X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=e39d9008ee666a84069a3402a21bd8b7d9f8cfb9;hb=1730be35c0c3fda8f9c63f1fb6dcea7b5fb2ba35;hp=38b27b197def9a4b2e8eacc87bbe1e0402618333;hpb=d6e6893d922a0fca8fa0c716b714c162ad2b9714;p=jalview.git

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 38b27b1..e39d900 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -67,6 +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;
@@ -1547,6 +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);
@@ -1691,10 +1730,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     // 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);
+    // 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);
     
   }