import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
{
return null;
}
- Alignment al = null;
+ AlignmentI al = null;
ColumnSelection alcsel = null;
int FirstSeq = -1; // the position of the query sequence in Alignment al
* @param al
* @param profileseq
*/
- private void alignToProfileSeq(Alignment al, SequenceI profileseq)
+ private void alignToProfileSeq(AlignmentI al, SequenceI profileseq)
{
char gc = al.getGapCharacter();
int[] gapMap = profileseq.gapMap();