Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 1a18fb9..4273e6c 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -60,7 +60,7 @@ public class StockholmFileTest
   public void pfamFileIO() throws Exception
   {
     testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0,
-            false);
+            false, false, false);
   }
 
   @Test(groups = { "Functional" })
@@ -86,7 +86,7 @@ public class StockholmFileTest
   public void rfamFileIO() throws Exception
   {
     testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1,
-            false);
+            false, false, false);
   }
 
   /**
@@ -98,11 +98,14 @@ public class StockholmFileTest
    * @param ioformat
    *          - label for IO class used to write and read back in the data from
    *          f
+   * @param ignoreFeatures
    * @param ignoreRowVisibility
+   * @param allowNullAnnotations
    */
 
   public static void testFileIOwithFormat(File f, FileFormatI ioformat,
-          int naliannot, int nminseqann, boolean ignoreRowVisibility)
+          int naliannot, int nminseqann, boolean ignoreFeatures,
+          boolean ignoreRowVisibility, boolean allowNullAnnotations)
   {
     System.out.println("Reading file: " + f);
     String ff = f.getPath();
@@ -136,7 +139,8 @@ public class StockholmFileTest
               "Identify routine could not recognise output generated by '"
                       + ioformat + "' writer",
               ioformat.equals(identifyoutput));
-      testAlignmentEquivalence(al, al_input, false);
+      testAlignmentEquivalence(al, al_input, ignoreFeatures,
+              ignoreRowVisibility, allowNullAnnotations);
       int numaliannot = 0, numsqswithali = 0;
       for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
       {
@@ -283,7 +287,8 @@ public class StockholmFileTest
     seq_original = al.getSequencesArray();
     SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
     seq_new = al_input.getSequencesArray();
-    SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new;
+    List<SequenceFeature> sequenceFeatures_original;
+    List<SequenceFeature> sequenceFeatures_new;
     AlignmentAnnotation annot_original, annot_new;
     //
     for (int i = 0; i < al.getSequencesArray().length; i++)
@@ -319,23 +324,20 @@ public class StockholmFileTest
                   && seq_new[in].getSequenceFeatures() != null)
           {
             System.out.println("There are feature!!!");
-            sequenceFeatures_original = new SequenceFeature[seq_original[i]
-                    .getSequenceFeatures().length];
             sequenceFeatures_original = seq_original[i]
                     .getSequenceFeatures();
-            sequenceFeatures_new = new SequenceFeature[seq_new[in]
-                    .getSequenceFeatures().length];
             sequenceFeatures_new = seq_new[in].getSequenceFeatures();
 
-            assertEquals("different number of features",
-                    seq_original[i].getSequenceFeatures().length,
-                    seq_new[in].getSequenceFeatures().length);
+            assertEquals("different number of features", seq_original[i]
+                    .getSequenceFeatures().size(), seq_new[in]
+                    .getSequenceFeatures().size());
 
-            for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
+            for (int feat = 0; feat < seq_original[i].getSequenceFeatures()
+                    .size(); feat++)
             {
               assertEquals("Different features",
-                      sequenceFeatures_original[feat],
-                      sequenceFeatures_new[feat]);
+                      sequenceFeatures_original.get(feat),
+                      sequenceFeatures_new.get(feat));
             }
           }
           // compare alignment annotation