void updateCgviewSize() {
cgview.setWidth(getWidth());
cgview.setHeight(getHeight());
cgview.setBackboneRadius(Math.min(getWidth(), getHeight()) * 0.35);
System.out.println("repainting plasmidpanel line 161 " + (count++));
repaint();
}
/**
* Writes this map to a JPG file.
*
* @param filename the path and name of the file to create.
*/
public void writeToJPGFile(String filename) throws IOException {
this.prepareToDraw();
BufferedImage buffImage =
new BufferedImage(p.getWidth(), p.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D graphics2D = buffImage.createGraphics();
try {
p.draw(graphics2D);
System.out.println("Writing picture to " + filename);
ImageIO.write(buffImage, "JPG", new File(filename));
} finally {
graphics2D.dispose();
}
}
/**
* Overridden paint component method. Update the size, then repaint the plasmid
*
* @param g graphics object
*/
public void paintComponent(Graphics g) {
// super.paintComponent(g);
System.out.println("paint component called");
// if((previousWidth == -1 && previousHeight == -1) || (homePanel.getWidth() != previousWidth)
// || (homePanel.getHeight() != previousHeight)) {
super.paintComponent(g);
System.out.println("calling paint component because " + previousWidth + " " + previousHeight);
setSize(homePanel.getWidth(), homePanel.getHeight());
cgview.setWidth(getWidth());
cgview.setHeight(getHeight());
cgview.setBackboneRadius(Math.min(getWidth(), getHeight()) * 0.28);
cgview.setTitleFont(new Font("Georgia", Font.PLAIN, 16));
// updateCgviewSize();
cgview.draw((Graphics2D) g);
previousWidth = homePanel.getWidth();
previousHeight = homePanel.getHeight();
// }
}
/* 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());
}
}
/* 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();
}
/* 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();
}
private void prepareToDraw() {
if (forwardSlot0 != null) {
forwardSlot0.setCgview(p);
forwardSlot0.setFeatureThickness(featureThickness);
}
if (forwardSlot1 != null) {
forwardSlot1.setCgview(p);
forwardSlot1.setFeatureThickness(featureThickness);
}
if (forwardSlot2 != null) {
forwardSlot2.setCgview(p);
forwardSlot2.setFeatureThickness(featureThickness);
}
if (forwardSlot3 != null) {
forwardSlot3.setCgview(p);
forwardSlot3.setFeatureThickness(featureThickness);
}
if (forwardSlot4 != null) {
forwardSlot4.setCgview(p);
forwardSlot4.setFeatureThickness(featureThickness);
}
if (forwardSlot5 != null) {
forwardSlot5.setCgview(p);
forwardSlot5.setFeatureThickness(featureThickness);
}
if (forwardSlot6 != null) {
forwardSlot6.setCgview(p);
forwardSlot6.setFeatureThickness(featureThickness);
}
if (forwardSlot7 != null) {
forwardSlot7.setCgview(p);
forwardSlot7.setFeatureThickness(featureThickness);
}
if (reverseSlot0 != null) {
reverseSlot0.setCgview(p);
reverseSlot0.setFeatureThickness(featureThickness);
}
if (reverseSlot1 != null) {
reverseSlot1.setCgview(p);
reverseSlot1.setFeatureThickness(featureThickness);
}
if (reverseSlot2 != null) {
reverseSlot2.setCgview(p);
reverseSlot2.setFeatureThickness(featureThickness);
}
if (reverseSlot3 != null) {
reverseSlot3.setCgview(p);
reverseSlot3.setFeatureThickness(featureThickness);
}
if (reverseSlot4 != null) {
reverseSlot4.setCgview(p);
reverseSlot4.setFeatureThickness(featureThickness);
}
if (reverseSlot5 != null) {
reverseSlot5.setCgview(p);
reverseSlot5.setFeatureThickness(featureThickness);
}
if (reverseSlot6 != null) {
reverseSlot6.setCgview(p);
reverseSlot6.setFeatureThickness(featureThickness);
}
if (reverseSlot7 != null) {
reverseSlot7.setCgview(p);
reverseSlot7.setFeatureThickness(featureThickness);
}
if (restrictionSlot != null) {
restrictionSlot.setCgview(p);
restrictionSlot.setFeatureThickness(featureThickness);
}
// send settings to p
if (showTitle) {
p.setTitle(title);
}
p.setWidth(imageWidth);
p.setHeight(imageHeight);
p.setLabelsToKeep(MAXLABELS);
p.setDrawTickMarks(drawTickMarks);
p.setTitleFont(titleFont);
p.setLabelFont(labelFont);
p.setFeatureThickness(featureThickness);
p.setBackboneThickness(backboneThickness);
p.setFeatureSlotSpacing(featureSpacing);
p.setLegendFont(legendFont);
p.setTickLength(tickLength);
p.setLabelLineLength(labelLineLength);
p.setLabelPlacementQuality(labelPlacementQuality);
p.setUseColoredLabelBackgrounds(useColoredLabelBackground);
p.setShowBorder(showBorder);
p.setShowShading(showShading);
p.setShadingProportion(shadingProportion);
p.setUseInnerLabels(useInnerLabels);
p.setMoveInnerLabelsToOuter(moveInnerLabelsToOuter);
p.setWarningFont(rulerFont);
p.setRulerFont(rulerFont);
// if not drawing labels, don't show message.
