X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=22fe5689bed5a072f79a5a2f065df6fa3376d7b5;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=ec9ace4b29dd7514033c8e8ac4867619b20ee00d;hpb=f2f654875a6eb5f4e90b2c5c545bfed3a70f2b5f;p=jalview.git

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index ec9ace4..22fe568 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -1,20 +1,33 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * 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.util;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.api.AlignViewportI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.commands.EditCommand.Edit;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -28,59 +41,70 @@ import jalview.gui.AlignViewport;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FormatAdapter;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.annotations.Test;
+
 public class MappingUtilsTest
 {
   private AlignViewportI dnaView;
+
   private AlignViewportI proteinView;
 
   /**
    * Simple test of mapping with no intron involved.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testBuildSearchResults()
   {
-    final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
+    final Sequence seq1 = new Sequence("Seq1/5-10", "C-G-TA-GC");
     seq1.createDatasetSequence();
 
-    final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+    final Sequence aseq1 = new Sequence("Seq1/12-13", "-P-R");
     aseq1.createDatasetSequence();
 
     /*
-     * Map dna bases 1-6 to protein residues 1-2
+     * Map dna bases 5-10 to protein residues 12-13
      */
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    MapList map = new MapList(new int[]
-    { 1, 6 }, new int[]
-    { 1, 2 }, 3, 1);
+    MapList map = new MapList(new int[] { 5, 10 }, new int[] { 12, 13 }, 3,
+            1);
     acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
     Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
 
     /*
-     * Check protein residue 1 maps to codon 1-3, 2 to codon 4-6
+     * Check protein residue 12 maps to codon 5-7, 13 to codon 8-10
      */
-    SearchResults sr = MappingUtils.buildSearchResults(aseq1, 1, acfList);
+    SearchResults sr = MappingUtils.buildSearchResults(aseq1, 12, acfList);
     assertEquals(1, sr.getResults().size());
     Match m = sr.getResults().get(0);
     assertEquals(seq1.getDatasetSequence(), m.getSequence());
-    assertEquals(1, m.getStart());
-    assertEquals(3, m.getEnd());
-    sr = MappingUtils.buildSearchResults(aseq1, 2, acfList);
+    assertEquals(5, m.getStart());
+    assertEquals(7, m.getEnd());
+    sr = MappingUtils.buildSearchResults(aseq1, 13, acfList);
     assertEquals(1, sr.getResults().size());
     m = sr.getResults().get(0);
     assertEquals(seq1.getDatasetSequence(), m.getSequence());
-    assertEquals(4, m.getStart());
-    assertEquals(6, m.getEnd());
+    assertEquals(8, m.getStart());
+    assertEquals(10, m.getEnd());
 
     /*
-     * Check inverse mappings, from codons 1-3, 4-6 to protein 1, 2
+     * Check inverse mappings, from codons 5-7, 8-10 to protein 12, 13
      */
-    for (int i = 1; i < 7; i++)
+    for (int i = 5; i < 11; i++)
     {
       sr = MappingUtils.buildSearchResults(seq1, i, acfList);
       assertEquals(1, sr.getResults().size());
       m = sr.getResults().get(0);
       assertEquals(aseq1.getDatasetSequence(), m.getSequence());
-      int residue = i > 3 ? 2 : 1;
+      int residue = i > 7 ? 13 : 12;
       assertEquals(residue, m.getStart());
       assertEquals(residue, m.getEnd());
     }
@@ -89,65 +113,64 @@ public class MappingUtilsTest
   /**
    * Simple test of mapping with introns involved.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testBuildSearchResults_withIntron()
   {
-    final Sequence seq1 = new Sequence("Seq1", "C-G-TAGA-GCAGCTT");
+    final Sequence seq1 = new Sequence("Seq1/5-17", "c-G-tAGa-GcAgCtt");
     seq1.createDatasetSequence();
-  
-    final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+
+    final Sequence aseq1 = new Sequence("Seq1/8-9", "-E-D");
     aseq1.createDatasetSequence();
-  
+
     /*
-     * Map dna bases [2, 4, 5], [7, 9, 11] to protein residues 1 and 2
+     * Map dna bases [6, 8, 9], [11, 13, 115] to protein residues 8 and 9
      */
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    MapList map = new MapList(new int[]
-    { 2, 2, 4, 5, 7, 7, 9, 9, 11, 11 }, new int[]
-    { 1, 2 }, 3, 1);
+    MapList map = new MapList(new int[] { 6, 6, 8, 9, 11, 11, 13, 13, 15,
+        15 }, new int[] { 8, 9 }, 3, 1);
     acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
     Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
-  
+
     /*
-     * Check protein residue 1 maps to [2, 4, 5]
+     * Check protein residue 8 maps to [6, 8, 9]
      */
-    SearchResults sr = MappingUtils.buildSearchResults(aseq1, 1, acfList);
+    SearchResults sr = MappingUtils.buildSearchResults(aseq1, 8, acfList);
     assertEquals(2, sr.getResults().size());
     Match m = sr.getResults().get(0);
     assertEquals(seq1.getDatasetSequence(), m.getSequence());
-    assertEquals(2, m.getStart());
-    assertEquals(2, m.getEnd());
+    assertEquals(6, m.getStart());
+    assertEquals(6, m.getEnd());
     m = sr.getResults().get(1);
     assertEquals(seq1.getDatasetSequence(), m.getSequence());
-    assertEquals(4, m.getStart());
-    assertEquals(5, m.getEnd());
+    assertEquals(8, m.getStart());
+    assertEquals(9, m.getEnd());
 
