X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignedCodonIteratorTest.java;h=113cb2a363886d1f46ab91354481bf8d614970e1;hb=d9c7868a610eff29a8eddb160b6dc78a94a72470;hp=3e3a46dfbee92eda8d618127f992b38f97398922;hpb=3412b273e964fb1a9d22564b04a5f0c827ec2461;p=jalview.git

diff --git a/test/jalview/datamodel/AlignedCodonIteratorTest.java b/test/jalview/datamodel/AlignedCodonIteratorTest.java
index 3e3a46d..113cb2a 100644
--- a/test/jalview/datamodel/AlignedCodonIteratorTest.java
+++ b/test/jalview/datamodel/AlignedCodonIteratorTest.java
@@ -1,13 +1,35 @@
+/*
+ * 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.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
-import org.testng.annotations.Test;
-import org.testng.Assert;
+
 import jalview.util.MapList;
 
 import java.util.Iterator;
 
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
 /**
  * Unit tests for Mapping$AlignedCodonIterator
  * 
@@ -19,16 +41,16 @@ public class AlignedCodonIteratorTest
   /**
    * Test normal case for iterating over aligned codons.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testNext()
   {
     SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc");
     from.createDatasetSequence();
     SequenceI to = new Sequence("Seq1", "-PQ-R-");
     to.createDatasetSequence();
-    MapList map = new MapList(new int[]
-    { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[]
-    { 1, 3 }, 3, 1);
+    MapList map = new MapList(
+            new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 },
+            new int[] { 1, 3 }, 3, 1);
     Mapping m = new Mapping(to.getDatasetSequence(), map);
 
     Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
@@ -47,16 +69,16 @@ public class AlignedCodonIteratorTest
   /**
    * Test weird case where the mapping skips over a peptide.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testNext_unmappedPeptide()
   {
     SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc");
     from.createDatasetSequence();
     SequenceI to = new Sequence("Seq1", "-PQ-TR-");
     to.createDatasetSequence();
-    MapList map = new MapList(new int[]
-    { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[]
-    { 1, 2, 4, 4 }, 3, 1);
+    MapList map = new MapList(
+            new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[] { 1,
+                2, 4, 4 }, 3, 1);
     Mapping m = new Mapping(to.getDatasetSequence(), map);
 
     Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
@@ -71,20 +93,19 @@ public class AlignedCodonIteratorTest
     assertEquals("R", codon.product);
     assertFalse(codons.hasNext());
   }
-  
+
   /**
    * Test for exception thrown for an incomplete codon.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testNext_incompleteCodon()
   {
     SequenceI from = new Sequence("Seq1", "-CgC-C-cCgTt");
     from.createDatasetSequence();
     SequenceI to = new Sequence("Seq1", "-PQ-R-");
     to.createDatasetSequence();
-    MapList map = new MapList(new int[]
-    { 1, 1, 3, 4, 6, 6, 8, 8 }, new int[]
-    { 1, 3 }, 3, 1);
+    MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 8 },
+            new int[] { 1, 3 }, 3, 1);
     Mapping m = new Mapping(to.getDatasetSequence(), map);
 
     Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
@@ -104,18 +125,16 @@ public class AlignedCodonIteratorTest
   /**
    * Test normal case for iterating over aligned codons.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testAnother()
   {
     SequenceI from = new Sequence("Seq1", "TGCCATTACCAG-");
     from.createDatasetSequence();
     SequenceI to = new Sequence("Seq1", "CHYQ");
     to.createDatasetSequence();
-    MapList map = new MapList(new int[]
-    { 1, 12 }, new int[]
-    { 1, 4 }, 3, 1);
+    MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
     Mapping m = new Mapping(to.getDatasetSequence(), map);
-  
+
     Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
     AlignedCodon codon = codons.next();
     assertEquals("[0, 1, 2]", codon.toString());
@@ -131,4 +150,31 @@ public class AlignedCodonIteratorTest
     assertEquals("Q", codon.product);
     assertFalse(codons.hasNext());
   }
+
+  /**
+   * Test for a case with sequence (and mappings) not starting at 1
+   */
+  @Test(groups = { "Functional" })
+  public void testNext_withOffset()
+  {
+    SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc", 7, 20);
+    from.createDatasetSequence();
+    SequenceI to = new Sequence("Seq1/10-12", "-PQ-R-");
+    to.createDatasetSequence();
+    MapList map = new MapList(new int[] { 7, 7, 9, 10, 12, 12, 14, 16, 18,
+        19 }, new int[] { 10, 12 }, 3, 1);
+    Mapping m = new Mapping(to.getDatasetSequence(), map);
+
+    Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
+    AlignedCodon codon = codons.next();
+    assertEquals("[1, 3, 5]", codon.toString());
+    assertEquals("P", codon.product);
+    codon = codons.next();
+    assertEquals("[8, 10, 11]", codon.toString());
+    assertEquals("Q", codon.product);
+    codon = codons.next();
+    assertEquals("[13, 15, 17]", codon.toString());
+    assertEquals("R", codon.product);
+    assertFalse(codons.hasNext());
+  }
 }