null));
seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
0f, null));
+ // disulfide bond is a 'contact feature' - only select its 'start' and 'end'
+ seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc", 8, 12,
+ 0f, null));
/*
* select the first three columns --> Metal in seq1 2-3
assertEquals(0, bs.cardinality());
/*
+ * columns 9-11 should not match disulfide bond at 8/12
+ */
+ sg.setStartRes(8);
+ sg.setEndRes(10);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
+ sg, bs);
+ assertEquals(0, seqCount);
+ assertEquals(0, bs.cardinality());
+
+ /*
+ * columns 6-14 should match disulfide bond at 8/12
+ */
+ sg.setStartRes(5);
+ sg.setEndRes(13);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
+ sg, bs);
+ assertEquals(1, seqCount);
+ assertEquals(2, bs.cardinality());
+ assertTrue(bs.get(7));
+ assertTrue(bs.get(11));
+
+ /*
* look for a feature that isn't there
*/
sg.setStartRes(0);