import jalview.analysis.AlignmentSorter;
import jalview.commands.OrderCommand;
import jalview.datamodel.*;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
public class FeatureSettings extends Panel implements ItemListener,
MouseListener, MouseMotionListener, ActionListener,
g.drawString("(Features can be added from searches or", 10, 40);
g.drawString("from Jalview / GFF features files)", 10, 60);
}
- protected void popupSort(final String type, final Hashtable minmax,
+
+ protected void popupSort(final MyCheckbox check, final Hashtable minmax,
int x, int y)
{
+ final String type = check.type;
java.awt.PopupMenu men = new PopupMenu("Settings for " + type);
java.awt.MenuItem scr = new MenuItem("Sort by Score");
men.add(scr);
if (minmax != null)
{
final Object typeMinMax = minmax.get(type);
- final java.awt.CheckboxMenuItem chb = new java.awt.CheckboxMenuItem("Vary Height");
- // this is broken at the moment
- chb.setState(minmax.get(type) != null);
- chb.addActionListener(new ActionListener()
- {
-
- public void actionPerformed(ActionEvent e)
- {
- chb.setState(chb.getState());
- if (chb.getState())
- {
- minmax.put(type, null);
- }
- else
- {
- minmax.put(type, typeMinMax);
- }
- }
-
- });
- men.add(chb);
+ /*
+ * final java.awt.CheckboxMenuItem chb = new
+ * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the
+ * moment chb.setState(minmax.get(type) != null);
+ * chb.addActionListener(new ActionListener() {
+ *
+ * public void actionPerformed(ActionEvent e) {
+ * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type,
+ * null); } else { minmax.put(type, typeMinMax); } }
+ *
+ * }); men.add(chb);
+ */
if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
{
- // graduated colourschemes for those where minmax exists for the positional features
- MenuItem mxcol = new MenuItem("Min Max Colour");
+ // graduated colourschemes for those where minmax exists for the
+ // positional features
+ MenuItem mxcol = new MenuItem("Graduated Colour");
men.add(mxcol);
mxcol.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
new FeatureColourChooser(me, type);
+ // write back the current colour object to update the table
+ check.updateColor(fr.getFeatureStyle(type));
}
});
Component[] comps;
int cSize = featurePanel.getComponentCount();
- Checkbox check;
+ MyCheckbox check;
// This will remove any checkboxes which shouldn't be
// visible
for (int i = 0; i < cSize; i++)
{
comps = featurePanel.getComponents();
- check = (Checkbox) comps[i];
- if (!visibleChecks.contains(check.getLabel()))
+ check = (MyCheckbox) comps[i];
+ if (!visibleChecks.contains(check.type))
{
featurePanel.remove(i);
cSize--;
* update the checklist of feature types with the given type
*
* @param groupsChanged
- * true means if the type is not in the display list then it
- * will be added and displayed
+ * true means if the type is not in the display list then it will be
+ * added and displayed
* @param type
- * feature type to be checked for in the list.
+ * feature type to be checked for in the list.
*/
void addCheck(boolean groupsChanged, String type)
{
boolean addCheck;
Component[] comps = featurePanel.getComponents();
- Checkbox check;
+ MyCheckbox check;
addCheck = true;
for (int i = 0; i < featurePanel.getComponentCount(); i++)
{
- check = (Checkbox) comps[i];
- if (check.getLabel().equals(type))
+ check = (MyCheckbox) comps[i];
+ if (check.type.equals(type))
{
addCheck = false;
break;
check = new MyCheckbox(
type,
selected,
- (fr.featureLinks != null && fr.featureLinks.containsKey(type)));
+ (fr.featureLinks != null && fr.featureLinks.containsKey(type)),
+ fr.getFeatureStyle(type));
check.addMouseListener(this);
check.addMouseMotionListener(this);
- check.setBackground(fr.getColour(type));
check.addItemListener(this);
if (groupsChanged)
{
int tmpSize = 0;
for (int i = 0; i < cSize; i++)
{
- Checkbox check = (Checkbox) comps[i];
- tmp[tmpSize][0] = check.getLabel();
- tmp[tmpSize][1] = fr.getColour(check.getLabel());
+ MyCheckbox check = (MyCheckbox) comps[i];
+ tmp[tmpSize][0] = check.type;
+ tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
