JAL-3438 spotless for 2.11.2.0

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

diff --git a/test/jalview/datamodel/AlignedCodonIteratorTest.java b/test/jalview/datamodel/AlignedCodonIteratorTest.java
index d9c7e12..af9bbb7 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonIteratorTest.java
+++ b/test/jalview/datamodel/AlignedCodonIteratorTest.java
@@ -1,13 +1,35 @@
+/*
+ * 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;
 import static org.testng.AssertJUnit.assertFalse;
 
+import jalview.gui.JvOptionPane;
 import jalview.util.MapList;
 
 import java.util.Iterator;
 
 import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 /**
@@ -18,19 +40,27 @@ import org.testng.annotations.Test;
  */
 public class AlignedCodonIteratorTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * Test normal case for iterating over aligned codons.
    */
-  @Test(groups ={ "Functional" })
+  @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, '-');
@@ -49,16 +79,16 @@ public class AlignedCodonIteratorTest
   /**
    * Test weird case where the mapping skips over a peptide.
    */
-  @Test(groups ={ "Functional" })
+  @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, '-');
@@ -73,20 +103,20 @@ public class AlignedCodonIteratorTest
     assertEquals("R", codon.product);
     assertFalse(codons.hasNext());
   }
-  
+
   /**
    * Test for exception thrown for an incomplete codon.
    */
-  @Test(groups ={ "Functional" })
+  @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, '-');
@@ -106,18 +136,17 @@ public class AlignedCodonIteratorTest
   /**
    * Test normal case for iterating over aligned codons.
    */
-  @Test(groups ={ "Functional" })
+  @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());
@@ -133,4 +162,33 @@ 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());
+  }
 }