if (stretchGroup == null)
{
- stretchGroup = av.getAlignment().findGroup(sequence);
- if (stretchGroup != null && res > stretchGroup.getStartRes()
- && res < stretchGroup.getEndRes())
- {
- av.setSelectionGroup(stretchGroup);
- }
- else
- {
- stretchGroup = null;
- }
+ stretchGroup = av.getAlignment().findGroup(sequence, res);
+ av.setSelectionGroup(stretchGroup);
}
- else if (!stretchGroup.getSequences(null).contains(sequence)
+ if (stretchGroup == null
+ || !stretchGroup.getSequences(null).contains(sequence)
|| stretchGroup.getStartRes() > res
|| stretchGroup.getEndRes() < res)
{
* @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
*/
@Override
- public SequenceGroup findGroup(SequenceI s)
+ public SequenceGroup findGroup(SequenceI seq, int position)
{
synchronized (groups)
{
- for (int i = 0; i < this.groups.size(); i++)
+ for (SequenceGroup sg : groups)
{
- SequenceGroup sg = groups.get(i);
-
- if (sg.getSequences(null).contains(s))
+ if (sg.getSequences(null).contains(seq))
{
- return sg;
+ if (position >= sg.getStartRes() && position <= sg.getEndRes())
+ {
+ return sg;
+ }
}
}
}
int findIndex(SequenceI s);
/**
- * Finds group that given sequence is part of.
+ * Returns the first group (in the order in which groups were added) that
+ * includes the given sequence and aligned position (base 0), or null if none
+ * found
*
- * @param s
- * Sequence in alignment.
+ * @param seq
+ * @param position
*
- * @return First group found for sequence. WARNING : Sequences may be members
- * of several groups. This method is incomplete.
+ * @return
*/
- SequenceGroup findGroup(SequenceI s);
+ SequenceGroup findGroup(SequenceI seq, int position);
/**
* Finds all groups that a given sequence is part of.
if (stretchGroup == null)
{
- stretchGroup = av.getAlignment().findGroup(sequence);
-
- if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
- && (res < stretchGroup.getEndRes()))
- {
- av.setSelectionGroup(stretchGroup);
- }
- else
- {
- stretchGroup = null;
- }
+ stretchGroup = av.getAlignment().findGroup(sequence, res);
+ av.setSelectionGroup(stretchGroup);
}
- else if (!stretchGroup.getSequences(null).contains(sequence)
+ if (stretchGroup == null
+ || !stretchGroup.getSequences(null).contains(sequence)
|| (stretchGroup.getStartRes() > res)
|| (stretchGroup.getEndRes() < res))
{
assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to);
}
+ @Test(groups = { "Functional" })
+ public void testFindGroup()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI");
+ SequenceI seq2 = new Sequence("seq2", "---JKLMNO---");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 });
+
+ assertNull(a.findGroup(null, 0));
+ assertNull(a.findGroup(seq1, 1));
+ assertNull(a.findGroup(seq1, -1));
+
+ /*
+ * add a group consisting of just "DEF"
+ */
+ SequenceGroup sg1 = new SequenceGroup();
+ sg1.addSequence(seq1, false);
+ sg1.setStartRes(3);
+ sg1.setEndRes(5);
+ a.addGroup(sg1);
+
+ assertNull(a.findGroup(seq1, 2)); // position not in group
+ assertNull(a.findGroup(seq1, 6)); // position not in group
+ assertNull(a.findGroup(seq2, 5)); // sequence not in group
+ assertSame(a.findGroup(seq1, 3), sg1); // yes
+ assertSame(a.findGroup(seq1, 4), sg1);
+ assertSame(a.findGroup(seq1, 5), sg1);
+
+ /*
+ * add a group consisting of
+ * EF--
+ * KLMN
+ */
+ SequenceGroup sg2 = new SequenceGroup();
+ sg2.addSequence(seq1, false);
+ sg2.addSequence(seq2, false);
+ sg2.setStartRes(4);
+ sg2.setEndRes(7);
+ a.addGroup(sg2);
+
+ assertNull(a.findGroup(seq1, 2)); // unchanged
+ assertSame(a.findGroup(seq1, 3), sg1); // unchanged
+ /*
+ * if a residue is in more than one group, method returns
+ * the first found (in order groups were added)
+ */
+ assertSame(a.findGroup(seq1, 4), sg1);
+ assertSame(a.findGroup(seq1, 5), sg1);
+
+ /*
+ * seq2 only belongs to the second group
+ */
+ assertSame(a.findGroup(seq2, 4), sg2);
+ assertSame(a.findGroup(seq2, 5), sg2);
+ assertSame(a.findGroup(seq2, 6), sg2);
+ assertSame(a.findGroup(seq2, 7), sg2);
+ assertNull(a.findGroup(seq2, 3));
+ assertNull(a.findGroup(seq2, 8));
+ }
+
}