- private Vector<String> getAnnotationItems(boolean isSeqAssociated) {
- Vector<String> list = new Vector<String>();
- int index = 1;
- int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
- boolean enableSeqAss=false;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
- {
- if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef==null)
- {
- if (isSeqAssociated)
- {
- continue;
- }
- } else {
- enableSeqAss=true;
- }
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
- if (!list.contains(label))
- {anmap[list.size()] = i;
- list.addElement(label);
-
- }else {
- if (!isSeqAssociated) {
- anmap[list.size()] = i;
- list.addElement(label + "_" + (index++));
- }
- }
- }
- seqAssociated.setEnabled(enableSeqAss);
- annmap = new int[list.size()];
- System.arraycopy(anmap, 0, annmap, 0, annmap.length);
- return list;
- }
- private void setDefaultMinMax()