JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 982be0c..924dd37 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -51,8 +51,8 @@ public class Jalview2xmlTests
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[]
-    { "-props", "test/jalview/io/testProps.jvprops" });
+    jalview.bin.Jalview.main(new String[] { "-props",
+        "test/jalview/io/testProps.jvprops" });
   }
 
   /**
@@ -84,7 +84,7 @@ public class Jalview2xmlTests
     return numdsann;
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testRNAStructureRecovery() throws Exception
   {
     String inFile = "examples/RF00031_folded.stk";
@@ -119,7 +119,7 @@ public class Jalview2xmlTests
             af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testTCoffeeScores() throws Exception
   {
     String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
@@ -155,7 +155,7 @@ public class Jalview2xmlTests
             .println("T-Coffee score shading successfully recovered from project.");
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testColourByAnnotScores() throws Exception
   {
     String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
@@ -241,7 +241,7 @@ public class Jalview2xmlTests
             .println("Per sequence (Group) colourscheme successfully applied and recovered.");
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void gatherViewsHere() throws Exception
   {
     int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
@@ -254,7 +254,7 @@ public class Jalview2xmlTests
 
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void viewRefPdbAnnotation() throws Exception
   {
     Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
@@ -276,7 +276,8 @@ public class Jalview2xmlTests
     assertTrue("Couldn't find the structure view", sps != null);
     SequenceI sq = sps.getAlignment().findName("1A70|");
     AlignmentAnnotation refan = null;
-    for (AlignmentAnnotation ra:sps.getAlignment().getAlignmentAnnotation())
+    for (AlignmentAnnotation ra : sps.getAlignment()
+            .getAlignmentAnnotation())
     {
       if (ra.graph != 0)
       {
@@ -284,7 +285,7 @@ public class Jalview2xmlTests
         break;
       }
     }
-    assertTrue("Annotation secondary structure not found.",refan!=null);
+    assertTrue("Annotation secondary structure not found.", refan != null);
     assertTrue("Couldn't find 1a70 null chain", sq != null);
     // compare the manually added temperature factor annotation
     // to the track automatically transferred from the pdb structure on load
@@ -298,25 +299,25 @@ public class Jalview2xmlTests
         for (int p = 0; p < ala.annotations.length; p++)
         {
           sq.findPosition(p);
-          try {
+          try
+          {
             assertTrue(
                     "Mismatch at alignment position " + p,
-                  (alaa.annotations[p] == null && refan.annotations[p] == null)
+                    (alaa.annotations[p] == null && refan.annotations[p] == null)
                             || alaa.annotations[p].value == refan.annotations[p].value);
-          }
-          catch (NullPointerException q)
+          } catch (NullPointerException q)
           {
-            Assert.fail("Mismatch of alignment annotations at position " + p
-                    + " Ref seq ann: " + refan.annotations[p]
+            Assert.fail("Mismatch of alignment annotations at position "
+                    + p + " Ref seq ann: " + refan.annotations[p]
                     + " alignment " + alaa.annotations[p]);
           }
-          }
+        }
       }
     }
-    
+
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testCopyViewSettings() throws Exception
   {
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
@@ -350,18 +351,16 @@ public class Jalview2xmlTests
   }
 
   /**
-   * test store and recovery of expanded views - 
-   * currently this is disabled since the 
-   * Desktop.explodeViews method doesn't seem 
-   * to result in the views being expanded to 
-   * distinct align frames when executed programmatically.
+   * test store and recovery of expanded views - currently this is disabled
+   * since the Desktop.explodeViews method doesn't seem to result in the views
+   * being expanded to distinct align frames when executed programmatically.
+   * 
    * @throws Exception
    */
   @Test(groups = { "Functional" }, enabled = false)
   public void testStoreAndRecoverExpandedviews() throws Exception
   {
-    AlignFrame af = new jalview.io.FileLoader()
-            .LoadFileWaitTillLoaded(
+    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
     assertTrue("Didn't read in the example file correctly.", af != null);
     String afid = af.getViewport().getSequenceSetId();
@@ -369,12 +368,12 @@ public class Jalview2xmlTests
       final AlignFrame xaf = af;
       af = null;
       new Thread(new Runnable()
-    {
-      @Override
-      public void run()
       {
+        @Override
+        public void run()
+        {
           Desktop.instance.explodeViews(xaf);
-      }
+        }
       }).start();
       Thread.sleep(1000);
     }
@@ -384,8 +383,7 @@ public class Jalview2xmlTests
     // Thread.sleep(300);
     // }
     int oldviews = Desktop.getAlignFrames().length;
-    Assert.assertEquals(
-            Desktop.getAlignFrames().length,
+    Assert.assertEquals(Desktop.getAlignFrames().length,
             Desktop.getAlignmentPanels(afid).length);
     File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
     try
@@ -406,9 +404,11 @@ public class Jalview2xmlTests
     af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
             tfile.getAbsolutePath(), FormatAdapter.FILE);
     Assert.assertNotNull(af);
-    Assert.assertEquals(Desktop.getAlignFrames().length,
+    Assert.assertEquals(
+            Desktop.getAlignFrames().length,
             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
-    Assert.assertEquals(oldviews,
+    Assert.assertEquals(
+            oldviews,
             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
   }