JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/test/jalview/analysis/GroupingTest.java b/test/jalview/analysis/GroupingTest.java
index 4698d0d..1a04517 100644 (file)
--- a/test/jalview/analysis/GroupingTest.java
+++ b/test/jalview/analysis/GroupingTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 jalview.datamodel.Alignment;
@@ -25,19 +45,18 @@ 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 sg1 = 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 sg2 = 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 };
+  int[] positions = new int[] { 1, 7, 9 };
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testMakeGroupsWithBoth()
   {
     ArrayList<String> str = new ArrayList<String>();
@@ -53,8 +72,7 @@ public class GroupingTest
     SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
             alignment.getSequencesArray(),
             str.toArray(new String[str.size()]),
-            Arrays.asList(new SequenceGroup[]
-            { sg1, sg2 }));
+            Arrays.asList(new SequenceGroup[] { sg1, sg2 }));
     ColumnSelection cs = new ColumnSelection();
     for (int p : positions)
     {
@@ -62,9 +80,9 @@ public class GroupingTest
     }
     SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
             alignment.getSequencesArray(), cs,
-            Arrays.asList(new SequenceGroup[]
-            { sg1, sg2 }));
-    AssertJUnit.assertEquals(seqgroupsString.length, seqgroupsColSel.length);
+            Arrays.asList(new SequenceGroup[] { sg1, sg2 }));
+    AssertJUnit
+            .assertEquals(seqgroupsString.length, seqgroupsColSel.length);
     for (int p = 0; p < seqgroupsString.length; p++)
     {
       AssertJUnit.assertEquals(seqgroupsString[p].getName(),