/**
* 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);
}
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);
}
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);
}
/** Scrolls the window to the start/end of the next annotation to the right. */
public void nextAnnotation() {
int basepair = getVisibleBase();
if (getType().equals("AA")) {
basepair += 3 * getAnnotationPanel().getStrand().toInt();
}
int position =
getAnnotationPanel()
.tierPositionToPixelPosition(getAnnotationPanel().basePairToTierPosition(basepair));
SeqFeatureI feature = getAnnotationPanel().getNextFeature(position);
if (feature != null) {
if (getAnnotationPanel().getOrientation() == Orientation.FIVE_TO_THREE) {
scrollToBase(feature.getStart());
} else {
scrollToBase(feature.getEnd());
}
AnnotatedFeatureI selection = null;
if (feature instanceof AnnotatedFeatureI) {
selection = getTransOrOneLevelAnn((AnnotatedFeatureI) feature);
}
if (selection != null
&& selection.isTranscript()
&& ((Transcript) selection).haveWholeSequence()) {
setSelection((AnnotatedFeatureI) feature);
getCurationState().getSelectionManager().select(feature, this);
} else if (selection != null && selection != getSelection()) {
nextAnnotation();
}
}
}
/* Start AnnotationChangeListenter interface */
public boolean handleAnnotationChangeEvent(AnnotationChangeEvent evt) {
if (this.isVisible() && evt.getSource() != this) {
if (evt.isCompound()) {
for (int i = 0; i < evt.getNumberOfChildren(); ++i) {
handleAnnotationChangeEvent(evt.getChildChangeEvent(i));
}
reformatAnnotationPanel();
return true;
}
// can probably be done better, this will reformat the panel a lot
reformatAnnotationPanel();
if (evt.isEndOfEditSession()) {
getOverview().updateState();
setSelection(getSelection());
updateEditRegion();
repaint();
updateTitle();
}
if (evt.isAdd()) {
AnnotatedFeatureI annotToDisplay = null;
AnnotatedFeatureI gene = evt.getChangedAnnot();
int trans_count = gene.size();
for (int i = 0; i < trans_count; ++i) {
Transcript t = (Transcript) gene.getFeatureAt(i);
if (evt.isUndo()) {
// System.out.printf("Attaching %s(%d)\n", t, t.hashCode());
// addFeatureToPanel(t, getAnnotationPanel());
if (getSelection() != null && t.getName().equals(getSelection().getName())) {
annotToDisplay = t;
}
}
}
if (annotToDisplay == null) {
annotToDisplay = (AnnotatedFeatureI) evt.getChangedAnnot().getFeatureAt(0);
} else {
setSelection(annotToDisplay);
}
getOverview().updateState();
}
if (evt.isDelete()) {}
}
repaint();
return true;
}
/** 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
}
public static void test(
GuiCurationState curationState, int strand, Selection selection, String type) {
JFrame frame = new JFrame("TopLevelDemo");
MultiSequenceAlignerFrame msa =
MultiSequenceAlignerFrame.makeAligner(
curationState, strand,
selection, type);
msa.setPreferredSize(new Dimension(1000, 800));
msa.pack();
msa.setVisible(true);
AnnotatedFeatureI gai = getFirstAnnot(selection);
if (gai != null) {
msa.getPanel().scrollToBase(gai.getStart());
msa.getPanel().setSelection(gai);
}
}
public void setGene(AnnotatedFeatureI g) {
this.gene = g;
if (g == null) return;
if (!g.isProteinCodingGene()) {
setText("NOT A PEPTIDE");
setEnabled(false);
} else {
