+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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 static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResults.Match;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
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 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");
* Map dna bases 1-6 to protein residues 1-2
*/
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);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
/**
* Simple test of mapping with introns involved.
*/
- @Test
- public void testBuildSearchResults_withIntro()
+ @Test(groups = { "Functional" })
+ public void testBuildSearchResults_withIntron()
{
final Sequence seq1 = new Sequence("Seq1", "C-G-TAGA-GCAGCTT");
seq1.createDatasetSequence();
-
+
final Sequence aseq1 = new Sequence("Seq1", "-P-R");
aseq1.createDatasetSequence();
-
+
/*
* Map dna bases [2, 4, 5], [7, 9, 11] to protein residues 1 and 2
*/
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[] { 2, 2, 4, 5, 7, 7, 9, 9, 11, 11 },
+ new int[] { 1, 2 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
-
+
/*
* Check protein residue 1 maps to [2, 4, 5]
*/
assertEquals(seq1.getDatasetSequence(), m.getSequence());
assertEquals(11, m.getStart());
assertEquals(11, m.getEnd());
-
+
/*
* Check inverse mappings, from codons to protein
*/
}
/**
- * Test mapping a sequence group.
+ * Test mapping a sequence group made of entire sequences.
*
* @throws IOException
*/
- @Test
- public void testMapSequenceGroup() throws IOException
+ @Test(groups = { "Functional" })
+ public void testMapSequenceGroup_sequences() throws IOException
{
/*
* Set up dna and protein Seq1/2/3 with mappings (held on the protein
"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
protein.setCodonFrames(acfList);
/*
- * Select Seq1 and Seq3 in the protein
+ * Select Seq1 and Seq3 in the protein (startRes=endRes=0)
*/
SequenceGroup sg = new SequenceGroup();
sg.setColourText(true);
/*
* 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());
assertEquals(2, mappedGroup.getSequences().size());
assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(1));
+ assertEquals(0, mappedGroup.getStartRes());
+ assertEquals(2, mappedGroup.getEndRes());
/*
* Verify mapping sequence group from dna to protein
sg.clear();
sg.addSequence(cdna.getSequenceAt(1), false);
sg.addSequence(cdna.getSequenceAt(0), false);
+ sg.setStartRes(0);
+ sg.setEndRes(2);
mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
assertTrue(mappedGroup.getColourText());
assertSame(sg.getIdColour(), mappedGroup.getIdColour());
assertEquals(2, mappedGroup.getSequences().size());
assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(0));
assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(1));
+ assertEquals(0, mappedGroup.getStartRes());
+ assertEquals(0, mappedGroup.getEndRes());
}
/**
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();
/*
* viewport). Lower case for introns.
*/
AlignmentI cdna = loadAlignment(">Seq1\nAC-GctGtC-T\n"
- + ">Seq2\nTc-GA-G-T-Tc\n" + ">Seq3\nTtTT-AaCGg-\n",
- "FASTA");
+ + ">Seq2\nTc-GA-G-T-Tc\n" + ">Seq3\nTtTT-AaCGg-\n", "FASTA");
cdna.setDataset(null);
AlignmentI protein = loadAlignment(
- ">Seq1\n-K-P\n>Seq2\nL--Q\n>Seq3\nG--S\n",
- "FASTA");
+ ">Seq1\n-K-P\n>Seq2\nL--Q\n>Seq3\nG--S\n", "FASTA");
protein.setDataset(null);
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[] { 1, 3, 6, 6, 8, 9 }, new int[] {
+ 1, 2 }, 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 = new MapList(new int[] { 1, 1, 3, 4, 5, 7 }, new int[] { 1, 2 },
+ 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 = new MapList(new int[] { 1, 1, 3, 4, 5, 5, 7, 8 }, new int[] { 1,
+ 2 }, 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(groups = { "Functional" })
+ public void testMapColumnSelection_null() throws IOException
+ {
+ setupMappedAlignments();
+ ColumnSelection cs = MappingUtils.mapColumnSelection(null, dnaView,
+ proteinView);
+ assertTrue("mapped selection not empty", cs.getSelected().isEmpty());
+ }
+
/**
* 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 })));
+ }
+
+ /**
+ * Test mapping a sequence group made of entire columns.
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testMapSequenceGroup_columns() throws IOException
+ {
+ /*
+ * Set up dna and protein Seq1/2/3 with mappings (held on the protein
+ * viewport).
