X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignedCodonFrameTest.java;h=a0757ccf19f2cf05feb8588fc59a7baa99c0aaf2;hb=de0e24ab7826daa950257b9659c7e0937f15fb2f;hp=35d92d35af96f9d4b971abdac6709b04aa15e0e6;hpb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;p=jalview.git

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index 35d92d3..a0757cc 100644
--- a/test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/test/jalview/datamodel/AlignedCodonFrameTest.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.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -15,11 +35,10 @@ public class AlignedCodonFrameTest
   /**
    * Test the method that locates the first aligned sequence that has a mapping.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testFindAlignedSequence()
   {
-    AlignmentI cdna = new Alignment(new SequenceI[]
-    {});
+    AlignmentI cdna = new Alignment(new SequenceI[] {});
     final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
     seq1.createDatasetSequence();
     cdna.addSequence(seq1);
@@ -27,8 +46,7 @@ public class AlignedCodonFrameTest
     seq2.createDatasetSequence();
     cdna.addSequence(seq2);
 
-    AlignmentI aa = new Alignment(new SequenceI[]
-    {});
+    AlignmentI aa = new Alignment(new SequenceI[] {});
     final Sequence aseq1 = new Sequence("Seq1", "-P-R");
     aseq1.createDatasetSequence();
     aa.addSequence(aseq1);
@@ -43,27 +61,23 @@ public class AlignedCodonFrameTest
 
     assertNull(acf.findAlignedSequence(seq1, aa));
 
-    MapList map = new MapList(new int[]
-    { 1, 6 }, new int[]
-    { 1, 2 }, 3, 1);
+    MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
     acf.addMap(seq1.getDatasetSequence(), aseq2.getDatasetSequence(), map);
 
     /*
      * DNA seq1 maps to AA seq2
      */
-    assertEquals(aa.getSequenceAt(1),
- acf.findAlignedSequence(cdna
+    assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(cdna
             .getSequenceAt(0).getDatasetSequence(), aa));
 
-    assertEquals(cdna.getSequenceAt(0),
- acf.findAlignedSequence(aa
+    assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(aa
             .getSequenceAt(1).getDatasetSequence(), cdna));
   }
 
   /**
    * Test the method that locates the mapped codon for a protein position.
    */
-    @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testGetMappedRegion()
   {
     // introns lower case, exons upper case
@@ -87,13 +101,11 @@ public class AlignedCodonFrameTest
     /*
      * Set up the mappings for the exons (upper-case bases)
      */
-    MapList map = new MapList(new int[]
-    { 2, 4, 6, 6, 8, 9 }, new int[]
-    { 1, 2 }, 3, 1);
+    MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
+        1, 2 }, 3, 1);
     acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
-    map = new MapList(new int[]
-    { 1, 2, 4, 5, 7, 8 }, new int[]
-    { 1, 2 }, 3, 1);
+    map = new MapList(new int[] { 1, 2, 4, 5, 7, 8 }, new int[] { 1, 2 },
+            3, 1);
     acf.addMap(seq2.getDatasetSequence(), aseq2.getDatasetSequence(), map);
 
     assertEquals("[2, 4]",
@@ -111,7 +123,7 @@ public class AlignedCodonFrameTest
     assertNull(acf.getMappedRegion(seq1, aseq2, 1));
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testGetMappedCodon()
   {
     final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
@@ -129,14 +141,39 @@ public class AlignedCodonFrameTest
     /*
      * Set up the mappings for the exons (upper-case bases)
      */
-    MapList map = new MapList(new int[]
-    { 2, 4, 6, 6, 8, 9 }, new int[]
-    { 1, 2 }, 3, 1);
+    MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
+        1, 2 }, 3, 1);
     acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
-    
+
     assertEquals("[G, T, A]", Arrays.toString(acf.getMappedCodon(
             aseq1.getDatasetSequence(), 1)));
     assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(
             aseq1.getDatasetSequence(), 2)));
   }
+
+  /**
+   * Test for the case where sequences have start > 1
+   */
+  @Test(groups = { "Functional" })
+  public void testGetMappedCodon_forSubSequences()
+  {
+    final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T", 27, 35);
+    seq1.createDatasetSequence();
+
+    final Sequence aseq1 = new Sequence("Seq1", "-P-R", 12, 13);
+    aseq1.createDatasetSequence();
+
+    /*
+     * Set up the mappings for the exons (upper-case bases)
+     */
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    MapList map = new MapList(new int[] { 28, 30, 32, 32, 34, 35 },
+            new int[] { 12, 13 }, 3, 1);
+    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+
+    assertEquals("[G, T, A]", Arrays.toString(acf.getMappedCodon(
+            aseq1.getDatasetSequence(), 12)));
+    assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(
+            aseq1.getDatasetSequence(), 13)));
+  }
 }