X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotatedPDBFileInputTest.java;h=fe5e7ab08f0938ad0513912d6fd9193e32ea8ec9;hb=3ab582bfeeab1563bedf60e97994e63e672d2e31;hp=d3d9ff81102f2bd4ec6bba31b5ce8d13e73467e1;hpb=7f7f02ea0804ccff0f891f83b05662ab484cf6f1;p=jalview.git

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index d3d9ff8..fe5e7ab 100644
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -85,8 +85,8 @@ public class AnnotatedPDBFileInputTest
     {
       for (int q = p + 1; q < avec.length; q++)
       {
-        assertTrue("Found a duplicate annotation row "
-                + avec[p].label, avec[p] != avec[q]);
+        assertTrue("Found a duplicate annotation row " + avec[p].label,
+                avec[p] != avec[q]);
       }
     }
   }
@@ -104,7 +104,7 @@ public class AnnotatedPDBFileInputTest
         if (StructureImportSettings.getDefaultPDBFileParser().equals(
                 StructureParser.JALVIEW_PARSER))
         {
-        assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+          assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
         }
       }
     }
@@ -122,9 +122,9 @@ public class AnnotatedPDBFileInputTest
     SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
     assertEquals(296, sf.length);
     assertEquals("RESNUM", sf[0].getType());
-    assertEquals("GLU:19 1gaqA", sf[0].getDescription());
+    assertEquals("GLU:  19  1gaqA", sf[0].getDescription());
     assertEquals("RESNUM", sf[295].getType());
-    assertEquals("TYR:314 1gaqA", sf[295].getDescription());
+    assertEquals("TYR: 314  1gaqA", sf[295].getDescription());
 
     /*
      * 1GAQ/B
@@ -132,9 +132,9 @@ public class AnnotatedPDBFileInputTest
     sf = al.getSequenceAt(1).getSequenceFeatures();
     assertEquals(98, sf.length);
     assertEquals("RESNUM", sf[0].getType());
-    assertEquals("ALA:1 1gaqB", sf[0].getDescription());
+    assertEquals("ALA:   1  1gaqB", sf[0].getDescription());
     assertEquals("RESNUM", sf[97].getType());
-    assertEquals("ALA:98 1gaqB", sf[97].getDescription());
+    assertEquals("ALA:  98  1gaqB", sf[97].getDescription());
 
     /*
      * 1GAQ/C
@@ -142,9 +142,9 @@ public class AnnotatedPDBFileInputTest
     sf = al.getSequenceAt(2).getSequenceFeatures();
     assertEquals(296, sf.length);
     assertEquals("RESNUM", sf[0].getType());
-    assertEquals("GLU:19 1gaqC", sf[0].getDescription());
+    assertEquals("GLU:  19  1gaqC", sf[0].getDescription());
     assertEquals("RESNUM", sf[295].getType());
-    assertEquals("TYR:314 1gaqC", sf[295].getDescription());
+    assertEquals("TYR: 314  1gaqC", sf[295].getDescription());
   }
 
   @Test(groups = { "Functional" })
@@ -221,8 +221,8 @@ public class AnnotatedPDBFileInputTest
         sq = sq.getDatasetSequence();
       }
       assertNotNull(sq.getAllPDBEntries());
-      assertEquals("Expected only one PDB ID",
-              sq.getAllPDBEntries().size(), 1);
+      assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
+              .size());
       for (PDBEntry pdbentry : sq.getAllPDBEntries())
       {
         System.err.println("PDB Entry " + pdbentry.getId() + " "