X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentAnnotationTests.java;h=d5e9d036f3cb808136798610d7f09deb1025e220;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=4c9eabead412c49706a2285854446050fda5d77b;hpb=c93b9ad2ebfab4cad4608a8890132918589576be;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index 4c9eabe..d5e9d03 100644
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * 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.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -10,7 +30,7 @@ import org.testng.annotations.Test;
 
 public class AlignmentAnnotationTests
 {
-  @Test
+  @Test(groups = { "Functional" })
   public void testCopyConstructor()
   {
     SequenceI sq = new Sequence("Foo", "ARAARARARAWEAWEAWRAWEAWE");
@@ -23,6 +43,7 @@ public class AlignmentAnnotationTests
               alc.getProperty(key));
     }
   }
+
   /**
    * create some dummy annotation derived from the sequence
    * 
@@ -74,7 +95,7 @@ public class AlignmentAnnotationTests
    * different dataset frames (annotation transferred by mapping between
    * sequences)
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testLiftOver()
   {
     SequenceI sqFrom = new Sequence("fromLong", "QQQCDEWGH");
@@ -97,9 +118,9 @@ public class AlignmentAnnotationTests
     alSeq2.setStart(sqTo.getStart() + align.getSeq2Start() - 1);
     alSeq2.setEnd(sqTo.getStart() + align.getSeq2End() - 1);
     alSeq2.setDatasetSequence(sqTo);
-    System.out.println(new AppletFormatAdapter().formatSequences("STH",
-            new Alignment(new SequenceI[]
-            { sqFrom, alSeq1, sqTo, alSeq2 }), true));
+    System.out.println(new AppletFormatAdapter()
+            .formatSequences("STH", new Alignment(new SequenceI[] { sqFrom,
+                alSeq1, sqTo, alSeq2 }), true));
 
     Mapping mp = align.getMappingFromS1(false);
 
@@ -119,8 +140,7 @@ public class AlignmentAnnotationTests
     almap2.setSequenceRef(alSeq2);
     almap2.adjustForAlignment();
 
-    AlignmentI all = new Alignment(new SequenceI[]
-    { alSeq1, alSeq2 });
+    AlignmentI all = new Alignment(new SequenceI[] { alSeq1, alSeq2 });
     all.addAnnotation(almap1);
     all.addAnnotation(almap2);
     System.out.println(new AppletFormatAdapter().formatSequences("STH",
@@ -157,7 +177,7 @@ public class AlignmentAnnotationTests
     }
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testAdjustForAlignment()
   {
     SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
@@ -166,8 +186,8 @@ public class AlignmentAnnotationTests
     /*
      * Annotate positions 3/4/5 (CDE) with values 1/2/3
      */
-    Annotation[] anns = new Annotation[]
-    { null, null, new Annotation(1), new Annotation(2), new Annotation(3) };
+    Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
+        new Annotation(2), new Annotation(3) };
     AlignmentAnnotation ann = new AlignmentAnnotation("SS",
             "secondary structure", anns);
     seq.addAlignmentAnnotation(ann);