JAL-1479 SiftClient house keeping

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

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index 23aa889..a0757cc 100644 (file)
--- 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;
@@ -130,4 +150,30 @@ public class AlignedCodonFrameTest
     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)));
+  }
 }