private Annotation findAnnotationOfFeature(Feature f) {
List<Annotation> annotations = plasmid.getAnnotations();
for (int i = 0; i < annotations.size(); i++) {
org.autogene.core.bio.entities.Feature o = annotations.get(i).getFeature();
if (f.getLabel().equals(o.getDisplayName())) return annotations.get(i);
}
return null;
}
/* Set up the CGView to display the plasmid */
private void initCgview() {
int length = plasmid.getSequence().length();
cgview = new Cgview(length);
// some optional settings
cgview.setWidth(getWidth());
cgview.setHeight(getHeight());
cgview.setTitle(plasmid.getName());
cgview.setLabelPlacementQuality(100);
cgview.setShowWarning(true);
cgview.setLabelLineLength(8.0d);
cgview.setLabelLineThickness(0.5f);
cgview.setLabelShuffle(false);
// create a FeatureSlot to hold sequence features
FeatureSlot featureSlot = new FeatureSlot(cgview, CgviewConstants.DIRECT_STRAND);
// create random sequence features
List<org.autogene.core.bio.entities.Annotation> annotations = plasmid.getAnnotations();
HashMap<String, Integer> counts = new HashMap<String, Integer>();
// create the feature annotations to view in the plasmid
for (int i = 0; i < annotations.size(); i++) {
// update the label names such as Aapl (1) and Aapl (2) in the case that
// there is more than one of the same annotation in two different locations
Annotation a = annotations.get(i);
String name = a.getFeature().getName();
int cur = 1;
if (counts.containsKey(name)) {
cur = counts.get(name);
cur++;
counts.put(name, cur);
// Log.addText("plasmidpanel: " + name + "," + cur);
} else {
counts.put(name, cur);
// Log.addText("plasmidpanel: " + name + "," + cur);
}
// simply create the feature
System.out.println("ABCD creating feature with " + name + " " + cur);
Feature feature = new Feature(featureSlot, (name + " (" + cur + ")"));
feature.setColor(
a.getScore() == 1.0
? ColorConstants.NEUTRAL_COLOR_PERFECT_MATCH
: ColorConstants.NEUTRAL_COLOR_IMPERFECT_MATCH);
FeatureRange featureRange = new FeatureRange(feature, a.getStart(), a.getEnd());
}
}