setEnabled(true);
Hashtable curator_values = Config.getPeptideStates();
String pep_status = g.getProperty("sp_status");
PeptideStatus this_status = Config.getPeptideStatus(pep_status);
JMenuItem item;
/* these are the computed values that cannot be over-ridden
by a curator
*/
item = new JMenuItem(this_status.getText());
add(item);
item.addActionListener(this);
/* these are the possible values to be selected
by a curator */
Enumeration e = curator_values.keys();
while (e.hasMoreElements()) {
String key = (String) e.nextElement();
PeptideStatus a_status = (PeptideStatus) curator_values.get(key);
if (a_status.getPrecedence() >= this_status.getPrecedence()
&& !a_status.getText().equals(this_status.getText())
&& a_status.getCurated()) {
item = new JMenuItem(a_status.getText());
add(item);
item.addActionListener(this);
}
}
setText(this_status.getText());
}
}
/** Scrolls the window to the start/end of the next annotation to the left */
public void prevAnnotation() {
int basepair = getVisibleBase();
int offset = getType().equals("AA") ? 3 : 1;
basepair += (getVisibleBaseCount() - offset) * getStrand().toInt();
int position =
getAnnotationPanel()
.tierPositionToPixelPosition(getAnnotationPanel().basePairToTierPosition(basepair));
SeqFeatureI feature = getAnnotationPanel().getPrevFeature(position);
if (feature != null) {
// get highest pixel position
position = getAnnotationPanel().getHigh(feature);
position =
getType().equals("AA")
? position - (getVisibleBaseCount() / 3)
: position - getVisibleBaseCount();
position = getAnnotationPanel().pixelPositionToTierPosition(position);
int bp = getAnnotationPanel().tierPositionToBasePair(position);
scrollToBase(bp);
AnnotatedFeatureI selection = null;
if (feature instanceof AnnotatedFeatureI) {
selection = getTransOrOneLevelAnn((AnnotatedFeatureI) feature);
}
if (selection != null
&& selection.isTranscript()
&& ((Transcript) selection).haveWholeSequence()) {
setSelection((AnnotatedFeatureI) feature);
getCurationState().getSelectionManager().select(feature, this);
} else if (selection != null && selection != getSelection()) {
prevAnnotation();
}
}
}
public void actionPerformed(ActionEvent e) {
JMenuItem item = (JMenuItem) e.getSource();
// This should probably be done in AnnotationEditor changeSpStatus(gene,item...
gene.addProperty("sp_status", item.getText());
// AnnotationChangeEvent ace = AnnotationChangeEvent.getSessionDoneEvent(this);
AnnotSessionDoneEvent de = new AnnotSessionDoneEvent(this);
// = new AnnotationChangeEvent(this,
// gene,
// FeatureChangeEvent.REDRAW,
// AnnotationChangeEvent.ANNOTATION,
// gene);
getController().handleAnnotationChangeEvent(de);
}
/**
* 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;
}
/**
* 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);
}
}
});
}
public boolean handleAnnotationChangeEvent(AnnotationChangeEvent evt) {
if (this.isVisible() && evt.getSource() != this) {
if (evt.isCompound()) {
for (int i = 0; i < evt.getNumberOfChildren(); ++i) {
handleAnnotationChangeEvent(evt.getChildChangeEvent(i));
}
return true;
}
if (evt.isEndOfEditSession()) {
// Dont want scrolling on ann change, also sf for redraw is the
// gene, so it just goes to 1st trans which is problematic.
