JAL-4124 MappableContactMatrix equivalence and hashCode ensuring non-redundant set...

[jalview.git] / test / jalview / project / Jalview2xmlTests.java

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index c9532cc..38b27b1 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -47,6 +47,7 @@ import org.testng.AssertJUnit;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.analysis.AlignmentUtils;
 import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -1646,6 +1647,55 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
     Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
     Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
+
+    // verify no duplicate PAE matrix data when new view created and saved
+    
+    // add reference annotations to view first, then copy
+    AlignmentUtils.addReferenceAnnotationTo(newAl, newAl.getSequenceAt(0), newSeq.getAnnotation()[0],null);
+    
+    AlignmentViewPanel newview = af.newView("copy of PAE", true);
+    
+    // redundant asserts here check all is good with the new view firest...
+    AlignmentI newviewAl = newview.getAlignment();
+    SequenceI newviewSeq = newviewAl.getSequenceAt(0);
+    // check annotation of the expected type exists
+    Assert.assertEquals(newviewSeq.getAnnotation().length, 1);
+    Assert.assertEquals(newviewSeq.getAnnotation()[0].graph, paeCm.graph);
+    // check we have just one contact matrix mapping
+    Assert.assertEquals(newviewSeq.getContactMaps().size(), 1);
+    
+    // and can be found for the annotation on the sequence
+    ContactMatrixI newviewMat = newviewSeq
+            .getContactMatrixFor(newviewSeq.getAnnotation()[0]);
+    Assert.assertNotNull(newviewMat);
+
+    Assert.assertTrue(newviewMat == restoredMat);
+    
+    // save the two views and restore. Now look at visible annotation to check all views have shared refs.
+    
+    tfile = File.createTempFile("testStoreAndRecoverPAEmatrixTwoViews",
+            ".jvp");
+    new Jalview2XML(false).saveState(tfile);
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+    newAl = af.getAlignPanels().get(0).getAlignment();
+    AlignmentAnnotation view1aa = newAl.getSequenceAt(0).getAnnotation()[0];
+
+    newviewAl = af.getAlignPanels().get(1).getAlignment();
+    AlignmentAnnotation view2aa = newviewAl.getSequenceAt(0).getAnnotation()[0];
+
+    // annotations are shared across alignment views - so should still have an identical pair of annotations.
+    Assert.assertTrue(view1aa==view2aa);
+    // identical annotations means identical contact matrix mappings
+    Assert.assertEquals(newAl.getDataset().getSequenceAt(0).getContactMaps().size(), 1);
+
+    Assert.assertTrue(view1aa!=view2aa);
+    restoredMat = newAl.getContactMatrixFor(view1aa);
+    newviewMat = newviewAl.getContactMatrixFor(view2aa);
+    Assert.assertTrue(restoredMat!=newviewMat);
+    
   }
 
 }