X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=92ee5e018f761d9f34dc4a45286a348f87986c25;hb=94b92afb860aed95bc9f615a8cc1f97e6b69550f;hp=caeb18429570a67fea048ba1a467c96cbc5862ac;hpb=1d210cc4ad4423f300976afb8c7e62a7119a5494;p=jalview.git

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index caeb184..92ee5e0 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -22,19 +22,26 @@ public class StockholmFileTest
   @Test
   public void pfamFileIO() throws Exception
   {
-      test(new File(PfamFile));
-      AppletFormatAdapter af = new AppletFormatAdapter();
-      AlignmentI al = af.readFile(PfamFile, af.FILE, new IdentifyFile().Identify(PfamFile, af.FILE));
-      int numpdb=0;
-      for (SequenceI sq:al.getSequences())
+    testFileIOwithFormat(new File(PfamFile), "STH");
+  }
+  @Test
+  public void pfamFileDataExtraction() throws Exception
+  {  AppletFormatAdapter af = new AppletFormatAdapter();
+    AlignmentI al = af.readFile(PfamFile, af.FILE,
+            new IdentifyFile().Identify(PfamFile, af.FILE));
+    int numpdb = 0;
+    for (SequenceI sq : al.getSequences())
+    {
+      if (sq.getPDBId() != null)
       {
-        if (sq.getPDBId()!=null)
-        {
-          numpdb+=sq.getPDBId().size();
-        }
+        numpdb += sq.getPDBId().size();
       }
-      assertTrue("PF00111 seed alignment has at least 1 PDB file, but the reader found none.",numpdb>0);
+    }
+    assertTrue(
+            "PF00111 seed alignment has at least 1 PDB file, but the reader found none.",
+            numpdb > 0);
   }
+
   @Test
   public void rfamFileIO() throws Exception
   {