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

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

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index 04ab3bf..2d64d28 100644 (file)
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -1,13 +1,35 @@
-
+/*
+ * 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 static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
 import java.util.Hashtable;
 
+import org.testng.annotations.Test;
+
 public class AAFrequencyTest
 {
   private static final String C = AAFrequency.MAXCOUNT;
@@ -20,17 +42,16 @@ public class AAFrequencyTest
 
   private static final String P = AAFrequency.PROFILE;
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testCalculate_noProfile()
   {
     SequenceI seq1 = new Sequence("Seq1", "CAGT");
     SequenceI seq2 = new Sequence("Seq2", "CACT");
     SequenceI seq3 = new Sequence("Seq3", "C--G");
     SequenceI seq4 = new Sequence("Seq4", "CA-t");
-    SequenceI[] seqs = new SequenceI[]
-    { seq1, seq2, seq3, seq4 };
+    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
     Hashtable[] result = new Hashtable[seq1.getLength()];
-    
+
     AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
 
     // col 0 is 100% C
@@ -63,15 +84,14 @@ public class AAFrequencyTest
     assertEquals("T", col.get(R));
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testCalculate_withProfile()
   {
     SequenceI seq1 = new Sequence("Seq1", "CAGT");
     SequenceI seq2 = new Sequence("Seq2", "CACT");
     SequenceI seq3 = new Sequence("Seq3", "C--G");
     SequenceI seq4 = new Sequence("Seq4", "CA-t");
-    SequenceI[] seqs = new SequenceI[]
-    { seq1, seq2, seq3, seq4 };
+    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
     Hashtable[] result = new Hashtable[seq1.getLength()];
 
     AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
@@ -98,15 +118,14 @@ public class AAFrequencyTest
     assertEquals(4, profile[1][1]);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testCalculate_withProfileTiming()
   {
     SequenceI seq1 = new Sequence("Seq1", "CAGT");
     SequenceI seq2 = new Sequence("Seq2", "CACT");
     SequenceI seq3 = new Sequence("Seq3", "C--G");
     SequenceI seq4 = new Sequence("Seq4", "CA-t");
-    SequenceI[] seqs = new SequenceI[]
-    { seq1, seq2, seq3, seq4 };
+    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
     Hashtable[] result = new Hashtable[seq1.getLength()];
 
     // ensure class loaded and initialized
@@ -120,7 +139,7 @@ public class AAFrequencyTest
     System.out.println(System.currentTimeMillis() - start);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testGetPercentageFormat()
   {
     assertNull(AAFrequency.getPercentageFormat(0));