{
private Alignment dataset;
- protected List<SequenceI> sequences;
+ private List<SequenceI> sequences;
protected List<SequenceGroup> groups;
return sequences.get(i);
}
}
+
return null;
}
public int getWidth()
{
int maxLength = -1;
-
+
for (int i = 0; i < sequences.size(); i++)
{
- if (getSequenceAt(i).getLength() > maxLength)
- {
- maxLength = getSequenceAt(i).getLength();
- }
+ maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
}
-
return maxLength;
}
AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
annot.hasText = false;
- annot.setCalcId(new String(calcId));
+ if (calcId != null)
+ {
+ annot.setCalcId(new String(calcId));
+ }
annot.autoCalculated = autoCalc;
if (seqRef != null)
{