if (!(showLabels)) {
p.setShowWarning(false);
}
// set backboneRadius based on smallest image dimension
int smallestDimension = Math.min(imageWidth, imageHeight);
if (smallestDimension <= 750) {
p.setBackboneRadius(0.50d * (double) smallestDimension / 2.0d);
} else {
p.setBackboneRadius(0.50d * 750.0d / 2.0d);
}
// check coloredLabels
if (!(useColoredLabels)) {
if (colorScheme == REGULAR) {
p.setGlobalLabelColor((Color) MAP_ITEM_COLORS.get("titleFont"));
} else if (colorScheme == INVERSE) {
p.setGlobalLabelColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
}
}
// set map item colors
if (colorScheme == REGULAR) {
p.setLongTickColor((Color) MAP_ITEM_COLORS.get("tick"));
p.setShortTickColor((Color) MAP_ITEM_COLORS.get("partialTick"));
p.setZeroTickColor((Color) MAP_ITEM_COLORS.get("zeroLine"));
p.setRulerFontColor((Color) MAP_ITEM_COLORS.get("rulerFont"));
p.setBackboneColor((Color) MAP_ITEM_COLORS.get("backbone"));
p.setTitleFontColor((Color) MAP_ITEM_COLORS.get("titleFont"));
p.setWarningFontColor((Color) MAP_ITEM_COLORS.get("titleFont"));
p.setBackgroundColor((Color) MAP_ITEM_COLORS.get("background"));
} else if (colorScheme == INVERSE) {
p.setLongTickColor((Color) MAP_ITEM_COLORS_INVERSE.get("tick"));
p.setShortTickColor((Color) MAP_ITEM_COLORS_INVERSE.get("partialTick"));
p.setZeroTickColor((Color) MAP_ITEM_COLORS_INVERSE.get("zeroLine"));
p.setRulerFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("rulerFont"));
p.setBackboneColor((Color) MAP_ITEM_COLORS_INVERSE.get("backbone"));
p.setTitleFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
p.setWarningFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
p.setBackgroundColor((Color) MAP_ITEM_COLORS_INVERSE.get("background"));
}
// build legend
if ((showLegend) && (DRAW_LEGEND_ITEMS.size() > 0)) {
// create legend
legend = new Legend(p);
legend.setAllowLabelClash(allowLabelClashLegend);
legend.setBackgroundOpacity(0.5f);
legend.setFont(legendFont);
legend.setPosition(legendPosition);
if (colorScheme == REGULAR) {
legend.setBackgroundColor((Color) MAP_ITEM_COLORS.get("background"));
legend.setFontColor((Color) MAP_ITEM_COLORS.get("titleFont"));
} else if (colorScheme == INVERSE) {
legend.setBackgroundColor((Color) MAP_ITEM_COLORS_INVERSE.get("background"));
legend.setFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
}
LegendItem legendItem;
Enumeration legendEntries = DRAW_LEGEND_ITEMS.keys();
ArrayList list = new ArrayList();
while (legendEntries.hasMoreElements()) {
list.add(legendEntries.nextElement());
}
Collections.sort(list);
Iterator i = list.iterator();
while (i.hasNext()) {
String key = (String) i.next();
legendItem = new LegendItem(legend);
legendItem.setDrawSwatch(SWATCH_SHOW);
legendItem.setLabel((String) LEGEND_ITEM_NAMES.get(key));
if (colorScheme == REGULAR) {
legendItem.setSwatchColor((Color) FEATURE_COLORS.get(key));
} else if (colorScheme == INVERSE) {
legendItem.setSwatchColor((Color) FEATURE_COLORS_INVERSE.get(key));
}
}
}
// set message
if (showMessage) {
legend = new Legend(p);
legend.setAllowLabelClash(false);
legend.setBackgroundOpacity(0.5f);
legend.setFont(messageFont);
legend.setPosition(LEGEND_LOWER_RIGHT);
LegendItem legendItem;
if (colorScheme == REGULAR) {
legend.setBackgroundColor((Color) MAP_ITEM_COLORS.get("background"));
legend.setFontColor((Color) MAP_ITEM_COLORS.get("titleFont"));
legendItem = new LegendItem(legend);
legendItem.setLabel(message);
legendItem.setDrawSwatch(SWATCH_NO_SHOW);
} else if (colorScheme == INVERSE) {
legend.setBackgroundColor((Color) MAP_ITEM_COLORS_INVERSE.get("background"));
legend.setFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
legendItem = new LegendItem(legend);
legendItem.setLabel(message);
legendItem.setDrawSwatch(SWATCH_NO_SHOW);
}
}
}
@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");
}
}
