X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=4505f169e8c5737944e22847ab612088b3f1f934;hb=ab271f65ad7519b988efbfa04e32a0199d9bd8d4;hp=fc2ffdaffd2187e3e1af4ad057c5e584575a2841;hpb=3c2de0e2204842f88e58c1e8f5ef6251c99a84d5;p=jalview.git

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index fc2ffda..4505f16 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -1,6 +1,7 @@
 package jalview.io;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -9,8 +10,9 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 
 import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.Map;
 
 import org.junit.Test;
 
@@ -109,7 +111,7 @@ public class StockholmFileTest
    *          'secondary' or generated alignment from some datapreserving
    *          transformation
    */
-  private static void testAlignmentEquivalence(AlignmentI al,
+  public static void testAlignmentEquivalence(AlignmentI al,
           AlignmentI al_input)
   {
     assertNotNull("Original alignment was null", al);
@@ -133,6 +135,7 @@ public class StockholmFileTest
     // we might want to revise this in future
     int aa_new_size = (aa_new == null ? 0 : aa_new.length), aa_original_size = (aa_original == null ? 0
             : aa_original.length);
+    Map<Integer,java.util.BitSet> orig_groups=new HashMap<Integer,java.util.BitSet>(),new_groups=new HashMap<Integer,java.util.BitSet>();
 
     if (aa_new != null && aa_original != null)
     {
@@ -141,6 +144,25 @@ public class StockholmFileTest
         if (aa_new.length>i) {
           assertTrue("Different alignment annotation at position "+i,
                 equalss(aa_original[i], aa_new[i]));
+          // compare graphGroup or graph properties - needed to verify JAL-1299
+          assertTrue("Graph type not identical.",aa_original[i].graph==aa_new[i].graph);
+          assertTrue("Visibility not identical.", aa_original[i].visible==aa_new[i].visible);
+          assertTrue(
+                  "Threshold line not identical.",
+                  aa_original[i].threshold == null ? aa_new[i].threshold == null
+                          : aa_original[i].threshold
+                                  .equals(aa_new[i].threshold));
+          // graphGroup may differ, but pattern should be the same
+          Integer o_ggrp=new Integer(aa_original[i].graphGroup+2),n_ggrp=new Integer(aa_new[i].graphGroup+2);
+          BitSet orig_g=orig_groups.get(o_ggrp),new_g=new_groups.get(n_ggrp);
+          if (orig_g==null) {
+            orig_groups.put(o_ggrp,orig_g= new BitSet());
+          }
+          if (new_g==null) {
+            new_groups.put(n_ggrp, new_g=new BitSet());
+          }
+          assertTrue("Graph Group pattern differs at annotation "+i, orig_g.equals(new_g));
+          orig_g.set(i); new_g.set(i);
         } else {
           System.err.println("No matching annotation row for "+aa_original[i].toString());
         }
@@ -209,7 +231,6 @@ public class StockholmFileTest
                               .equals(sequenceFeatures_new[feat]));
             }
           }
-
           // compare alignment annotation
           if (al.getSequenceAt(i).getAnnotation() != null
                   && al_input.getSequenceAt(in).getAnnotation() != null)
@@ -221,7 +242,7 @@ public class StockholmFileTest
               {
                 annot_original = al.getSequenceAt(i).getAnnotation()[j];
                 annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
-                assertTrue("Different annotation",
+                assertTrue("Different annotation elements",
                         equalss(annot_original, annot_new));
               }
             }
@@ -255,17 +276,15 @@ public class StockholmFileTest
       System.err.println("Different lengths for annotation row elements: "+annot_or.annotations.length +"!="+ annot_new.annotations.length);
       return false;
     }
-    // TODO: does not compare graphGroup or graph properties
-    // TODO: does not compare visibility
     for (int i = 0; i < annot_or.annotations.length; i++)
     {
       Annotation an_or=annot_or.annotations[i],an_new=annot_new.annotations[i];
       if (an_or != null
               && an_new!= null)
       {
-        if (!an_or.displayCharacter
-                .equals(an_new.displayCharacter)
-                || an_or.secondaryStructure != an_new.secondaryStructure
+        if (!an_or.displayCharacter.trim()
+                .equals(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))))