JAL-1925 update source version in license

[jalview.git] / test / jalview / datamodel / AlignmentAnnotationTests.java

diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index f23b3d2..4981db6 100644 (file)
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -1,14 +1,36 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * 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.junit.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+
 import jalview.analysis.AlignSeq;
 import jalview.io.AppletFormatAdapter;
 
-import org.junit.Test;
+import org.testng.annotations.Test;
 
 public class AlignmentAnnotationTests
 {
-  @Test
+  @Test(groups = { "Functional" })
   public void testCopyConstructor()
   {
     SequenceI sq = new Sequence("Foo", "ARAARARARAWEAWEAWRAWEAWE");
@@ -21,6 +43,7 @@ public class AlignmentAnnotationTests
               alc.getProperty(key));
     }
   }
+
   /**
    * create some dummy annotation derived from the sequence
    * 
@@ -72,7 +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");
@@ -95,9 +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);
 
@@ -117,8 +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",
@@ -153,7 +175,48 @@ public class AlignmentAnnotationTests
                       : "Out of range");
       assertEquals("Position " + p + " " + alm1 + " " + alm2, alm1, alm2);
     }
-    // new jalview.io.FormatAdapter().formatSequences("STOCKHOLM", n)
   }
 
+  @Test(groups = { "Functional" })
+  public void testAdjustForAlignment()
+  {
+    SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
+    seq.createDatasetSequence();
+
+    /*
+     * 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) };
+    AlignmentAnnotation ann = new AlignmentAnnotation("SS",
+            "secondary structure", anns);
+    seq.addAlignmentAnnotation(ann);
+
+    /*
+     * Check annotation map before modifying aligned sequence
+     */
+    assertNull(ann.getAnnotationForPosition(1));
+    assertNull(ann.getAnnotationForPosition(2));
+    assertNull(ann.getAnnotationForPosition(6));
+    assertNull(ann.getAnnotationForPosition(7));
+    assertEquals(1, ann.getAnnotationForPosition(3).value, 0.001d);
+    assertEquals(2, ann.getAnnotationForPosition(4).value, 0.001d);
+    assertEquals(3, ann.getAnnotationForPosition(5).value, 0.001d);
+
+    /*
+     * Trim the displayed sequence to BCD and adjust annotations
+     */
+    seq.setSequence("BCD");
+    seq.setStart(2);
+    seq.setEnd(4);
+    ann.adjustForAlignment();
+
+    /*
+     * Should now have annotations for aligned positions 2, 3Q (CD) only
+     */
+    assertEquals(3, ann.annotations.length);
+    assertNull(ann.annotations[0]);
+    assertEquals(1, ann.annotations[1].value, 0.001);
+    assertEquals(2, ann.annotations[2].value, 0.001);
+  }
 }