tmp[tmpSize][2] = new Boolean(check.getState());
tmpSize++;
}
selectedCheck = (MyCheckbox) evt.getSource();
if (fr.featureLinks != null
- && fr.featureLinks.containsKey(selectedCheck.getLabel()))
+ && fr.featureLinks.containsKey(selectedCheck.type))
{
if (evt.getX() > selectedCheck.stringWidth + 20)
{
public void mouseClicked(MouseEvent evt)
{
MyCheckbox check = (MyCheckbox) evt.getSource();
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK)!=0)
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
{
- this.popupSort(check.getLabel(), fr.minmax, evt.getX(), evt.getY());
+ this.popupSort(check, fr.minmax, evt.getX(), evt.getY());
}
if (fr.featureLinks != null
- && fr.featureLinks.containsKey(check.getLabel()))
+ && fr.featureLinks.containsKey(check.type))
{
if (evt.getX() > check.stringWidth + 20)
{
evt.consume();
- String link = fr.featureLinks.get(check.getLabel()).toString();
+ String link = fr.featureLinks.get(check.type).toString();
ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), link
.substring(0, link.indexOf("|")));
}
if (evt.getClickCount() > 1)
{
- new UserDefinedColours(this, check.getLabel(), fr.getColour(check
- .getLabel()));
+ Object fcol = fr.getFeatureStyle(check.type);
+ if (fcol instanceof Color)
+ {
+ new UserDefinedColours(this, check.type, (Color) fcol);
+ } else {
+ new FeatureColourChooser(this, check.type);
+ // write back the current colour object to update the table
+ check.updateColor(fr.getFeatureStyle(check.type));
+ }
}
}
class MyCheckbox extends Checkbox
{
+ public String type;
public int stringWidth;
boolean hasLink;
+ GraduatedColor gcol;
+
+ Color col;
+
+ public void updateColor(Object newcol)
+ {
+ if (newcol instanceof Color)
+ {
+ col = (Color) newcol;
+ gcol = null;
+ }
+ else if (newcol instanceof GraduatedColor)
+ {
+ gcol = (GraduatedColor) newcol;
+ col = null;
+ }
+ else
+ {
+ throw new Error("Invalid color for MyCheckBox");
+ }
+ if (col != null)
+ {
+ setBackground(col);
+ }
+ else
+ {
+ String vlabel = type;
+ if (gcol.getThreshType()!=AnnotationColourGradient.NO_THRESHOLD)
+ {
+ vlabel += " "+((gcol.getThreshType()==AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" : "(<)");
+ }
+ if (gcol.isColourByLabel()) {
+ setBackground(Color.white);
+ vlabel += " (by Label)";
+ } else {
+ setBackground(gcol.getMinColor());
+ }
+ this.setLabel(vlabel);
+ }
+ repaint();
+ }
+
public MyCheckbox(String label, boolean checked, boolean haslink)
{
super(label, checked);
-
+ type = label;
FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
stringWidth = fm.stringWidth(label);
this.hasLink = haslink;
}
+ public MyCheckbox(String type, boolean selected, boolean b,
+ Object featureStyle)
+ {
+ this(type,selected,b);
+ updateColor(featureStyle);
+ }
+
public void paint(Graphics g)
{
+ int width = getWidth(), height = getHeight();
+ if (gcol != null)
+ {
+ if (gcol.isColourByLabel())
+ {
+ g.setColor(Color.white);
+ g.fillRect(width/2, 0,width/2, height);
+ /*g.setColor(Color.black);
+ Font f=g.getFont().deriveFont(9);
+ g.setFont(f);
+
+ // g.setFont(g.getFont().deriveFont(
+ // AffineTransform.getScaleInstance(
+ // width/g.getFontMetrics().stringWidth("Label"),
+ // height/g.getFontMetrics().getHeight())));
+ g.drawString("Label", width/2, 0); */
+
+ }
+ else
+ {
+ Color maxCol = gcol.getMaxColor();
+ g.setColor(maxCol);
+ g.fillRect(width/2, 0,width/2, height);
+
+ }
+ }
+
if (hasLink)
{
g.drawImage(linkImage, stringWidth + 25,
}
}
}
+
protected void sortByDens(String[] typ)
{
sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
}
+
private String[] getDisplayedFeatureTypes()
{
String[] typ = null;
return typ;
}
-
protected void sortBy(String[] typ, String methodText, final String method)
{
if (typ == null)
}
SequenceI[] oldOrder = al.getSequencesArray();
AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
- this.ap.alignFrame.addHistoryItem(new OrderCommand(methodText, oldOrder, alignPanel.av
- .getAlignment()));
+ this.ap.alignFrame.addHistoryItem(new OrderCommand(methodText,
+ oldOrder, alignPanel.av.getAlignment()));
alignPanel.paintAlignment(true);
}
git://source.jalview.org / jalview.git / blobdiff