JAL-1712 fixes/tests for Castor binding of EMBL XML / show flanking

[jalview.git] / test / jalview / analysis / AlignmentUtilsTests.java

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 6c06955..02955f1 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -195,9 +195,7 @@ public class AlignmentUtilsTests
      * Expand the subsequence to the full sequence abcDEFghi
      */
     AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
-    // FIXME expandContext adds an unnecessary gap; need tests to cover all
-    // cases for which 'maxOffset' is computed
-    assertEquals("-abcDEFghi", expanded.getSequenceAt(0)
+    assertEquals("abcDEFghi", expanded.getSequenceAt(0)
             .getSequenceAsString());
 
     /*
@@ -215,13 +213,12 @@ public class AlignmentUtilsTests
     assertNull(ann.annotations[0]);
     assertNull(ann.annotations[1]);
     assertNull(ann.annotations[2]);
-    assertNull(ann.annotations[3]);
-    assertEquals(4, ann.annotations[4].value, 0.001);
-    assertEquals(5, ann.annotations[5].value, 0.001);
-    assertEquals(6, ann.annotations[6].value, 0.001);
+    assertEquals(4, ann.annotations[3].value, 0.001);
+    assertEquals(5, ann.annotations[4].value, 0.001);
+    assertEquals(6, ann.annotations[5].value, 0.001);
+    assertNull(ann.annotations[6]);
     assertNull(ann.annotations[7]);
     assertNull(ann.annotations[8]);
-    assertNull(ann.annotations[9]);
 
     /*
      * sequence position mappings should be unchanged