public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
- this(av,ap,null);
+ this(av, ap, null);
}
- public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,AnnotationColourGradient initSettings)
+
+ public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,
+ AnnotationColourGradient initSettings)
{
super(av, ap);
oldcs = av.getGlobalColourScheme();
setDefaultMinMax();
adjusting = true;
- if (oldcs instanceof AnnotationColourGradient && initSettings==null)
+ if (oldcs instanceof AnnotationColourGradient && initSettings == null)
{
// init from oldcs
initialiseFrom((AnnotationColourGradient) oldcs);
- } else {
+ }
+ else
+ {
// use initial colour gradient - if any..
initialiseFrom(initSettings);
}
-
+
jbInit();
adjusting = false;
frame.invalidate();
frame.pack();
}
+
private void initialiseFrom(AnnotationColourGradient acg)
{
- if (acg!=null)
+ if (acg != null)
{
useOriginalColours.setSelected(
- acg.isPredefinedColours() || acg.getBaseColour() != null);
+ acg.isPredefinedColours() || acg.getBaseColour() != null);
if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
populateThresholdComboBox(threshold);
- if (acg!=null)
+ if (acg != null)
{
String label = getAnnotationMenuLabel(acg.getAnnotation());
- // TODO: workaround below shouldn't be necessary - there's a bug in getAnnotationMenuLabel!
+ // TODO: workaround below shouldn't be necessary - there's a bug in
+ // getAnnotationMenuLabel!
if (acg.isSeqAssociated())
{
label = acg.getAnnotation().label;
return;
}
- int selIndex = annotations
- .getSelectedIndex();
+ int selIndex = annotations.getSelectedIndex();
int annIndex = annmap[selIndex];
setCurrentAnnotation(
av.getAlignment().getAlignmentAnnotation()[annIndex]);
* @param av
* @param ap
* @param alignmentAnnotation
- * @param perseq - when true, enable per-sequence if alignment annotation is per sequence
+ * @param perseq
+ * - when true, enable per-sequence if alignment annotation is per
+ * sequence
*/
public static void displayFor(AlignViewport av, AlignmentPanel ap,
AlignmentAnnotation alignmentAnnotation, boolean perSeq)
{
ColourSchemeI global = av.getGlobalColourScheme();
- AnnotationColourGradient newCS = new AnnotationColourGradient(alignmentAnnotation, global, alignmentAnnotation.threshold!=null ? AnnotationColourGradient.ABOVE_THRESHOLD:AnnotationColourGradient.NO_THRESHOLD);
- if (alignmentAnnotation.sequenceRef!=null)
+ AnnotationColourGradient newCS = new AnnotationColourGradient(
+ alignmentAnnotation, global,
+ alignmentAnnotation.threshold != null
+ ? AnnotationColourGradient.ABOVE_THRESHOLD
+ : AnnotationColourGradient.NO_THRESHOLD);
+ if (alignmentAnnotation.sequenceRef != null)
{
newCS.setSeqAssociated(perSeq);
}
- for (int i=0;i<alignmentAnnotation.annotations.length;i++)
+ for (int i = 0; i < alignmentAnnotation.annotations.length; i++)
{
Annotation ann = alignmentAnnotation.annotations[i];
- if (ann!=null && ann.colour!=null && !ann.colour.equals(Color.white))
+ if (ann != null && ann.colour != null
+ && !ann.colour.equals(Color.white))
{
newCS.setPredefinedColours(true);
break;
}
}
- AnnotationColourChooser achooser = new AnnotationColourChooser(av,ap,newCS);
+ AnnotationColourChooser achooser = new AnnotationColourChooser(av, ap,
+ newCS);
}
}