X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=e39d9008ee666a84069a3402a21bd8b7d9f8cfb9;hb=1730be35c0c3fda8f9c63f1fb6dcea7b5fb2ba35;hp=37ef06927a8e79dc20192b70aa788072ed569628;hpb=80b889f0cca49103e1b20ed806755a0719789906;p=jalview.git

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 37ef069..e39d900 100644
--- 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;
@@ -66,6 +67,7 @@ import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Sequence;
 import jalview.datamodel.Sequence.DBModList;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
@@ -114,6 +116,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
     JvOptionPane.setInteractiveMode(false);
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
@@ -1544,6 +1548,44 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   }
 
   @Test(groups = { "Functional" })
+  public void testMatrixToFloatsAndBack()
+  {
+    int imax=2000;
+    int i=imax;
+    SequenceI sq = new Sequence("dummy","SEQ");
+    while (sq.getLength()<i)
+    {
+      sq.setSequence(sq.getSequenceAsString()+'Q');
+    }
+    float[][] paevals = new float[i][i];
+    for (i = imax - 1; i >= 0; i--)
+    {
+      for (int j = 0; j <= i; j++)
+      {
+        paevals[i][j] = ((i - j < 2)
+                || ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f;
+        paevals[j][i] = -paevals[i][j];
+      }
+    }
+    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]);
+    assertEquals(vals[4][3], paevals[4][3]);
+    
+    // test recovery
+    for (i=0;i<imax;i++)
+    {
+      for (int j=0;j<imax;j++)
+      {
+        assertEquals(vals[i][j],paevals[i][j]);
+      }
+    }
+  }
+  @Test(groups = { "Functional" })
   public void testPAEsaveRestore() throws Exception
   {
     Desktop.instance.closeAll_actionPerformed(null);
@@ -1561,7 +1603,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       {
         paevals[i][j] = ((i - j < 2)
                 || ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f;
-        paevals[j][i] = paevals[i][j];
+        paevals[j][i] = -paevals[i][j];
       }
     }
     PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
@@ -1571,7 +1613,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
             sq.getLength(), sq.getLength());
     assertEquals(vals[3][4], paevals[3][4]);
-    dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, 0.5f, false));
+    assertEquals(vals[4][3], paevals[4][3]);
+    dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false,0.5f, false));
     Assert.assertNotSame(dummyMat.getNewick(), "");
     AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
     al.addAnnotation(paeCm);
@@ -1602,7 +1645,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       BitSet newGp = BitSet.valueOf(newlongvals);
       assertTrue(gp.equals(newGp));
     }
-
     File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
             ".jvp");
     new Jalview2XML(false).saveState(tfile);
@@ -1629,7 +1671,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertEquals(oldMap.getToRanges(), newMap.getToRanges());
     Assert.assertEquals(oldMap.getFromRatio(), newMap.getFromRatio());
     Assert.assertEquals(oldMap.getToRatio(), newMap.getToRatio());
-
     for (i = sq.getLength() - 1; i >= 0; i--)
     {
       ContactListI oldCM = dummyMat.getContactList(i),
@@ -1646,6 +1687,55 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     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);
+
+    // TODO Verify when distinct mappable PAEs are created, only one PAE dataset is actually held.
+    // Assert.assertTrue(view1aa!=view2aa);
+    // restoredMat = newAl.getContactMatrixFor(view1aa);
+    // newviewMat = newviewAl.getContactMatrixFor(view2aa);
+    // Assert.assertTrue(restoredMat!=newviewMat);
+    
   }
 
 }