assertEquals(0, ranges.getStartSeq());
assertEquals(2, ranges.getEndSeq());
}
- @Test(groups = {"Functional"})
+
+ @Test(groups = { "Functional" })
public void testGetSelectionAsNewSequences_withContactMatrices()
{
- SequenceI seq = new Sequence("seq","ACADA");
+ SequenceI seq = new Sequence("seq", "ACADA");
ContactMatrixI cmat = new SeqDistanceContactMatrix(5);
seq.addContactList(cmat);
- Alignment al = new Alignment(new SequenceI[] {seq.deriveSequence() });
+ Alignment al = new Alignment(new SequenceI[] { seq.deriveSequence() });
al.addAnnotation(al.getSequenceAt(0).getAnnotation()[0]);
- AlignFrame af = new AlignFrame(al,500,500);
-
+ AlignFrame af = new AlignFrame(al, 500, 500);
+
SequenceI selseqs[] = af.getViewport().getSelectionAsNewSequence();
assertNotNull(selseqs[0].getAnnotation());
assertNotNull(selseqs[0].getAnnotation()[0]);
- assertEquals(cmat,selseqs[0].getContactMatrixFor(selseqs[0].getAnnotation()[0]));
-
- assertNotNull(selseqs[0].getContactListFor(selseqs[0].getAnnotation()[0], 2));
-
+ assertEquals(cmat,
+ selseqs[0].getContactMatrixFor(selseqs[0].getAnnotation()[0]));
+
+ assertNotNull(
+ selseqs[0].getContactListFor(selseqs[0].getAnnotation()[0], 2));
+
// now select everything and test again
af.selectAllSequenceMenuItem_actionPerformed(null);
selseqs = af.getViewport().getSelectionAsNewSequence();
assertNotNull(selseqs[0].getAnnotation());
assertNotNull(selseqs[0].getAnnotation()[0]);
- assertEquals(cmat,selseqs[0].getContactMatrixFor(selseqs[0].getAnnotation()[0]));
- assertNotNull(selseqs[0].getContactListFor(selseqs[0].getAnnotation()[0], 2));
+ assertEquals(cmat,
+ selseqs[0].getContactMatrixFor(selseqs[0].getAnnotation()[0]));
+ assertNotNull(
+ selseqs[0].getContactListFor(selseqs[0].getAnnotation()[0], 2));
}
}