X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FGroupingTest.java;h=df39b810feb1c149b59712d1953ae79a13662435;hb=6b5f772a654104d856da1651c3d411981be463df;hp=61bd480b1de7a7d85e07fdcc5038b04de4e47527;hpb=f21eb611044169a07a7d4c6e2f69dd772fa7c872;p=jalview.git

diff --git a/test/jalview/analysis/GroupingTest.java b/test/jalview/analysis/GroupingTest.java
index 61bd480..df39b81 100644
--- a/test/jalview/analysis/GroupingTest.java
+++ b/test/jalview/analysis/GroupingTest.java
@@ -1,6 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis;
 
-import static org.junit.Assert.fail;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
@@ -8,11 +27,10 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
-import java.util.ArrayList;
 import java.util.Arrays;
 
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
 
 public class GroupingTest
 {
@@ -26,22 +44,26 @@ public class GroupingTest
 
   Sequence s5 = new Sequence("s5", "AAAADDEDTTEE");
 
-  SequenceGroup sg1 = new SequenceGroup(Arrays.asList(new SequenceI[]
-  { s1, s2 }), "Group1", null, false, false, false, 0, 5);
+  SequenceGroup sg_12 = new SequenceGroup(Arrays.asList(new SequenceI[] { s1,
+      s2 }), "Group1", null, false, false, false, 0, 5);
 
-  SequenceGroup sg2 = new SequenceGroup(Arrays.asList(new SequenceI[]
-  { s3, s4, s5 }), "Group2", null, false, false, false, 0, 5);
+  SequenceGroup sg_345 = new SequenceGroup(Arrays.asList(new SequenceI[] { s3,
+      s4, s5 }), "Group2", null, false, false, false, 0, 5);
 
-  AlignmentI alignment = new Alignment(new SequenceI[]
-  { s1, s2, s3, s4, s5 });
+  AlignmentI alignment = new Alignment(
+          new SequenceI[] { s1, s2, s3, s4, s5 });
 
-  int[] positions = new int[]
-  { 1, 7, 9 };
+  /*
+   * test for the case where column selections are not added in
+   * left to right order
+   */
+  int[] positions = new int[] { 7, 9, 1 };
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testMakeGroupsWithBoth()
   {
-    ArrayList<String> str = new ArrayList<String>();
+    String[] str = new String[alignment.getHeight()];
+    int seq = 0;
     for (SequenceI s : alignment.getSequences())
     {
       StringBuilder sb = new StringBuilder();
@@ -49,13 +71,12 @@ public class GroupingTest
       {
         sb.append(s.getCharAt(p));
       }
-      str.add(sb.toString());
+      str[seq++] = sb.toString();
     }
     SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
-            alignment.getSequencesArray(),
-            str.toArray(new String[str.size()]),
-            Arrays.asList(new SequenceGroup[]
-            { sg1, sg2 }));
+            alignment.getSequencesArray(), str,
+            Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
+
     ColumnSelection cs = new ColumnSelection();
     for (int p : positions)
     {
@@ -63,27 +84,21 @@ public class GroupingTest
     }
     SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
             alignment.getSequencesArray(), cs,
-            Arrays.asList(new SequenceGroup[]
-            { sg1, sg2 }));
-    Assert.assertEquals(seqgroupsString.length, seqgroupsColSel.length);
+            Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
+    AssertJUnit
+            .assertEquals(seqgroupsString.length, seqgroupsColSel.length);
     for (int p = 0; p < seqgroupsString.length; p++)
     {
-      Assert.assertEquals(seqgroupsString[p].getName(),
+      AssertJUnit.assertEquals(seqgroupsString[p].getName(),
               seqgroupsColSel[p].getName());
-      Assert.assertArrayEquals(
+      AssertJUnit.assertArrayEquals(
               seqgroupsString[p].getSequencesInOrder(alignment),
               seqgroupsColSel[p].getSequencesInOrder(alignment));
       if (seqgroupsString[p].getSequences().contains(s2))
       {
-        Assert.assertTrue(seqgroupsString[p].getSize() == 2);
+        AssertJUnit.assertTrue(seqgroupsString[p].getSize() == 2);
       }
     }
   }
 
-  @Test
-  public void testMakeGroupsFromCols()
-  {
-    fail("Not yet implemented"); // TODO
-  }
-
 }