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 84af3e4..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;
@@ -600,9 +601,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase
      * test for patch release versions
      */
     assertFalse(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.2"));
-    assertTrue(Jalview2XML.isVersionStringLaterThan("2.11.3.0","2.11.4"));
-    assertFalse(Jalview2XML.isVersionStringLaterThan("2.12.2.0b1","2.12.2.0"));
-    assertFalse(Jalview2XML.isVersionStringLaterThan("2.12.2.3","2.12.2.2"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.4"));
+    assertFalse(
+            Jalview2XML.isVersionStringLaterThan("2.12.2.0b1", "2.12.2.0"));
+    assertFalse(
+            Jalview2XML.isVersionStringLaterThan("2.12.2.3", "2.12.2.2"));
 
   }
 
@@ -870,8 +873,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     acg.setPredefinedColours(true);
     af.changeColour(acg);
     Color seqcol[] = new Color[3];
-    for (int iStart=fsq.findIndex(fsq.getStart()),i=0;i<3;i++) {
-      seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null);
+    for (int iStart = fsq.findIndex(fsq.getStart()), i = 0; i < 3; i++)
+    {
+      seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas
+              .getSequenceRenderer()
+              .getResidueColour(fsq, iStart + i, null);
     }
     /*
      * save project, close windows, reload project, verify
@@ -880,7 +886,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             "testStoreAndRecoverAnnotRowElemColors", ".jvp");
     tfile.deleteOnExit();
     new Jalview2XML(false).saveState(tfile);
-    //Desktop.instance.closeAll_actionPerformed(null);
+    // Desktop.instance.closeAll_actionPerformed(null);
     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
             DataSourceType.FILE);
     Assert.assertNotNull(af, "Failed to reload project");
@@ -888,9 +894,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase
      * verify alignment annotation has colors
      */
     av = af.getViewport();
-    
+
     ColourSchemeI loadedCscheme = av.getGlobalColourScheme();
-    Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient,"Didn't apply Annotation colour gradient");
+    Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient,
+            "Didn't apply Annotation colour gradient");
     acg = (AnnotationColourGradient) loadedCscheme;
     assertTrue(acg.isSeqAssociated());
     assertTrue(acg.isPredefinedColours());
@@ -903,13 +910,16 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     for (int iStart = al.getSequenceAt(0)
             .findIndex(al.getSequenceAt(0).getStart()), i = 0; i < 3; i++)
     {
-      Assert.assertTrue(ala.annotations[i].colour!=null);
+      Assert.assertTrue(ala.annotations[i].colour != null);
       Assert.assertTrue(ala.annotations[i].colour.equals(annots[i].colour));
-      Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null);
-      Assert.assertTrue(seqcol[i].equals(newseqcol),"Sequence shading is different");
+      Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas
+              .getSequenceRenderer()
+              .getResidueColour(fsq, iStart + i, null);
+      Assert.assertTrue(seqcol[i].equals(newseqcol),
+              "Sequence shading is different");
 
     }
-    
+
   }
 
   /**
@@ -1490,7 +1500,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   }
 
   /**
-   * Test that a view from an older version of Jalview is restored with Overview automatically shown when the preference is set
+   * Test that a view from an older version of Jalview is restored with Overview
+   * automatically shown when the preference is set
    * 
    * @throws Exception
    */
@@ -1515,7 +1526,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
    * 
    * @throws Exception
    */
-  @Test(groups = {"Functional"}, enabled=false)
+  @Test(groups = { "Functional" }, enabled = false)
   public void testReloadActuallyReloads() throws Exception
   {
     Desktop.instance.closeAll_actionPerformed(null);
@@ -1537,7 +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--)
@@ -1550,6 +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",
@@ -1560,15 +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--)
@@ -1580,6 +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());
+    
+    
   }
 
 }