From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 15 Feb 2013 15:43:27 +0000 (+0000)
Subject: split test for general Stockholm IO consistency (JAL-1199) from test for IO of sequen... 
X-Git-Tag: Release_2_8_0b1~1^2~65^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d1718072ef2d5d921de0c253ccba3af665dbc6ac;p=jalview.git

split test for general Stockholm IO consistency (JAL-1199) from test for IO of sequence metadata (JAL-1265)
---

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
   {