}
/**
- * Add s to this sequence group
+ * Add s to this sequence group. If aligment sequence is already contained in
+ * group, it will not be added again, but recalculation may happen if the flag
+ * is set.
*
* @param s
* alignment sequence to be added
{
return getSequencesInOrder(al, true);
}
+
/**
- * return an array representing the intersection of the group with al, optionally returning an array the size of al.getHeight()
- * where nulls mark the non-intersected sequences
+ * return an array representing the intersection of the group with al,
+ * optionally returning an array the size of al.getHeight() where nulls mark
+ * the non-intersected sequences
+ *
* @param al
* @param trim
* @return null or array
private boolean showConsensusHistogram;
/**
+ * set this alignmentAnnotation object as the one used to render consensus annotation
+ * @param aan
+ */
+ public void setConsensus(AlignmentAnnotation aan)
+ {
+ if (consensus==null)
+ {
+ consensus=aan;
+ }
+ }
+
+ /**
*
* @return automatically calculated consensus row
*/
}
/**
+ * set this alignmentAnnotation object as the one used to render consensus annotation
+ * @param aan
+ */
+ public void setConservationRow(AlignmentAnnotation aan)
+ {
+ if (conservation==null)
+ {
+ conservation=aan;
+ }
+ }
+ /**
* get the conservation annotation row for this group
*
* @return autoCalculated annotation row