JAL-3070 JAL-2507 fix up test output and honour the ‘ignoreFeatures’ flag when testin...

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

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index e86c8ad..96c6828 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -257,8 +257,8 @@ public class StockholmFileTest
           assertEquals("Threshold line not identical.",
                   aa_original[i].threshold, aa_new[i].threshold);
           // graphGroup may differ, but pattern should be the same
-          Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2);
-          Integer n_ggrp = new Integer(aa_new[i].graphGroup + 2);
+          Integer o_ggrp = Integer.valueOf(aa_original[i].graphGroup + 2);
+          Integer n_ggrp = Integer.valueOf(aa_new[i].graphGroup + 2);
           BitSet orig_g = orig_groups.get(o_ggrp);
           BitSet new_g = new_groups.get(n_ggrp);
           if (orig_g == null)
@@ -323,10 +323,11 @@ public class StockholmFileTest
                           || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
                                   .getSequenceFeatures() != null));
           // compare sequence features
-          if (seq_original[i].getSequenceFeatures() != null
+          if (!ignoreFeatures
+                  && seq_original[i].getSequenceFeatures() != null
                   && seq_new[in].getSequenceFeatures() != null)
           {
-            System.out.println("There are feature!!!");
+            System.out.println("Checking feature equivalence.");
             sequenceFeatures_original = seq_original[i]
                     .getSequenceFeatures();
             sequenceFeatures_new = seq_new[in].getSequenceFeatures();