+ @Override
+ public AlignmentAnnotation findOrCreateAnnotation(String name,
+ String calcId, boolean autoCalc, SequenceI seqRef,
+ SequenceGroup groupRef)
+ {
+ assert (name != null);
+ for (AlignmentAnnotation annot : getAlignmentAnnotation())
+ {
+ if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+ && (calcId == null || annot.getCalcId().equals(calcId))
+ && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+ {
+ return annot;
+ }
+ }
+ AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
+ new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
+ annot.hasText = false;
+ annot.setCalcId(new String(calcId));
+ annot.autoCalculated = autoCalc;
+ if (seqRef != null)
+ {
+ annot.setSequenceRef(seqRef);
+ }
+ annot.groupRef = groupRef;
+ addAnnotation(annot);
+
+ return annot;
+ }
+
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
+ {
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
+ {
+ if (a.getCalcId() == calcId
+ || (a.getCalcId() != null && calcId != null && a.getCalcId()
+ .equals(calcId)))
+ {
+ aa.add(a);
+ }
+ }
+ return aa;
+ }
+
+ @Override
+ public void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map<SequenceI, SequenceCollectionI> map, boolean up)
+ {
+ synchronized (sequences)
+ {
+ if (up)
+ {
+
+ for (int i = 1, iSize = sequences.size(); i < iSize; i++)
+ {
+ SequenceI seq = sequences.get(i);
+ if (!sg.getSequences(map).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = sequences.get(i - 1);
+ if (sg.getSequences(null).contains(temp))
+ {
+ continue;
+ }
+
+ sequences.set(i, temp);
+ sequences.set(i - 1, seq);
+ }
+ }
+ else
+ {
+ for (int i = sequences.size() - 2; i > -1; i--)
+ {
+ SequenceI seq = sequences.get(i);
+ if (!sg.getSequences(map).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = sequences.get(i + 1);
+ if (sg.getSequences(map).contains(temp))
+ {
+ continue;
+ }
+
+ sequences.set(i, temp);
+ sequences.set(i + 1, seq);
+ }
+ }
+
+ }
+ }
+