X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=344d74ddd67dea28a749aa63736eb89bd39e0f13;hb=19c22459dca6c69d6f1fd0eed029c01e21c99854;hp=0151a12280b665a63802dda3f97dd7e8c39295de;hpb=7440c240e784fa663228f579b51694e023a30ae3;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 0151a12..344d74d 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1052,6 +1052,38 @@ public class SequenceTest
     assertEquals("ABCDEF",
             derived.getDatasetSequence().getSequenceAsString());
   }
+  
+  /**
+   * test that creating a copy of an existing sequence with dataset sequence and
+   * associated contact matrix yields annotation associated with the same
+   * contact matrix in the copy
+   */
+  @Test(groups= {"Functional"})
+  public void testCopyPasteStyleDerivesequence_withcontactMatrixAnn()
+  {
+    SequenceI seq1=new Sequence("seq1","ACDACDACD");
+    seq1.createDatasetSequence();
+    ContactMatrixI cm = new SeqDistanceContactMatrix(seq1.getLength());
+    // addContactList needs to return annotation addable to the sequence reference it was called from
+    AlignmentAnnotation aann = seq1.addContactList(cm);
+    assertTrue(aann.sequenceRef==seq1);
+    assertEquals(1,seq1.getAnnotation().length);
+    assertNotNull(seq1.getContactListFor(seq1.getAnnotation()[0], 1));
+    
+    SequenceI seq_derived=seq1.deriveSequence();
+    assertEquals(1,seq_derived.getAnnotation().length);
+    assertTrue(cm==seq_derived.getContactMatrixFor(seq_derived.getAnnotation()[0]));
+    assertNotNull(seq_derived.getContactListFor(seq_derived.getAnnotation()[0], 1));
+    
+    // copy paste actually uses the copy constructor .. so
+    
+    SequenceI seq_copied=new Sequence((Sequence)seq_derived);
+    assertEquals(1,seq_copied.getAnnotation().length);
+    assertTrue(cm==seq_copied.getContactMatrixFor(seq_copied.getAnnotation()[0]));
+    assertNotNull(seq_copied.getContactListFor(seq_copied.getAnnotation()[0], 1));
+    
+    
+  }
 
   @Test(groups = { "Functional" })
   public void testCopyConstructor_noDataset()