     /*
-     * Check protein residue 2 maps to [7, 9, 11]
+     * Check protein residue 9 maps to [11, 13, 15]
      */
-    sr = MappingUtils.buildSearchResults(aseq1, 2, acfList);
+    sr = MappingUtils.buildSearchResults(aseq1, 9, acfList);
     assertEquals(3, sr.getResults().size());
     m = sr.getResults().get(0);
     assertEquals(seq1.getDatasetSequence(), m.getSequence());
-    assertEquals(7, m.getStart());
-    assertEquals(7, m.getEnd());
+    assertEquals(11, m.getStart());
+    assertEquals(11, m.getEnd());
     m = sr.getResults().get(1);
     assertEquals(seq1.getDatasetSequence(), m.getSequence());
-    assertEquals(9, m.getStart());
-    assertEquals(9, m.getEnd());
+    assertEquals(13, m.getStart());
+    assertEquals(13, m.getEnd());
     m = sr.getResults().get(2);
     assertEquals(seq1.getDatasetSequence(), m.getSequence());
-    assertEquals(11, m.getStart());
-    assertEquals(11, m.getEnd());
-  
+    assertEquals(15, m.getStart());
+    assertEquals(15, m.getEnd());
+
     /*
      * Check inverse mappings, from codons to protein
      */
-    for (int i = 1; i < 14; i++)
+    for (int i = 5; i < 18; i++)
     {
       sr = MappingUtils.buildSearchResults(seq1, i, acfList);
-      int residue = (i == 2 || i == 4 || i == 5) ? 1 : (i == 7 || i == 9
-              || i == 11 ? 2 : 0);
+      int residue = (i == 6 || i == 8 || i == 9) ? 8 : (i == 11 || i == 13
+              || i == 15 ? 9 : 0);
       if (residue == 0)
       {
         assertEquals(0, sr.getResults().size());
@@ -166,7 +189,7 @@ public class MappingUtilsTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testMapSequenceGroup_sequences() throws IOException
   {
     /*
@@ -180,9 +203,7 @@ public class MappingUtilsTest
             "FASTA");
     protein.setDataset(null);
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    MapList map = new MapList(new int[]
-    { 1, 3 }, new int[]
-    { 1, 1 }, 3, 1);
+    MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 3, 1);
     for (int seq = 0; seq < 3; seq++)
     {
       acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
@@ -207,7 +228,8 @@ public class MappingUtilsTest
     /*
      * Verify the mapped sequence group in dna
      */
-    SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView);
+    SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
+            proteinView, dnaView);
     assertTrue(mappedGroup.getColourText());
     assertSame(sg.getIdColour(), mappedGroup.getIdColour());
     assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
@@ -248,7 +270,7 @@ public class MappingUtilsTest
   protected AlignmentI loadAlignment(final String data, String format)
           throws IOException
   {
-    Alignment a = new FormatAdapter().readFile(data,
+    AlignmentI a = new FormatAdapter().readFile(data,
             AppletFormatAdapter.PASTE, format);
     a.setDataset(null);
     return a;
@@ -259,11 +281,11 @@ public class MappingUtilsTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testMapColumnSelection_proteinToDna() throws IOException
   {
     setupMappedAlignments();
-  
+
     ColumnSelection colsel = new ColumnSelection();
 