displayAnnot(currentAnnot);
repaint(); // this is the needed repaint after the changes
return true;
}
/*
AnnotatedFeatureI gene = evt.getChangedAnnot();
for (Object o : szap.getAnnotations().getFeatures()) {
AnnotatedFeatureI feat = (AnnotatedFeatureI)o;
if (feat.getId().equals(gene.getId())) {
//gene = feat;
break;
}
}
*/
if (evt.isAdd()) {
AnnotatedFeatureI annotToDisplay = null;
AnnotatedFeatureI gene = evt.getChangedAnnot();
int trans_count = gene.size();
for (int i = 0; i < trans_count; ++i) {
Transcript t = (Transcript) gene.getFeatureAt(i);
if (evt.isUndo()) {
// System.out.printf("Attaching %s(%d)\n", t, t.hashCode());
editorPanel.attachAnnot(t);
if (currentAnnot != null && t.getName().equals(currentAnnot.getName())) {
annotToDisplay = t;
}
}
}
if (annotToDisplay == null) {
annotToDisplay = (AnnotatedFeatureI) evt.getChangedAnnot().getFeatureAt(0);
}
displayAnnot(annotToDisplay);
return true;
}
if (evt.isDelete()) {
AnnotatedFeatureI gene = evt.getChangedAnnot();
int trans_count = gene.size();
for (int i = 0; i < trans_count; ++i) {
if (evt.isUndo()) {
Transcript t = (Transcript) gene.getFeatureAt(i);
// System.out.printf("Detaching %s(%d)\n", t, t.hashCode());
editorPanel.detachTranscript(t);
}
}
return true;
}
/*
// getAnnotation() can be null after a delete - return if null?
SeqFeatureI sf = evt.getAnnotTop();
// If the annotation event is not for the editors strand then return
boolean is_reverse = (sf.getStrand() == -1);
if (editorPanel.getReverseStrand() != is_reverse)
return false;
if (evt.isDelete() && evt.isRootAnnotChange()) {
AnnotatedFeatureI gene = evt.getChangedAnnot();
int trans_count = gene.size();
for (int i = 0; i < trans_count; i++) {
Transcript t = (Transcript) gene.getFeatureAt (i);
editorPanel.detachTranscript (t);
if (t == currentAnnot)
currentAnnot = null;
}
} else if (evt.isDelete() && evt.isTranscriptChange()) {
Transcript t = (Transcript) evt.getChangedAnnot();
editorPanel.detachTranscript (t);
if (t == currentAnnot)
currentAnnot = null;
} else if ((evt.isAdd() || evt.isSplit() || evt.isMerge()) &&
evt.isRootAnnotChange()) {
AnnotatedFeatureI gene = evt.getChangedAnnot();
int trans_count = gene.size();
for (int i = 0; i < trans_count; i++) {
Transcript t = (Transcript) gene.getFeatureAt (i);
int tier = editorPanel.attachAnnot (t);
}
} else if (evt.isAdd() && evt.isTranscriptChange()) {
Transcript t = (Transcript) evt.getChangedAnnot();
int tier = editorPanel.attachAnnot (t);
}
// Exon split or intron made - same thing isnt it?
else if (evt.isAdd() && evt.isExonChange()) {
Transcript t = (Transcript) evt.getParentFeature();
// removing and adding transcript will force editorPanel
// to pick up new exon
editorPanel.detachTranscript(t);
editorPanel.attachAnnot(t);
}
else if (evt.isDelete() && evt.isExonChange()) {
Transcript t = (Transcript) evt.getParentFeature();
// removing and adding transcript will force editorPanel to remove exon
editorPanel.detachTranscript(t);
editorPanel.attachAnnot(t);
// or editorPanel.removeFeature((Exon)evt.getSecondFeature());
}
// else if (evt.isReplace()) { //&&evt.isTopAnnotChange - always true of replace
// AnnotatedFeatureI old_gene = evt.getReplacedFeature();
// AnnotatedFeatureI new_gene = (AnnotatedFeatureI)evt.getChangedFeature();
// int trans_count = old_gene.size();
// /* This does assume that there are no changes in the number
// of transcripts between the old and the new. Might be safer
// to separate the 2 loops */
// for (int i = 0; i < trans_count; i++) {
// Transcript t;
// t = (Transcript) old_gene.getFeatureAt (i);
// editorPanel.detachTranscript (t);
// t = (Transcript) new_gene.getFeatureAt (i);
// int tier = editorPanel.attachTranscript (t);
// }
// // This is so that we don't select a different transcript
// AnnotatedFeatureI current_gene = (current_transcript != null ?
