Merge branch 'develop' into features/JAL-1705_ensembl

[jalview.git] / test / jalview / util / ComparisonTest.java

diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index 837cbe6..6618789 100644 (file)
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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.util;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -12,7 +32,7 @@ import org.testng.annotations.Test;
 public class ComparisonTest
 {
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testIsGap()
   {
     assertTrue(Comparison.isGap('-'));
@@ -28,64 +48,53 @@ public class ComparisonTest
    * Test for isNucleotide is that sequences in a dataset are more than 85%
    * AGCTU. Test is not case-sensitive and ignores gaps.
    */
-  @Test
-  public void testIsNucleotide() {
+  @Test(groups = { "Functional" })
+  public void testIsNucleotide()
+  {
     SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
-    assertFalse(Comparison.isNucleotide(new SequenceI[]
-    { seq }));
-    assertFalse(Comparison.isNucleotide(new SequenceI[][]
-    { new SequenceI[]
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+    assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
     { seq } }));
 
     seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
-    assertFalse(Comparison.isNucleotide(new SequenceI[]
-    { seq }));
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
 
     seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV");
-    assertTrue(Comparison.isNucleotide(new SequenceI[]
-    { seq }));
+    assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
 
     seq = new Sequence("eightyfivepercentgapped",
             "--agc--tuA--GCPV-a---gct-uA-GC---UV");
-    assertFalse(Comparison.isNucleotide(new SequenceI[]
-    { seq }));
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
 
     seq = new Sequence("nineypercentgapped",
             "ag--ct-u-A---GC---g----Vag--c---tuAGCUV");
-    assertTrue(Comparison.isNucleotide(new SequenceI[]
-    { seq }));
+    assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
 
     seq = new Sequence("allgap", "---------");
-    assertFalse(Comparison.isNucleotide(new SequenceI[]
-    { seq }));
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
 
     seq = new Sequence("DNA", "ACTugGCCAG");
     SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
     /*
      * 90% DNA:
      */
-    assertTrue(Comparison.isNucleotide(new SequenceI[]
-    { seq, seq, seq, seq, seq, seq, seq, seq, seq, seq2 }));
-    assertTrue(Comparison.isNucleotide(new SequenceI[][]
-    { new SequenceI[]
-    { seq }, new SequenceI[]
-    { seq, seq, seq }, new SequenceI[]
-    { seq, seq, seq, seq, seq, seq2 } }));
+    assertTrue(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
+        seq, seq, seq, seq, seq, seq, seq2 }));
+    assertTrue(Comparison.isNucleotide(new SequenceI[][] {
+        new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
+        new SequenceI[] { seq, seq, seq, seq, seq, seq2 } }));
     /*
      * 80% DNA:
      */
-    assertFalse(Comparison.isNucleotide(new SequenceI[]
-    { seq, seq, seq, seq, seq, seq, seq, seq, seq2, seq2 }));
-    assertFalse(Comparison.isNucleotide(new SequenceI[][]
-    { new SequenceI[]
-    { seq }, new SequenceI[]
-    { seq, seq, seq }, new SequenceI[]
-    { seq, seq, seq, seq, seq2, seq2, null } }));
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
+        seq, seq, seq, seq, seq, seq2, seq2 }));
+    assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
+    { seq }, new SequenceI[] { seq, seq, seq },
+        new SequenceI[] { seq, seq, seq, seq, seq2, seq2, null } }));
 
     seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
     // 12/14 = 85.7%
-    assertTrue(Comparison.isNucleotide(new SequenceI[]
-    { seq }));
+    assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
 
     assertFalse(Comparison.isNucleotide((SequenceI[]) null));
     assertFalse(Comparison.isNucleotide((SequenceI[][]) null));
@@ -94,7 +103,7 @@ public class ComparisonTest
   /**
    * Test percentage identity calculation for two sequences.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testPID_matchGaps()
   {
     String seq1 = "ABCDEF";