+ */
+ AlignmentI cdna = loadAlignment(
+ ">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);
+ 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
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setColourText(true);
+ sg.setIdColour(Color.GREEN);
+ sg.setOutlineColour(Color.LIGHT_GRAY);
+ sg.addSequence(protein.getSequenceAt(0), false);
+ sg.addSequence(protein.getSequenceAt(1), false);
+ 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);
+ assertTrue(mappedGroup.getColourText());
+ assertSame(sg.getIdColour(), mappedGroup.getIdColour());
+ assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
+ assertEquals(3, mappedGroup.getSequences().size());
+ assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
+ assertSame(cdna.getSequenceAt(1), mappedGroup.getSequences().get(1));
+ assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(2));
+ assertEquals(3, mappedGroup.getStartRes());
+ assertEquals(5, mappedGroup.getEndRes());
+
+ /*
+ * Verify mapping sequence group from dna to protein
+ */
+ sg.clear();
+ sg.addSequence(cdna.getSequenceAt(0), false);
+ sg.addSequence(cdna.getSequenceAt(1), false);
+ sg.addSequence(cdna.getSequenceAt(2), false);
+ // select columns 2 and 3 in DNA which span protein columns 0 and 1
+ sg.setStartRes(2);
+ sg.setEndRes(3);
+ mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
+ assertTrue(mappedGroup.getColourText());
+ assertSame(sg.getIdColour(), mappedGroup.getIdColour());
+ assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
+ assertEquals(3, mappedGroup.getSequences().size());
+ assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(0));
+ assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(1));
+ assertSame(protein.getSequenceAt(2), mappedGroup.getSequences().get(2));
+ assertEquals(0, mappedGroup.getStartRes());
+ assertEquals(1, mappedGroup.getEndRes());
+ }
+
+ /**
+ * Test mapping a sequence group made of a sequences/columns region.
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testMapSequenceGroup_region() throws IOException
+ {
+ /*
+ * Set up gapped dna and protein Seq1/2/3 with mappings (held on the protein
+ * viewport).
+ */
+ AlignmentI cdna = loadAlignment(
+ ">Seq1\nA-CG-GC--AT-CA\n>Seq2\n-TG-AC-AG-T-AT\n>Seq3\n-T--ACG-TAAT-G\n",
+ "FASTA");
+ cdna.setDataset(null);
+ AlignmentI protein = loadAlignment(
+ ">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);
+ 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
+ * only includes a gap in Seq2 there is no mappable selection region in the
+ * corresponding DNA.
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setColourText(true);
+ sg.setIdColour(Color.GREEN);
+ sg.setOutlineColour(Color.LIGHT_GRAY);
+ sg.addSequence(protein.getSequenceAt(0), false);
+ 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);
+ assertTrue(mappedGroup.getColourText());
+ assertSame(sg.getIdColour(), mappedGroup.getIdColour());
+ assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
+ assertEquals(1, mappedGroup.getSequences().size());
+ assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
+ // Seq2 in protein has a gap in column 1 - ignored
+ // 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.
+ */
+ sg.setStartRes(2);
+ sg.setEndRes(4);
+ mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView);
+ assertEquals(1, mappedGroup.getStartRes());
+ assertEquals(13, mappedGroup.getEndRes());
+
+ /*
+ * Verify mapping sequence group from dna to protein
+ */
+ sg.clear();
+ sg.addSequence(cdna.getSequenceAt(0), false);
+
+ // select columns 4,5 - includes Seq1:codon2 (A) only
+ sg.setStartRes(4);
+ sg.setEndRes(5);
+ mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
+ assertEquals(2, mappedGroup.getStartRes());
+ assertEquals(2, mappedGroup.getEndRes());
+
+ // add Seq2 to dna selection cols 4-5 include codons 1 and 2 (LQ)
+ sg.addSequence(cdna.getSequenceAt(1), false);
+ mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
+ assertEquals(2, mappedGroup.getStartRes());
+ assertEquals(4, mappedGroup.getEndRes());
+
+ // add Seq3 to dna selection cols 4-5 include codon 1 (Q)
+ sg.addSequence(cdna.getSequenceAt(2), false);
+ mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
+ assertEquals(0, mappedGroup.getStartRes());
+ assertEquals(4, mappedGroup.getEndRes());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFindMappingsForSequence()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "ABC");
+ SequenceI seq2 = new Sequence("Seq2", "ABC");
+ SequenceI seq3 = new Sequence("Seq3", "ABC");
+ SequenceI seq4 = new Sequence("Seq4", "ABC");
+ seq1.createDatasetSequence();
+ seq2.createDatasetSequence();
+ seq3.createDatasetSequence();
+ seq4.createDatasetSequence();
+
+ /*
+ * 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);
+ 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
+ */
+ List<AlignedCodonFrame> result = MappingUtils.findMappingsForSequence(
+ seq1, mappings);
+ assertEquals(3, result.size());
+ assertTrue(result.contains(acf1));
+ assertTrue(result.contains(acf2));
+ assertTrue(result.contains(acf3));
+
+ /*
+ * Seq2 has two mappings
+ */
+ result = MappingUtils.findMappingsForSequence(seq2, mappings);
+ assertEquals(2, result.size());
+ assertTrue(result.contains(acf1));
+ assertTrue(result.contains(acf2));
+
+ /*
+ * Seq3 has one mapping
+ */
+ result = MappingUtils.findMappingsForSequence(seq3, mappings);
+ assertEquals(1, result.size());
+ assertTrue(result.contains(acf3));
+
+ /*
+ * Seq4 has no mappings
+ */
+ result = MappingUtils.findMappingsForSequence(seq4, mappings);
+ assertEquals(0, result.size());
+
+ result = MappingUtils.findMappingsForSequence(null, mappings);
+ assertEquals(0, result.size());
+
+ result = MappingUtils.findMappingsForSequence(seq1, null);
+ assertEquals(0, result.size());
+
+ result = MappingUtils.findMappingsForSequence(null, null);
+ assertEquals(0, result.size());
}
}
git://source.jalview.org / jalview.git / blobdiff