JAL-1925 update source version in license

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

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 2537002..5ab4297 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.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.
  * 
@@ -43,13 +43,13 @@ public class StockholmFileTest
   static String PfamFile = "examples/PF00111_seed.stk",
           RfamFile = "examples/RF00031_folded.stk";
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void pfamFileIO() throws Exception
   {
     testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void pfamFileDataExtraction() throws Exception
   {
     AppletFormatAdapter af = new AppletFormatAdapter();
@@ -58,9 +58,9 @@ public class StockholmFileTest
     int numpdb = 0;
     for (SequenceI sq : al.getSequences())
     {
-      if (sq.getPDBId() != null)
+      if (sq.getAllPDBEntries() != null)
       {
-        numpdb += sq.getPDBId().size();
+        numpdb += sq.getAllPDBEntries().size();
       }
     }
     assertTrue(
@@ -68,7 +68,7 @@ public class StockholmFileTest
             numpdb > 0);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void rfamFileIO() throws Exception
   {
     testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
@@ -136,7 +136,7 @@ public class StockholmFileTest
       if (naliannot > -1)
       {
         assertEquals("Number of alignment annotations", naliannot,
-              numaliannot);
+                numaliannot);
       }
 
       assertTrue(
@@ -268,7 +268,7 @@ public class StockholmFileTest
                           + (ignoreFeatures ? " ignoring." : ""),
                   ignoreFeatures
                           || (seq_original[i].getSequenceFeatures() == null && seq_new[in]
-                          .getSequenceFeatures() == null)
+                                  .getSequenceFeatures() == null)
                           || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
                                   .getSequenceFeatures() != null));
           // compare sequence features