X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=1cfa77156eb165d79915660da2a8987725bae1da;hb=4962cfc45d6cfc4899272a9a7eb991824c8a6e6e;hp=660a69c1a564f29b6eb97199dca5171ad36f9374;hpb=33ea5042df2f15bab1b21770dfc93f28b8bf950e;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 660a69c..1cfa771 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -37,7 +37,6 @@ import jalview.io.FormatAdapter;
 import jalview.util.MapList;
 
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
@@ -658,7 +657,7 @@ public class AlignmentTest
     assertFalse(iter.hasNext());
 
     // search for annotation with a particular label - expect three
-    anns = al.findAnnotations(null, null, "secondary structure");
+    anns = al.findAnnotations(null, null, "Secondary Structure");
     iter = anns.iterator();
     assertTrue(iter.hasNext());
     iter.next();
@@ -1107,35 +1106,6 @@ public class AlignmentTest
             "addSequence broke dataset reference integrity");
   }
 
-  @Test(groups = "Functional")
-  public void getVisibleStartAndEndIndexTest()
-  {
-    Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
-    AlignmentI align = new Alignment(new SequenceI[] { seq });
-    ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
-
-    int[] startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
-    assertEquals(0, startEnd[0]);
-    assertEquals(25, startEnd[1]);
-
-    hiddenCols.add(new int[] { 0, 0 });
-    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
-    assertEquals(1, startEnd[0]);
-    assertEquals(25, startEnd[1]);
-
-    hiddenCols.add(new int[] { 6, 9 });
-    hiddenCols.add(new int[] { 11, 12 });
-    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
-    assertEquals(1, startEnd[0]);
-    assertEquals(25, startEnd[1]);
-
-    hiddenCols.add(new int[] { 24, 25 });
-    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
-    System.out.println(startEnd[0] + " : " + startEnd[1]);
-    assertEquals(1, startEnd[0]);
-    assertEquals(23, startEnd[1]);
-  }
-
   /**
    * Tests that dbrefs with mappings to sequence get updated if the sequence
    * acquires a dataset sequence