JAL-1358 monday morning commits :(

[jalview.git] / test / jalview / io / StockholmFileTest.java

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 9beb174..4505f16 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -147,6 +147,11 @@ public class StockholmFileTest
           // 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);
@@ -226,7 +231,6 @@ public class StockholmFileTest
                               .equals(sequenceFeatures_new[feat]));
             }
           }
-
           // compare alignment annotation
           if (al.getSequenceAt(i).getAnnotation() != null
                   && al_input.getSequenceAt(in).getAnnotation() != null)
@@ -238,7 +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));
               }
             }
@@ -278,9 +282,9 @@ public class StockholmFileTest
       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))))