JAL-2333 test beefed up with gaps

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index d7f7acb..8c81d51 100644 (file)
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -37,10 +37,10 @@ public class AlignViewControllerTest
   @Test(groups = "Functional")
   public void testFindColumnsWithFeature()
   {
-    SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
-    SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
-    SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
-    SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
+    SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa");
+    SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
+    SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
+    SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
 
     /*
      * features start/end are base 1
@@ -58,11 +58,11 @@ public class AlignViewControllerTest
             0f, null));
 
     /*
-     * select the first three columns --> Metal in seq1 2-3
+     * select the first five columns --> Metal in seq1 cols 4-5
      */
     SequenceGroup sg = new SequenceGroup();
     sg.setStartRes(0); // base 0
-    sg.setEndRes(2);
+    sg.setEndRes(4);
     sg.addSequence(seq1, false);
     sg.addSequence(seq2, false);
     sg.addSequence(seq3, false);
@@ -73,36 +73,37 @@ public class AlignViewControllerTest
             bs);
     assertEquals(1, seqCount);
     assertEquals(2, bs.cardinality());
-    assertTrue(bs.get(1));
-    assertTrue(bs.get(2));
+    assertTrue(bs.get(3)); // base 0
+    assertTrue(bs.get(4));
 
     /*
-     * select the first four columns: Metal in seq1 2:4, seq2 4:4
+     * select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7 
      */
-    sg.setEndRes(3);
+    sg.setEndRes(6);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
     assertEquals(2, seqCount);
-    assertEquals(3, bs.cardinality());
-    assertTrue(bs.get(1));
-    assertTrue(bs.get(2));
+    assertEquals(4, bs.cardinality());
     assertTrue(bs.get(3));
+    assertTrue(bs.get(4));
+    assertTrue(bs.get(5));
+    assertTrue(bs.get(6));
 
     /*
-     * select column 11: Metal in seq3 only
+     * select column 14: Metal in seq3 only
      */
-    sg.setStartRes(10);
-    sg.setEndRes(10);
+    sg.setStartRes(13);
+    sg.setEndRes(13);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
     assertEquals(1, seqCount);
     assertEquals(1, bs.cardinality());
-    assertTrue(bs.get(10));
+    assertTrue(bs.get(13));
 
     /*
-     * select columns 16-20: no Metal feature
+     * select columns 18-20: no Metal feature
      */
-    sg.setStartRes(15);
+    sg.setStartRes(17);
     sg.setEndRes(19);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
@@ -110,10 +111,10 @@ public class AlignViewControllerTest
     assertEquals(0, bs.cardinality());
 
     /*
-     * columns 9-11 should not match disulfide bond at 8/12
+     * columns 11-13 should not match disulfide bond at 8/12
      */
-    sg.setStartRes(8);
-    sg.setEndRes(10);
+    sg.setStartRes(10);
+    sg.setEndRes(12);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
             sg, bs);
@@ -121,17 +122,17 @@ public class AlignViewControllerTest
     assertEquals(0, bs.cardinality());
 
     /*
-     * columns 6-14 should match disulfide bond at 8/12
+     * columns 6-18 should match disulfide bond at columns 9, 14
      */
     sg.setStartRes(5);
-    sg.setEndRes(13);
+    sg.setEndRes(17);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
             sg, bs);
     assertEquals(1, seqCount);
     assertEquals(2, bs.cardinality());
-    assertTrue(bs.get(7));
-    assertTrue(bs.get(11));
+    assertTrue(bs.get(8));
+    assertTrue(bs.get(13));
 
     /*
      * look for a feature that isn't there