcript) {
Transcript trans = (Transcript) gene_sib.getFeatureAt(0);
if (trans.haveWholeSequence()) // szap.getCurationSet()))
neighbor_down = trans;
}
}
}
upstream_button.setLabel(
neighbor_up == null
? ""
: "Go to next 5' annotation (" + neighbor_up.getParent().getName() + ")");
upstream_button.setVisible(neighbor_up != null);
downstream_button.setLabel(
neighbor_down == null
? ""
: "Go to next 3' annotation (" + neighbor_down.getParent().getName() + ")");
downstream_button.setVisible(neighbor_down != null);
// }
// todo - translationViewer take in 1 level annot
if (currentAnnot.isTranscript())
translationViewer.setTranscript((Transcript) currentAnnot, editorPanel.getSelectedTier());
}
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);
}
}
});
}
