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Merge branch 'bug/JAL-4313_cme_in_tests' into patch/JAL-4311_import_pLDDT_scores_from...
[jalview.git]
/
test
/
jalview
/
datamodel
/
PAEContactMatrixTest.java
diff --git
a/test/jalview/datamodel/PAEContactMatrixTest.java
b/test/jalview/datamodel/PAEContactMatrixTest.java
index
67edb37
..
fa7aca5
100644
(file)
--- a/
test/jalview/datamodel/PAEContactMatrixTest.java
+++ b/
test/jalview/datamodel/PAEContactMatrixTest.java
@@
-73,7
+73,7
@@
public class PAEContactMatrixTest
verifyPAEmatrix(seq, aa, 0, 0, 4);
// test clustering
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");
// remap - test the MappableContactMatrix.liftOver method
SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
@@
-116,7
+116,11
@@
public class PAEContactMatrixTest
AlignmentI alForSeq = new Alignment(new SequenceI[] { alseq });
newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
null);
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);
assertNotNull(alcl);
mappedCl = alcl.getMappedPositionsFor(0, 4);
assertNotNull(mappedCl);