assertSame(seq, cds1.getDatasetSequence());
}
-
@Test(groups = "Functional")
public void testAddReferenceAnnotations()
{
- SequenceI longseq= new Sequence("longA","ASDASDASDASDAASDASDASDASDA");
+ SequenceI longseq = new Sequence("longA", "ASDASDASDASDAASDASDASDASDA");
Annotation[] aa = new Annotation[longseq.getLength()];
-
- for (int p=0;p<aa.length; p++)
+
+ for (int p = 0; p < aa.length; p++)
{
- aa[p] = new Annotation("P", "pos "+(p+1), (char)0, (float)p+1);
+ aa[p] = new Annotation("P", "pos " + (p + 1), (char) 0,
+ (float) p + 1);
}
- AlignmentAnnotation refAnnot=new AlignmentAnnotation("LongSeqAnnot","Annotations",aa);
+ AlignmentAnnotation refAnnot = new AlignmentAnnotation("LongSeqAnnot",
+ "Annotations", aa);
refAnnot.setCalcId("Test");
longseq.addAlignmentAnnotation(refAnnot);
verifyExpectedSequenceAnnotation(refAnnot);
- Alignment ourAl = new Alignment(new SequenceI[] { longseq.getSubSequence(5, 10),longseq.getSubSequence(7, 12)});
+ Alignment ourAl = new Alignment(
+ new SequenceI[]
+ { longseq.getSubSequence(5, 10),
+ longseq.getSubSequence(7, 12) });
ourAl.createDatasetAlignment();
-
+
// transfer annotation
SortedMap<String, String> tipEntries = new TreeMap<>();
Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
AlignmentUtils.addReferenceAnnotations(candidates, ourAl, null);
assertNotNull(ourAl.getAlignmentAnnotation());
- assertEquals(ourAl.getAlignmentAnnotation().length,2);
-
- for (AlignmentAnnotation alan:ourAl.getAlignmentAnnotation())
+ assertEquals(ourAl.getAlignmentAnnotation().length, 2);
+
+ for (AlignmentAnnotation alan : ourAl.getAlignmentAnnotation())
{
verifyExpectedSequenceAnnotation(alan);
}
// now simulate copy/paste to new alignment
SequenceI[] newSeqAl = new SequenceI[2];
// copy sequences but no annotation
- newSeqAl[0]=new Sequence(ourAl.getSequenceAt(0),ourAl.getSequenceAt(0).getAnnotation());
- newSeqAl[1]=new Sequence(ourAl.getSequenceAt(1),ourAl.getSequenceAt(1).getAnnotation());
-
+ newSeqAl[0] = new Sequence(ourAl.getSequenceAt(0),
+ ourAl.getSequenceAt(0).getAnnotation());
+ newSeqAl[1] = new Sequence(ourAl.getSequenceAt(1),
+ ourAl.getSequenceAt(1).getAnnotation());
+
Alignment newAl = new Alignment(newSeqAl);
// delete annotation
- for (SequenceI sq:newAl.getSequences())
+ for (SequenceI sq : newAl.getSequences())
{
sq.setAlignmentAnnotation(new AlignmentAnnotation[0]);
}
SequenceGroup sg = new SequenceGroup(Arrays.asList(newSeqAl));
sg.setStartRes(0);
sg.setEndRes(newAl.getWidth());
- AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0], newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
- AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1], newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
- for (AlignmentAnnotation alan:newAl.getAlignmentAnnotation())
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0],
+ newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1],
+ newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
+ for (AlignmentAnnotation alan : newAl.getAlignmentAnnotation())
{
verifyExpectedSequenceAnnotation(alan);
}
}
-
+
/**
- * helper - tests annotation is mapped to position it was originally created for
+ * helper - tests annotation is mapped to position it was originally created
+ * for
+ *
* @param alan
*/
private void verifyExpectedSequenceAnnotation(AlignmentAnnotation alan)
{
- for (int c=0;c<alan.annotations.length;c++)
+ for (int c = 0; c < alan.annotations.length; c++)
{
Annotation a = alan.annotations[c];
- if (a!=null)
+ if (a != null)
{
- assertEquals("Misaligned annotation at "+c,(float)alan.sequenceRef.findPosition(c),a.value);
- } else {
- assertTrue("Unexpected Null at position "+c,c>=alan.sequenceRef.getLength() || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
+ assertEquals("Misaligned annotation at " + c,
+ (float) alan.sequenceRef.findPosition(c), a.value);
+ }
+ else
+ {
+ assertTrue("Unexpected Null at position " + c,
+ c >= alan.sequenceRef.getLength()
+ || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
}
}
}
AlignmentAnnotation alan = al.findAnnotations(sq, null, cm_aan.label)
.iterator().next();
ContactMatrixI t_cm = al.getContactMatrixFor(alan);
- assertNotNull("No contact map for the transferred annotation row.",t_cm);
+ assertNotNull("No contact map for the transferred annotation row.",
+ t_cm);
assertTrue(t_cm instanceof SeqDistanceContactMatrix);
- assertTrue(((SeqDistanceContactMatrix)t_cm).hasReferenceSeq());
-
+ assertTrue(((SeqDistanceContactMatrix) t_cm).hasReferenceSeq());
+
ContactListI cl = al.getContactListFor(alan, 1);
assertNotNull(
"No contact matrix recovered after reference annotation transfer",
cl);
- // semantics of sequence associated contact list is slightly tricky - column 3 in alignment should have data
+ // semantics of sequence associated contact list is slightly tricky - column
+ // 3 in alignment should have data
cl = al.getContactListFor(alan, 3);
assertNotNull(
"Contact matrix should have data for last position in sequence",