private String generateAnalysisURL(SeqFeatureI f) {
// Figure out URL for getting more information about this feature.
// If more than one feature was selected, use the LAST one.
String id = getIdForURL(f);
FeatureProperty prop = Config.getPropertyScheme().getFeatureProperty(f.getFeatureType());
String urlPrefix = getURLPrefix(prop, f, id);
if (urlPrefix == null) {
String m =
"Sorry, no URL registered for type "
+ f.getFeatureType()
+ "\nin tiers file "
+ Config.getStyle().getTiersFile();
JOptionPane.showMessageDialog(null, m);
return null;
}
return URLQueryGenerator.getURL(urlPrefix, id);
}
/**
* This just returns sf.getBioType() (capitalized) unless its a transcript. For transcript it only
* returns "Transcript" if its part of a Gene. Otherwise it returns its parent's bio type +
* transcript. (should it not tack on the transcript?) Thus a tRNA's transcript would display
* "tRNA transcript", where a gene's transcript would display just "Transcript". Should it
* actually display "Gene transcript"? rename getTypeForDisplay?
*/
public String getBioTypeForDisplay(SeqFeatureI sf) {
String typeDisplay;
if (sf instanceof AnnotatedFeatureI) {
typeDisplay = sf.getTopLevelType();
typeDisplay = capitalize(typeDisplay);
if (!sf.getTopLevelType().equalsIgnoreCase(sf.getFeatureType()))
typeDisplay += " " + capitalize(sf.getFeatureType());
} else {
String db = sf.getDatabase();
// Don't bother showing db name if it is "dummy"
if (db != null && !db.equals("") && !db.equals("dummy"))
typeDisplay = sf.getProgramName() + ":" + sf.getDatabase();
// yet again, the users have requested a change
// Now instead of an enumeration it is the range of the feature
else {
typeDisplay = (sf.getProgramName() + ":" + sf.getStart() + "-" + sf.getEnd());
}
}
return typeDisplay;
}
/**
* 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());
}
