+++ /dev/null
-/*
- * 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 static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertSame;
-import static org.testng.AssertJUnit.assertTrue;
-import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
-
-import jalview.gui.JvOptionPane;
-import jalview.util.MapList;
-
-import java.util.Arrays;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class AlignedCodonFrameTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- /**
- * Test the method that locates the first aligned sequence that has a mapping.
- */
- @Test(groups = { "Functional" })
- public void testFindAlignedSequence()
- {
- AlignmentI cdna = new Alignment(new SequenceI[] {});
- final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
- seq1.createDatasetSequence();
- cdna.addSequence(seq1);
- final Sequence seq2 = new Sequence("Seq2", "-TA-GG-GG");
- seq2.createDatasetSequence();
- cdna.addSequence(seq2);
-
- AlignmentI aa = new Alignment(new SequenceI[] {});
- final Sequence aseq1 = new Sequence("Seq1", "-P-R");
- aseq1.createDatasetSequence();
- aa.addSequence(aseq1);
- final Sequence aseq2 = new Sequence("Seq2", "-LY-");
- aseq2.createDatasetSequence();
- aa.addSequence(aseq2);
-
- /*
- * Mapping from first DNA sequence to second AA sequence.
- */
- AlignedCodonFrame acf = new AlignedCodonFrame();
-
- assertNull(acf.findAlignedSequence(seq1, aa));
-
- MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
- acf.addMap(seq1.getDatasetSequence(), aseq2.getDatasetSequence(), map);
-
- /*
- * DNA seq1 maps to AA seq2
- */
- assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(cdna
- .getSequenceAt(0).getDatasetSequence(), aa));
- // can also find this from the dna aligned sequence
- assertEquals(aa.getSequenceAt(1),
- acf.findAlignedSequence(cdna.getSequenceAt(0), aa));
-
- assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(aa
- .getSequenceAt(1).getDatasetSequence(), cdna));
- }
-
- /**
- * Test the method that locates the mapped codon for a protein position.
- */
- @Test(groups = { "Functional" })
- public void testGetMappedRegion()
- {
- // introns lower case, exons upper case
- final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
- seq1.createDatasetSequence();
- final Sequence seq2 = new Sequence("Seq2", "-TA-gG-Gg-CG-a");
- seq2.createDatasetSequence();
-
- final Sequence aseq1 = new Sequence("Seq1", "-P-R");
- aseq1.createDatasetSequence();
- final Sequence aseq2 = new Sequence("Seq2", "-LY-Q");
- aseq2.createDatasetSequence();
-
- /*
- * First with no mappings
- */
- AlignedCodonFrame acf = new AlignedCodonFrame();
-
- assertNull(acf.getMappedRegion(seq1, aseq1, 1));
-
- /*
- * Set up the mappings for the exons (upper-case bases)
- * Note residue Q is unmapped
- */
- MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
- 1, 2 }, 3, 1);
- acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- map = new MapList(new int[] { 1, 2, 4, 5, 7, 8 }, new int[] { 1, 2 },
- 3, 1);
- acf.addMap(seq2.getDatasetSequence(), aseq2.getDatasetSequence(), map);
-
- assertArrayEquals(new int[] { 2, 4 },
- acf.getMappedRegion(seq1, aseq1, 1));
- assertArrayEquals(new int[] { 6, 6, 8, 9 },
- acf.getMappedRegion(seq1, aseq1, 2));
- assertArrayEquals(new int[] { 1, 2, 4, 4 },
- acf.getMappedRegion(seq2, aseq2, 1));
- assertArrayEquals(new int[] { 5, 5, 7, 8 },
- acf.getMappedRegion(seq2, aseq2, 2));
-
- /*
- * No mapping from seq2 to Q
- */
- assertNull(acf.getMappedRegion(seq2, aseq2, 3));
-
- /*
- * No mapping from sequence 1 to sequence 2
- */
- assertNull(acf.getMappedRegion(seq1, aseq2, 1));
- }
-
- @Test(groups = { "Functional" })
- public void testGetMappedCodons()
- {
- final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
- seq1.createDatasetSequence();
- final Sequence aseq1 = new Sequence("Seq1", "-V-L");
- aseq1.createDatasetSequence();
-
- /*
- * First with no mappings
- */
- AlignedCodonFrame acf = new AlignedCodonFrame();
-
- assertNull(acf.getMappedCodons(seq1.getDatasetSequence(), 0));