     /*
@@ -313,6 +335,9 @@ public class MappingUtilsTest
   }
 
   /**
+   * Set up mappings for tests from 3 dna to 3 protein sequences. Sequences have
+   * offset start positions for a more general test case.
+   * 
    * @throws IOException
    */
   protected void setupMappedAlignments() throws IOException
@@ -321,32 +346,35 @@ public class MappingUtilsTest
      * Set up dna and protein Seq1/2/3 with mappings (held on the protein
      * viewport). Lower case for introns.
      */
-    AlignmentI cdna = loadAlignment(">Seq1\nAC-GctGtC-T\n"
-            + ">Seq2\nTc-GA-G-T-Tc\n" + ">Seq3\nTtTT-AaCGg-\n",
+    AlignmentI cdna = loadAlignment(">Seq1/10-18\nAC-GctGtC-T\n"
+            + ">Seq2/20-27\nTc-GA-G-T-Tc\n" + ">Seq3/30-38\nTtTT-AaCGg-\n",
             "FASTA");
     cdna.setDataset(null);
     AlignmentI protein = loadAlignment(
-            ">Seq1\n-K-P\n>Seq2\nL--Q\n>Seq3\nG--S\n",
+            ">Seq1/40-41\n-K-P\n>Seq2/50-51\nL--Q\n>Seq3/60-61\nG--S\n",
             "FASTA");
     protein.setDataset(null);
+
+    // map first dna to first protein seq
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    MapList map = new MapList(new int[]
-    { 1, 3, 6, 6, 8, 9 }, new int[]
-    { 1, 2 }, 3, 1);
+    MapList map = new MapList(new int[] { 10, 12, 15, 15, 17, 18 },
+            new int[] { 40, 41 }, 3, 1);
     acf.addMap(cdna.getSequenceAt(0).getDatasetSequence(), protein
             .getSequenceAt(0).getDatasetSequence(), map);
-    map = new MapList(new int[]
-    { 1, 1, 3, 4, 5, 7 }, new int[]
-    { 1, 2 }, 3, 1);
+
+    // map second dna to second protein seq
+    map = new MapList(new int[] { 20, 20, 22, 23, 24, 26 }, new int[] { 50,
+        51 }, 3, 1);
     acf.addMap(cdna.getSequenceAt(1).getDatasetSequence(), protein
             .getSequenceAt(1).getDatasetSequence(), map);
-    map = new MapList(new int[]
-    { 1, 1, 3, 4, 5, 5, 7, 8 }, new int[]
-    { 1, 2 }, 3, 1);
+
+    // map third dna to third protein seq
+    map = new MapList(new int[] { 30, 30, 32, 34, 36, 37 }, new int[] { 60,
+        61 }, 3, 1);
     acf.addMap(cdna.getSequenceAt(2).getDatasetSequence(), protein
             .getSequenceAt(2).getDatasetSequence(), map);
     Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
-  
+
     dnaView = new AlignViewport(cdna);
     proteinView = new AlignViewport(protein);
     protein.setCodonFrames(acfList);
@@ -357,13 +385,13 @@ public class MappingUtilsTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testMapColumnSelection_dnaToProtein() throws IOException
   {
     setupMappedAlignments();
-  
+
     ColumnSelection colsel = new ColumnSelection();
-  
+
     /*
      * Column 0 in dna picks up first bases which map to residue 1, columns 0-1
      * in protein.
@@ -384,7 +412,7 @@ public class MappingUtilsTest
     assertEquals("[0, 1, 3]", cs.getSelected().toString());
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testMapColumnSelection_null() throws IOException
   {
     setupMappedAlignments();
@@ -397,25 +425,28 @@ public class MappingUtilsTest
    * Tests for the method that converts a series of [start, end] ranges to
    * single positions
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testFlattenRanges()
   {
     assertEquals("[1, 2, 3, 4]",
-            Arrays.toString(MappingUtils.flattenRanges(new int[]
-            { 1, 4 })));
-    assertEquals("[1, 2, 3, 4]",
-            Arrays.toString(MappingUtils.flattenRanges(new int[]
-            { 1, 2, 3, 4 })));
-    assertEquals("[1, 2, 3, 4]",
-            Arrays.toString(MappingUtils.flattenRanges(new int[]
-            { 1, 1, 2, 2, 3, 3, 4, 4 })));
-    assertEquals("[1, 2, 3, 4, 7, 8, 9, 12]",
-            Arrays.toString(MappingUtils.flattenRanges(new int[]
-            { 1, 4, 7, 9, 12, 12 })));
+            Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4 })));
+    assertEquals(
+            "[1, 2, 3, 4]",
+            Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 2, 3,
+                4 })));
+    assertEquals(
+            "[1, 2, 3, 4]",
+            Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 1, 2,
+                2, 3, 3, 4, 4 })));
+    assertEquals(
+            "[1, 2, 3, 4, 7, 8, 9, 12]",
+            Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4, 7,
+                9, 12, 12 })));
     // unpaired start position is ignored:
-    assertEquals("[1, 2, 3, 4, 7, 8, 9, 12]",
-            Arrays.toString(MappingUtils.flattenRanges(new int[]
-            { 1, 4, 7, 9, 12, 12, 15 })));
+    assertEquals(
+            "[1, 2, 3, 4, 7, 8, 9, 12]",
+            Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4, 7,
+                9, 12, 12, 15 })));
   }
 
