X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=d7a9166a059437aeb4454d1d5a7380b8678f1f07;hb=e56b8db4f9c6e0a51cf538d95bd2e007a2c92495;hp=2537002d02b51a02117231293d7954caf3ad6f97;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 2537002..d7a9166 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -43,24 +43,24 @@ 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();
     AlignmentI al = af.readFile(PfamFile, af.FILE,
-            new IdentifyFile().Identify(PfamFile, af.FILE));
+            new IdentifyFile().identify(PfamFile, af.FILE));
     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);
@@ -95,7 +95,7 @@ public class StockholmFileTest
       AppletFormatAdapter rf = new AppletFormatAdapter();
 
       AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
-              new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+              new IdentifyFile().identify(ff, AppletFormatAdapter.FILE));
 
       assertNotNull("Couldn't read supplied alignment data.", al);
 
@@ -112,7 +112,7 @@ public class StockholmFileTest
               AppletFormatAdapter.PASTE, ioformat);
       assertNotNull("Couldn't parse reimported alignment data.", al_input);
 
-      String identifyoutput = new IdentifyFile().Identify(outputfile,
+      String identifyoutput = new IdentifyFile().identify(outputfile,
               AppletFormatAdapter.PASTE);
       assertNotNull("Identify routine failed for outputformat " + ioformat,
               identifyoutput);
@@ -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