// current_transcript.getGene() : null);
// if (current_gene != null && current_gene == old_gene) {
// int index = current_gene.getFeatureIndex(current_transcript);
// current_transcript = (Transcript) new_gene.getFeatureAt(index);
// }
// }
// this isnt possible - all replaces are for top annots
// else if (evt.isReplace() && evt.isTranscriptChange()) {
// Transcript old_trans = (Transcript)evt.getReplacedFeature();
// Transcript new_trans = (Transcript)evt.getChangedFeature();
// editorPanel.detachTranscript (old_trans);
// int tier = editorPanel.attachTranscript (new_trans);
// // This is so that we don't select a different transcript
// if (current_transcript != null && current_transcript == old_trans) {
// current_transcript = new_trans;
// }
// }
}
return true;
}
/** For annotations, try to find the appropriate identifier to add to the base URL. */
protected String generateAnnotURL(AnnotatedFeatureI g, String baseAnnotURL) {
if (baseAnnotURL == null || baseAnnotURL.equals("")) return null;
Hashtable id_hash = new Hashtable();
String id;
for (int i = 0; i < g.getDbXrefs().size(); i++) {
DbXref ref = (DbXref) g.getDbXrefs().elementAt(i);
id = ref.getIdValue();
// Apparently, if the id starts with FBan we want to replace "FBan" with "CG".
if (id.startsWith("FBan")) {
id = id.substring("FBan".length());
try {
int cg_num = Integer.parseInt(id);
id = "CG" + cg_num;
id_hash.put(id, id);
} catch (Exception e) {
}
} else if (id.startsWith("FB")) { // FBgn, FBab, etc.
id_hash.put(id, id);
} else if (id.startsWith("TE")) { // FBgn, FBab, etc.
id_hash.put(id, id);
}
}
id = getCG(g.getId(), "CG");
if (id != null) id_hash.put(id, id);
else {
id = getCG(g.getId(), "CR");
if (id != null) id_hash.put(id, id);
else {
id = getCG(g.getId(), "FB");
if (id != null) id_hash.put(id, id);
}
}
id = getCG(g.getName(), "CG");
if (id != null) id_hash.put(id, id);
else {
id = getCG(g.getName(), "CR");
if (id != null) id_hash.put(id, id);
}
for (int i = 0; i < g.getSynonyms().size(); i++) {
Synonym syn = (Synonym) (g.getSynonyms().elementAt(i));
id = getCG(syn.getName(), "CG");
if (id != null) id_hash.put(id, id);
else {
id = getCG(syn.getName(), "CR");
if (id != null) id_hash.put(id, id);
else {
id = getCG(g.getId(), "FB");
if (id != null) id_hash.put(id, id);
}
}
}
// The code here was glomming together all the elements into one
// big |ed string, but that's not what the FlyBase annotation report CGI wants.
// An FB or CG or CR identifier should be sufficient.
StringBuffer query_str = new StringBuffer();
for (Enumeration e = id_hash.elements(); e.hasMoreElements(); ) {
String namepart = (String) e.nextElement();
// System.out.println("Considering namepart " + namepart); // DEL
if (namepart.indexOf("FB") == 0
|| namepart.indexOf("CG") == 0
|| namepart.indexOf("CR") == 0) {
if (query_str.length() > 0) query_str.replace(0, query_str.length(), namepart);
else query_str.append(namepart);
break;
}
if (query_str.length() > 0) query_str.append('|');
query_str.append(namepart);
}
// if not FlyBase ID, use the annotation's regular ID
if (query_str.length() == 0) {
query_str.append(g.getId());
}
String url = null;
// System.out.println("generateAnnotUrl: query = " + query_str); // DEL
if (query_str.length() > 0) {
// if a custom URL is setup for this type in the tiers file, use that - otherwise use the
// global
// one setup in the style file
FeatureProperty fp = Config.getPropertyScheme().getFeatureProperty(g.getTopLevelType());
if (fp.getURLString() != null && fp.getURLString().length() > 0) {
url = fp.getURLString() + g.getId();
} else {
url = baseAnnotURL + query_str.toString();
}
}
return url;
}
