JAL-1780 JAL-653 Format/AppletFormat import and export pipeline regularised, uses...

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

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 00cbbb9..c3fd4e3 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,7 +23,6 @@ package jalview.io;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -93,7 +92,7 @@ public class StockholmFileTest
     {
       AppletFormatAdapter rf = new AppletFormatAdapter();
 
-      Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
+      AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
               new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
 
       assertNotNull("Couldn't read supplied alignment data.", al);
@@ -107,7 +106,7 @@ 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);
 
@@ -119,7 +118,7 @@ public class StockholmFileTest
               "Identify routine could not recognise output generated by '"
                       + ioformat + "' writer",
               ioformat.equals(identifyoutput));
-      testAlignmentEquivalence(al, al_input);
+      testAlignmentEquivalence(al, al_input, false);
       int numaliannot = 0, numsqswithali = 0;
       for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
       {
@@ -157,9 +156,11 @@ public class StockholmFileTest
    * @param al_input
    *          'secondary' or generated alignment from some datapreserving
    *          transformation
+   * @param ignoreFeatures
+   *          when true, differences in seuqence feature annotation are ignored.
    */
   public static void testAlignmentEquivalence(AlignmentI al,
-          AlignmentI al_input)
+          AlignmentI al_input, boolean ignoreFeatures)
   {
     assertNotNull("Original alignment was null", al);
     assertNotNull("Generated alignment was null", al_input);
@@ -261,8 +262,10 @@ public class StockholmFileTest
                   + " are not equal", ss_original.equals(ss_new));
 
           assertTrue(
-                  "Sequence Features were not equivalent",
-                  (seq_original[i].getSequenceFeatures() == null && seq_new[in]
+                  "Sequence Features were not equivalent"
+                          + (ignoreFeatures ? " ignoring." : ""),
+                  ignoreFeatures
+                          || (seq_original[i].getSequenceFeatures() == null && seq_new[in]
                           .getSequenceFeatures() == null)
                           || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
                                   .getSequenceFeatures() != null));