Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 81756e0..c9532cc 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -32,7 +32,9 @@ import java.awt.Color;
 import java.awt.Rectangle;
 import java.io.File;
 import java.io.IOException;
+import java.math.BigInteger;
 import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Locale;
@@ -59,6 +61,7 @@ import jalview.datamodel.ContactMatrix;
 import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLocus;
+import jalview.datamodel.GroupSet;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
@@ -100,6 +103,7 @@ import jalview.util.MapList;
 import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import jalview.ws.datamodel.MappableContactMatrixI;
 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 
 @Test(singleThreaded = true)
@@ -110,6 +114,8 @@ 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);
   }
@@ -243,9 +249,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
     boolean diffseqcols = false, diffgseqcols = false;
     SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
-    for (int p = 0,
-            pSize = af.getViewport().getAlignment().getWidth(); p < pSize
-                    && (!diffseqcols || !diffgseqcols); p++)
+    for (int p = 0, pSize = af.getViewport().getAlignment()
+            .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
     {
       if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
               .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
@@ -264,9 +269,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue(__rcs.isSeqAssociated(),
             "Group Annotation colourscheme wasn't sequence associated");
 
-    for (int p = 0,
-            pSize = af.getViewport().getAlignment().getWidth(); p < pSize
-                    && (!diffseqcols || !diffgseqcols); p++)
+    for (int p = 0, pSize = af.getViewport().getAlignment()
+            .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
     {
       if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
               0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
@@ -1559,18 +1563,48 @@ 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);
     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.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]);
+    dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false,0.5f, false));
     Assert.assertNotSame(dummyMat.getNewick(), "");
     AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
     al.addAnnotation(paeCm);
+    // verify store/restore of group bitsets
+    for (BitSet gp : dummyMat.getGroups())
+    {
+      StringBuilder sb = new StringBuilder();
+      for (long val : gp.toLongArray())
+      {
+        if (sb.length() > 0)
+        {
+          sb.append(",");
+        }
+        sb.append(val);
+      }
+      String[] longvals = sb.toString().split(",");
+      long[] newlongvals = new long[longvals.length];
+      for (int lv = 0; lv < longvals.length; lv++)
+      {
+        try
+        {
+          newlongvals[lv] = Long.valueOf(longvals[lv]);
+        } catch (Exception x)
+        {
+          Assert.fail("failed to deserialise bitset element ");
+        }
+      }
+      BitSet newGp = BitSet.valueOf(newlongvals);
+      assertTrue(gp.equals(newGp));
+    }
     File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
             ".jvp");
     new Jalview2XML(false).saveState(tfile);
@@ -1590,21 +1624,28 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     ContactMatrixI restoredMat = newSeq
             .getContactMatrixFor(newSeq.getAnnotation()[0]);
     Assert.assertNotNull(restoredMat);
+    MapList oldMap = ((MappableContactMatrixI) dummyMat).getMapFor(sq);
+    MapList newMap = ((MappableContactMatrixI) restoredMat)
+            .getMapFor(newSeq);
+    Assert.assertEquals(oldMap.getFromRanges(), newMap.getFromRanges());
+    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),
               newCM = restoredMat.getContactList(i);
       for (int j = oldCM.getContactHeight(); j >= 0; j--)
       {
-        Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j));
+        double old_j = oldCM.getContactAt(j);
+        double new_j = newCM.getContactAt(j);
+        Assert.assertEquals(old_j, new_j);
       }
     }
     Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups());
     Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
     Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
-    Assert.assertEquals( restoredMat.getNewick(),dummyMat.getNewick());
-    
-    
+    Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
   }
 
 }