   /**
@@ -423,7 +454,7 @@ public class MappingUtilsTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testMapSequenceGroup_columns() throws IOException
   {
     /*
@@ -431,27 +462,24 @@ public class MappingUtilsTest
      * viewport).
      */
     AlignmentI cdna = loadAlignment(
-            ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n",
-            "FASTA");
+            ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n", "FASTA");
     cdna.setDataset(null);
     AlignmentI protein = loadAlignment(">Seq1\nKA\n>Seq2\nLQ\n>Seq3\nQV\n",
             "FASTA");
     protein.setDataset(null);
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    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);
     for (int seq = 0; seq < 3; seq++)
     {
       acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
               .getSequenceAt(seq).getDatasetSequence(), map);
     }
     Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
-  
+
     AlignViewportI dnaView = new AlignViewport(cdna);
     AlignViewportI proteinView = new AlignViewport(protein);
     protein.setCodonFrames(acfList);
-  
+
     /*
      * Select all sequences, column 2 in the protein
      */
@@ -464,11 +492,12 @@ public class MappingUtilsTest
     sg.addSequence(protein.getSequenceAt(2), false);
     sg.setStartRes(1);
     sg.setEndRes(1);
-  
+
     /*
      * Verify the mapped sequence group in dna
      */
-    SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView);
+    SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
+            proteinView, dnaView);
     assertTrue(mappedGroup.getColourText());
     assertSame(sg.getIdColour(), mappedGroup.getIdColour());
     assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
@@ -478,7 +507,7 @@ public class MappingUtilsTest
     assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(2));
     assertEquals(3, mappedGroup.getStartRes());
     assertEquals(5, mappedGroup.getEndRes());
-  
+
     /*
      * Verify mapping sequence group from dna to protein
      */
@@ -506,7 +535,7 @@ public class MappingUtilsTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testMapSequenceGroup_region() throws IOException
   {
     /*
@@ -521,20 +550,18 @@ public class MappingUtilsTest
             ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", "FASTA");
     protein.setDataset(null);
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    MapList map = new MapList(new int[]
-    { 1, 9 }, new int[]
-    { 1, 3 }, 3, 1);
+    MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
     for (int seq = 0; seq < 3; seq++)
     {
       acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
               .getSequenceAt(seq).getDatasetSequence(), map);
     }
     Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
-  
+
     AlignViewportI dnaView = new AlignViewport(cdna);
     AlignViewportI proteinView = new AlignViewport(protein);
     protein.setCodonFrames(acfList);
-  
+
     /*
      * Select Seq1 and Seq2 in the protein, column 1 (K/-). Expect mapped
      * sequence group to cover Seq1, columns 0-3 (ACG). Because the selection
@@ -549,11 +576,12 @@ public class MappingUtilsTest
     sg.addSequence(protein.getSequenceAt(1), false);
     sg.setStartRes(1);
     sg.setEndRes(1);
-  
+
     /*
      * Verify the mapped sequence group in dna
      */
-    SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView);
+    SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
+            proteinView, dnaView);
     assertTrue(mappedGroup.getColourText());
     assertSame(sg.getIdColour(), mappedGroup.getIdColour());
     assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
@@ -563,7 +591,7 @@ public class MappingUtilsTest
     // Seq1 has K which should map to columns 0-3 in Seq1
     assertEquals(0, mappedGroup.getStartRes());
     assertEquals(3, mappedGroup.getEndRes());
-  
+
     /*
      * Now select cols 2-4 in protein. These cover Seq1:AS Seq2:LQ Seq3:VM which
      * extend over DNA columns 3-12, 1-7, 6-13 respectively, or 1-13 overall.
@@ -600,7 +628,7 @@ public class MappingUtilsTest
     assertEquals(4, mappedGroup.getEndRes());
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testFindMappingsForSequence()
   {
     SequenceI seq1 = new Sequence("Seq1", "ABC");
@@ -616,20 +644,18 @@ public class MappingUtilsTest
      * Create mappings from seq1 to seq2, seq2 to seq1, seq3 to seq1
      */
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
-    MapList map = new MapList(new int[]
-    { 1, 3 }, new int[]
-    { 1, 3 },1, 1);
+    MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 3 }, 1, 1);
     acf1.addMap(seq1.getDatasetSequence(), seq2.getDatasetSequence(), map);
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
     acf2.addMap(seq2.getDatasetSequence(), seq1.getDatasetSequence(), map);
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
     acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map);
-    
+
     Set<AlignedCodonFrame> mappings = new HashSet<AlignedCodonFrame>();
     mappings.add(acf1);
     mappings.add(acf2);
     mappings.add(acf3);
-    
+
     /*
      * Seq1 has three mappings
      */
@@ -669,5 +695,45 @@ public class MappingUtilsTest
 
