verifyPAEmatrix(seq, aa, 0, 0, 4);
// test clustering
- paematrix.setGroupSet(GroupSet.makeGroups(paematrix, 0.1f, false));
+ paematrix.setGroupSet(
+ GroupSet.makeGroups(paematrix, false, 0.1f, false));
// remap - test the MappableContactMatrix.liftOver method
SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
AlignmentI alForSeq = new Alignment(new SequenceI[] { alseq });
newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
null);
- ContactListI alcl = alForSeq.getContactListFor(newaa, 1);
+ // check for null on out of bounds
+ ContactListI alcl = alForSeq.getContactListFor(newaa,
+ newaa.annotations.length);
+ assertNull(alcl, "Should've gotten null!");
+ // now check for mapping
+ alcl = alForSeq.getContactListFor(newaa, 1);
assertNotNull(alcl);
mappedCl = alcl.getMappedPositionsFor(0, 4);
assertNotNull(mappedCl);
}
}
+ /**
+ * check mapping and resolution methods work
+ */
+ @Test(groups = { "Functional" })
+ public void testMappableContactMatrix()
+ {
+ SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+ MapList map = new MapList(new int[] { 5, 9 }, new int[] { 1, 5 }, 1, 1);
+ AlignmentAnnotation aa = newseq.addContactList(
+ new PAEContactMatrix(newseq, map, PAEdata, null));
+ ContactListI clist = newseq.getContactListFor(aa, 4);
+ assertNotNull(clist);
+ clist = newseq.getContactListFor(aa, 3);
+ assertNull(clist);
+
+ ContactMatrixI cm = newseq.getContactMatrixFor(aa);
+ MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
+ int[] pos = mcm.getMappedPositionsFor(newseq, 0);
+ assertNull(pos);
+
+ pos = mcm.getMappedPositionsFor(newseq, 1);
+ assertNotNull(pos);
+ assertEquals(pos[0], 4 + newseq.getStart());
+
+ pos = mcm.getMappedPositionsFor(newseq, 6); // after end of matrix
+ assertNull(pos);
+ pos = mcm.getMappedPositionsFor(newseq, 5); // at end of matrix
+ assertNotNull(pos);
+ assertEquals(pos[0], 8 + newseq.getStart());
+ SequenceI alseq = newseq.deriveSequence();
+ alseq.insertCharAt(5, '-');
+ pos = mcm.getMappedPositionsFor(alseq, 5); // at end of matrix
+ assertNotNull(pos);
+ assertEquals(pos[0], 8 + newseq.getStart());
+
+ }
}