/* Draws a feature called "SELECTED" when the user highlights DNA */
void paintSelectedFeature(int start, int end) {
// first see if a selected feature already exists
// if it does, remove it
removeSelectedFeature();
// paint the new one
Feature f = new Feature(cgview.getFeatureSlots().get(0), "SELECTED");
f.setColor(Color.green);
new FeatureRange(f, start, end);
repaint();
}
/* 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());
}
}
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");
}
}