     result = MappingUtils.findMappingsForSequence(null, null);
     assertEquals(0, result.size());
-}
+  }
+
+  @Test(groups = { "Functional" })
+  public void testMapEditCommand()
+  {
+    SequenceI dna = new Sequence("Seq1", "---ACG---GCATCA", 8, 16);
+    SequenceI protein = new Sequence("Seq2", "-T-AS", 5, 7);
+    dna.createDatasetSequence();
+    protein.createDatasetSequence();
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    MapList map = new MapList(new int[] { 8, 16 }, new int[] { 5, 7 }, 3, 1);
+    acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
+    Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+    mappings.add(acf);
+
+    AlignmentI prot = new Alignment(new SequenceI[] { protein });
+    prot.setCodonFrames(mappings);
+    AlignmentI nuc = new Alignment(new SequenceI[] { dna });
+
+    /*
+     * construct and perform the edit command to turn "-T-AS" in to "-T-A--S"
+     * i.e. insert two gaps at column 4
+     */
+    EditCommand ec = new EditCommand();
+    final Edit edit = ec.new Edit(Action.INSERT_GAP,
+            new SequenceI[] { protein }, 4, 2, '-');
+    ec.appendEdit(edit, prot, true, null);
+
+    /*
+     * the mapped edit command should be to insert 6 gaps before base 4 in the
+     * nucleotide sequence, which corresponds to aligned column 12 in the dna
+     */
+    EditCommand mappedEdit = MappingUtils.mapEditCommand(ec, false, nuc,
+            '-', mappings);
+    assertEquals(1, mappedEdit.getEdits().size());
+    Edit e = mappedEdit.getEdits().get(0);
+    assertEquals(1, e.getSequences().length);
+    assertEquals(dna, e.getSequences()[0]);
+    assertEquals(12, e.getPosition());
+    assertEquals(6, e.getNumber());
+  }
 }