/**
* 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;
}
/* 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;
}
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;
}