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;
}
/* Searches for the "SELECTED" feature and removes it if it exists */
void removeSelectedFeature() {
boolean found = true;
ArrayList<FeatureSlot> slots = cgview.getFeatureSlots();
for (int i = 0; i < slots.size(); i++) {
FeatureSlot fs = slots.get(i);
ArrayList<Feature> features = fs.getFeatures();
for (int j = 0; j < features.size(); j++) {
Feature f = features.get(j);
if (f.getLabel().equals("SELECTED")) {
found = true;
features.remove(j);
break;
}
}
if (found) break;
}
repaint();
}
@Override
public void mousePressed(MouseEvent me) {
/* Check to see if we clicked a label */
int x = me.getX(), y = me.getY();
Feature selectedFeature = null;
ArrayList<OuterLabel> outerLabels = cgview.getOuterLabels();
OuterLabel ol = null;
for (int o = 0; o < outerLabels.size(); o++) {
ol = outerLabels.get(o);
Rectangle2D rect = ol.getBounds();
double rectX = rect.getX(),
rectY = rect.getY(),
rectW = rect.getWidth(),
rectH = rect.getHeight();
if (x > rectX && x < (rectX + rectW) && y > rectY && y < (rectY + rectH)) {
ArrayList<FeatureSlot> featureSlots = cgview.getFeatureSlots();
for (int i = 0; i < featureSlots.size(); i++) {
FeatureSlot fs = featureSlots.get(i);
ArrayList<Feature> features = fs.getFeatures();
for (int j = 0; j < features.size(); j++) {
Feature f = features.get(j);
String featureLabel = f.getLabel();
if (featureLabel.equals(ol.getLabelText())) {
selectedFeature = f;
break;
}
if (selectedFeature != null) break;
}
if (selectedFeature != null) break;
}
}
if (selectedFeature != null) break;
}
/* If we have selected a feature, either make it appear selected or
* deselected. */
if (selectedFeature != null) {
// paint the feature on the cgview
Annotation a = findAnnotationOfFeature(selectedFeature);
Color toUse =
(a.getScore() == 1.0)
? ColorConstants.NEUTRAL_COLOR_PERFECT_MATCH
: ColorConstants.NEUTRAL_COLOR_IMPERFECT_MATCH;
Color fColor = selectedFeature.getColor();
Color blue =
(a.getScore() == 1.0)
? ColorConstants.NEUTRAL_COLOR_PERFECT_MATCH
: ColorConstants.NEUTRAL_COLOR_IMPERFECT_MATCH;
Color orange = ColorConstants.ROW_SELECTED_COLOR;
boolean isBlue =
fColor.getRed() == blue.getRed()
&& fColor.getGreen() == blue.getGreen()
&& fColor.getBlue() == blue.getBlue();
boolean isOrange =
fColor.getRed() == orange.getRed()
&& fColor.getGreen() == orange.getGreen()
&& fColor.getBlue() == orange.getBlue();
Color turq = ColorConstants.CUSTOM_ANNOTATION_COLOR;
boolean isTurquoise =
fColor.getRed() == turq.getRed()
&& fColor.getGreen() == turq.getGreen()
&& fColor.getBlue() == turq.getBlue();
Color ye = ColorConstants.VIEW_FEATURE_FROM_PRIVATE_REGISTRY_COLOR;
boolean isYellow =
fColor.getRed() == ye.getRed()
&& fColor.getGreen() == ye.getGreen()
&& fColor.getBlue() == ye.getBlue();
if (isBlue || isOrange || isTurquoise || isYellow) {
toUse = ColorConstants.SELECTED_COLOR;
selectedFeatures.add(selectedFeature.getLabel());
} else if (((MyTableModel) home.getTable().getModel())
.isFeatureSelected(selectedFeature.getLabel())) {
toUse = ColorConstants.ROW_SELECTED_COLOR;
selectedFeatures.remove(selectedFeature.getLabel());
} else {
toUse =
(a.getScore() == 1.0)
? ColorConstants.NEUTRAL_COLOR_PERFECT_MATCH
: ColorConstants.NEUTRAL_COLOR_IMPERFECT_MATCH;
selectedFeatures.remove(selectedFeature.getLabel());
}
selectedFeature.setColor(toUse);
ArrayList<FeatureRange> f = selectedFeature.getRanges();
for (int n = 0; n < f.size(); n++) {
f.get(n).setColor(toUse);
}
// ol.setColor(Color.red);
repaint();
// highlight text in the textpane
FeatureRange fr = (FeatureRange) selectedFeature.getRanges().get(0);
if (home != null) home.highlightDNA(fr);
} else {
System.out.println("selected feature is null");
}
}