X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=d7a9166a059437aeb4454d1d5a7380b8678f1f07;hb=90ad4273c7105b7763247192e1c6739eed30ba4c;hp=1c46d1f014073c76699f55cd17b2833a80b800b2;hpb=c93b9ad2ebfab4cad4608a8890132918589576be;p=jalview.git

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 1c46d1f..d7a9166 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -24,7 +24,6 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -44,24 +43,24 @@ public class StockholmFileTest
   static String PfamFile = "examples/PF00111_seed.stk",
           RfamFile = "examples/RF00031_folded.stk";
 
-  @Test
+  @Test(groups = { "Functional" })
   public void pfamFileIO() throws Exception
   {
     testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
   }
 
-  @Test
+  @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(
@@ -69,7 +68,7 @@ public class StockholmFileTest
             numpdb > 0);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void rfamFileIO() throws Exception
   {
     testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
@@ -95,8 +94,8 @@ public class StockholmFileTest
     {
       AppletFormatAdapter rf = new AppletFormatAdapter();
 
-      Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
-              new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+      AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
+              new IdentifyFile().identify(ff, AppletFormatAdapter.FILE));
 
       assertNotNull("Couldn't read supplied alignment data.", al);
 
@@ -109,11 +108,11 @@ public class StockholmFileTest
       System.out.println("Output file in '" + ioformat + "':\n"
               + outputfile + "\n<<EOF\n");
       // test for consistency in io
-      Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
+      AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
               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);
@@ -137,7 +136,7 @@ public class StockholmFileTest
       if (naliannot > -1)
       {
         assertEquals("Number of alignment annotations", naliannot,
-              numaliannot);
+                numaliannot);
       }
 
       assertTrue(
@@ -269,7 +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
@@ -352,9 +351,11 @@ public class StockholmFileTest
                 an_new.displayCharacter.trim())
                 || !("" + an_or.secondaryStructure).trim().equals(
                         ("" + an_new.secondaryStructure).trim())
-                || (an_or.description != an_new.description && (an_or.description == null
-                        || an_new.description == null || !an_or.description
-                          .equals(an_new.description))))
+                || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
+                        .trim().length() == 0)
+                        || (an_new.description == null && an_or.description
+                                .trim().length() == 0) || an_or.description
+                        .trim().equals(an_new.description.trim()))))
         {
           System.err.println("Annotation Element Mismatch\nElement " + i
                   + " in original: " + annot_or.annotations[i].toString()