/** 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();
}
}
}
/**
* 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;
}
/** 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();
}
}
}
/**
* 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());
}