- {
- if (sequences[i].getAnnotation() != null)
- {
- for (int a = 0; a < sequences[i].getAnnotation().length; a++)
- {
- AlignmentAnnotation newAnnot =
- new AlignmentAnnotation(
- sequences[i].getAnnotation()[a].label,
- sequences[i].getAnnotation()[a].description,
- sequences[i].getAnnotation()[a].annotations,
- sequences[i].getAnnotation()[a].graphMin,
- sequences[i].getAnnotation()[a].graphMax,
- sequences[i].getAnnotation()[a].graph);
-
- sequences[i].getAnnotation()[a] = newAnnot;
- newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
- sequenceMapping;
- newAnnot.sequenceRef = sequences[i];
- newAnnot.adjustForAlignment();
- alignment.addAnnotation(newAnnot);
- alignment.setAnnotationIndex(newAnnot, a);
- }
-
- alignPanel.annotationPanel.adjustPanelHeight();
- }
- }
-
- if(newAlignment)
- {
- AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- String newtitle = new String("Copied sequences");
-
- if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
- {
- Vector hc = (Vector)Desktop.jalviewClipboard[2];
- for(int i=0; i<hc.size(); i++)
- {
- int [] region = (int[]) hc.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
- }
- }
+ {
+ if (sequences[i].getAnnotation() != null)
+ {
+ for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+ {
+ AlignmentAnnotation newAnnot =
+ new AlignmentAnnotation(
+ sequences[i].getAnnotation()[a].label,
+ sequences[i].getAnnotation()[a].description,
+ sequences[i].getAnnotation()[a].annotations,
+ sequences[i].getAnnotation()[a].graphMin,
+ sequences[i].getAnnotation()[a].graphMax,
+ sequences[i].getAnnotation()[a].graph);
+
+ sequences[i].getAnnotation()[a] = newAnnot;
+ newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
+ sequenceMapping;
+ newAnnot.sequenceRef = sequences[i];
+ newAnnot.adjustForAlignment();
+ alignment.addAnnotation(newAnnot);
+ alignment.setAnnotationIndex(newAnnot, a);
+ }