JAL-2557 removal of Sequence.sequenceFeatures

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

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 228c935..4273e6c 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -287,7 +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++)
@@ -323,23 +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