X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=4537dcc68befa4b42be49ac5e128d4a58c73c99e;hb=19c22459dca6c69d6f1fd0eed029c01e21c99854;hp=b3c6b2ae1fb9fbe92c5ce1e03c8aa3ecc3c4d9db;hpb=7440c240e784fa663228f579b51694e023a30ae3;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index b3c6b2a..4537dcc 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -42,8 +42,10 @@ import jalview.datamodel.Alignment;
 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;
@@ -537,4 +539,29 @@ public class AlignViewportTest
     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));
+  }
 }