+/*
+ * 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;
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());
}
/**
* 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());
*
* @throws IOException
*/
- @Test
+ @Test(groups = { "Functional" })
public void testMapSequenceGroup_sequences() throws IOException
{
/*
"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
/*
* 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());
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;
*
* @throws IOException
*/
- @Test
+ @Test(groups = { "Functional" })
public void testMapColumnSelection_proteinToDna() throws IOException
{
setupMappedAlignments();
-
+
ColumnSelection colsel = new ColumnSelection();
/*
}
/**
+ * 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
* 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);
*
* @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.
assertEquals("[0, 1, 3]", cs.getSelected().toString());
}
- @Test
+ @Test(groups = { "Functional" })
public void testMapColumnSelection_null() throws IOException
{
setupMappedAlignments();
* 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 })));
}
/**
*
* @throws IOException
*/
- @Test
+ @Test(groups = { "Functional" })
public void testMapSequenceGroup_columns() throws IOException
{
/*
* 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
*/
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());
assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(2));
assertEquals(3, mappedGroup.getStartRes());
assertEquals(5, mappedGroup.getEndRes());
-
+
/*
* Verify mapping sequence group from dna to protein
*/
*
* @throws IOException
*/
- @Test
+ @Test(groups = { "Functional" })
public void testMapSequenceGroup_region() throws IOException
{
/*
">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
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());
// 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.
assertEquals(4, mappedGroup.getEndRes());
}
- @Test
+ @Test(groups = { "Functional" })
public void testFindMappingsForSequence()
{
SequenceI seq1 = new Sequence("Seq1", "ABC");
* 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
*/
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());
+ }
}
git://source.jalview.org / jalview.git / blobdiff