import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SeqDistanceContactMatrix;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
{
Jalview.main(
new String[]
- { "-nonews", "-props", "test/jalview/testProps.jvprops" });
+ { "--nonews", "--props", "test/jalview/testProps.jvprops" });
/*
* remove any sequence mappings left lying around by other tests
{
synchronized (this)
{
- while (viewport.getCalcManager().isWorking())
+ do
{
try
{
} catch (InterruptedException e)
{
}
- }
+ } while (viewport.getCalcManager().isWorking());
}
}
assertEquals(0, ranges.getStartSeq());
assertEquals(2, ranges.getEndSeq());
}
+ @Test(groups = {"Functional"})
+ public void testGetSelectionAsNewSequences_withContactMatrices()
+ {
+ SequenceI seq = new Sequence("seq","ACADA");
+ ContactMatrixI cmat = new SeqDistanceContactMatrix(5);
+ seq.addContactList(cmat);
+ Alignment al = new Alignment(new SequenceI[] {seq.deriveSequence() });
+ al.addAnnotation(al.getSequenceAt(0).getAnnotation()[0]);
+ 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));
+
+ // 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));
+ }
}