JAL-4134 store/restore Newick tree for PAE annotation row

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

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 6281c29..fa6c25c 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -55,6 +55,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrix;
 import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLocus;
@@ -1547,7 +1548,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE);
     AlignmentI al = af.getViewport().getAlignment();
-    SequenceI sq = al.getSequenceAt(0);
+    // PAE matrices are added as reference annotation to the dataset sequence
+    // at least for now.
+    SequenceI sq = al.getSequenceAt(0).getDatasetSequence();
     int i = sq.getLength();
     float[][] paevals = new float[i][i];
     for (i = i - 1; i >= 0; i--)
@@ -1560,6 +1563,12 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       }
     }
     PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
+    String content = ContactMatrix.contactToFloatString(dummyMat);
+    Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1
+    float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength());
+    assertEquals(vals[3][4],paevals[3][4]);
+    dummyMat.makeGroups(0.5f, false);
+    Assert.assertNotSame(dummyMat.getNewick(), "");
     AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
     al.addAnnotation(paeCm);
     File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
@@ -1570,15 +1579,15 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
             DataSourceType.FILE);
     AlignmentI newAl = af.getViewport().getAlignment();
-    SequenceI newSeq = newAl.getSequenceAt(0);
+    SequenceI newSeq = newAl.getSequenceAt(0).getDatasetSequence();
     // check annotation of the expected type exists
     Assert.assertEquals(newSeq.getAnnotation().length, 1);
     Assert.assertEquals(newSeq.getAnnotation()[0].graph, paeCm.graph);
 
     // check a contact matrix was recovered
     Assert.assertEquals(newSeq.getContactMaps().size(), 1);
-    // and can be found for the annotation
-    ContactMatrixI restoredMat = al
+    // and can be found for the annotation on the sequence
+    ContactMatrixI restoredMat = newSeq
             .getContactMatrixFor(newSeq.getAnnotation()[0]);
     Assert.assertNotNull(restoredMat);
     for (i = sq.getLength() - 1; i >= 0; i--)
@@ -1590,6 +1599,12 @@ public class Jalview2xmlTests extends Jalview2xmlBase
         Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j));
       }
     }
+    Assert.assertEquals(dummyMat.hasGroups(), restoredMat.hasGroups());
+    Assert.assertEquals(dummyMat.getGroups(), restoredMat.getGroups());
+    Assert.assertEquals(dummyMat.hasTree(), restoredMat.hasTree());
+    Assert.assertEquals(dummyMat.getNewick(), restoredMat.getNewick());
+    
+    
   }
 
 }