Merge branch 'feature/JAL-4307_hetatm_showhide' into develop

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

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 37ef069..aa4be3d 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -114,6 +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);
   }
@@ -285,12 +287,12 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void gatherViewsHere() throws Exception
   {
-    int origCount = Desktop.getAlignFrames() == null ? 0
-            : Desktop.getAlignFrames().length;
+    int origCount = Desktop.getDesktopAlignFrames() == null ? 0
+            : Desktop.getDesktopAlignFrames().length;
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
-    assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
+    assertTrue(Desktop.getDesktopAlignFrames().length == 1 + origCount,
             "Didn't gather the views in the example file.");
 
   }
@@ -428,7 +430,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
-    Assert.assertEquals(Desktop.getAlignFrames().length, 1);
+    Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 1);
     String afid = af.getViewport().getSequenceSetId();
 
     // check FileLoader returned a reference to the one alignFrame that is
@@ -438,8 +440,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
     Desktop.explodeViews(af);
 
-    int oldviews = Desktop.getAlignFrames().length;
-    Assert.assertEquals(Desktop.getAlignFrames().length,
+    int oldviews = Desktop.getDesktopAlignFrames().length;
+    Assert.assertEquals(Desktop.getDesktopAlignFrames().length,
             Desktop.getAlignmentPanels(afid).length);
     File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
     try
@@ -453,14 +455,14 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       Assert.fail("Didn't save the expanded view state", e);
     }
     Desktop.instance.closeAll_actionPerformed(null);
-    if (Desktop.getAlignFrames() != null)
+    if (Desktop.getDesktopAlignFrames() != null)
     {
-      Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+      Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
     }
     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
             DataSourceType.FILE);
     Assert.assertNotNull(af);
-    Assert.assertEquals(Desktop.getAlignFrames().length,
+    Assert.assertEquals(Desktop.getDesktopAlignFrames().length,
             Desktop.getAlignmentPanels(
                     af.getViewport().getSequenceSetId()).length);
     Assert.assertEquals(Desktop
@@ -517,9 +519,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       Assert.fail("Didn't save the expanded view state", e);
     }
     Desktop.instance.closeAll_actionPerformed(null);
-    if (Desktop.getAlignFrames() != null)
+    if (Desktop.getDesktopAlignFrames() != null)
     {
-      Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+      Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
     }
 
     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
@@ -696,9 +698,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       Assert.fail("Didn't save the expanded view state", e);
     }
     Desktop.instance.closeAll_actionPerformed(null);
-    if (Desktop.getAlignFrames() != null)
+    if (Desktop.getDesktopAlignFrames() != null)
     {
-      Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+      Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
     }
 
     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
@@ -790,9 +792,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       Assert.fail("Didn't save the state", e);
     }
     Desktop.instance.closeAll_actionPerformed(null);
-    if (Desktop.getAlignFrames() != null)
+    if (Desktop.getDesktopAlignFrames() != null)
     {
-      Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+      Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
     }
 
     AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
@@ -1215,7 +1217,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertNotNull(af);
 
     AlignmentI ds = null;
-    for (AlignFrame alignFrame : Desktop.getAlignFrames())
+    for (AlignFrame alignFrame : Desktop.getDesktopAlignFrames())
     {
       if (ds == null)
       {
@@ -1561,7 +1563,7 @@ 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 +1573,8 @@ 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 +1605,6 @@ 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 +1631,6 @@ 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),
@@ -1645,7 +1646,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
     Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
     Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
-
   }
 
 }