-
- /*
- * Set up the mappings for the exons (upper-case bases)
- */
- MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
- 1, 2 }, 3, 1);
- acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
-
- assertEquals(1, acf.getMappedCodons(aseq1.getDatasetSequence(), 1)
- .size());
- assertEquals(
- "[G, T, A]",
- Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
- 1).get(0)));
- assertEquals(
- "[C, T, T]",
- Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
- 2).get(0)));
- }
-
- /**
- * Test for the case where there is more than one variant of the DNA mapping
- * to a protein sequence
- */
- @Test(groups = { "Functional" })
- public void testGetMappedCodons_dnaVariants()
- {
- final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
- seq1.createDatasetSequence();
- final Sequence seq2 = new Sequence("Seq2", "c-G-TT-gT-gT-A");
- seq2.createDatasetSequence();
- final Sequence aseq1 = new Sequence("Seq1", "-V-L");
- aseq1.createDatasetSequence();
-
- AlignedCodonFrame acf = new AlignedCodonFrame();
-
- /*
- * Set up the mappings for the exons (upper-case bases)
- */
- MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
- 1, 2 }, 3, 1);
- acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- acf.addMap(seq2.getDatasetSequence(), aseq1.getDatasetSequence(), map);
-
- assertEquals(2, acf.getMappedCodons(aseq1.getDatasetSequence(), 1)
- .size());
- List<char[]> codonsForV = acf.getMappedCodons(
- aseq1.getDatasetSequence(), 1);
- assertEquals("[G, T, A]", Arrays.toString(codonsForV.get(0)));
- assertEquals("[G, T, T]", Arrays.toString(codonsForV.get(1)));
- List<char[]> codonsForL = acf.getMappedCodons(
- aseq1.getDatasetSequence(), 2);
- assertEquals("[C, T, T]", Arrays.toString(codonsForL.get(0)));
- assertEquals("[T, T, A]", Arrays.toString(codonsForL.get(1)));
- }
-
- /**
- * Test for the case where sequences have start > 1
- */
- @Test(groups = { "Functional" })
- public void testGetMappedCodons_forSubSequences()
- {
- final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T", 27, 35);
- seq1.createDatasetSequence();
-
- final Sequence aseq1 = new Sequence("Seq1", "-V-L", 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.getMappedCodons(aseq1.getDatasetSequence(),
- 12).get(0)));
- assertEquals(
- "[C, T, T]",
- Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
- 13).get(0)));
- }
-
- @Test(groups = { "Functional" })
- public void testCouldReplaceSequence()
- {
- SequenceI seq1 = new Sequence("Seq1/10-21", "aaacccgggttt");
- SequenceI seq1proxy = new SequenceDummy("Seq1");
-
- // map to region within sequence is ok
- assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
- 17));
- // map to region overlapping sequence is ok
- assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 5,
- 10));
- assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 21,
- 26));
- // map to region before sequence is not ok
- assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 4,
- 9));
- // map to region after sequence is not ok
- assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 22,
- 27));
-
- /*
- * test should fail if name doesn't match
- */
- seq1proxy.setName("Seq1a");
- assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
- 17));
- seq1proxy.setName("Seq1");
- seq1.setName("Seq1a");
- assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
- 17));
-
- /*
- * a dummy sequence can't replace a real one
- */
- assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1, seq1proxy, 12,
- 17));
-
- /*
- * a dummy sequence can't replace a dummy sequence
- */
- SequenceI seq1proxy2 = new SequenceDummy("Seq1");
- assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy,
- seq1proxy2, 12, 17));
-
- /*
- * a real sequence can't replace a real one
- */
- SequenceI seq1a = new Sequence("Seq1/10-21", "aaacccgggttt");
- assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1, seq1a, 12, 17));
- }
-
- /**
- * Tests for the method that tests whether any mapping to a dummy sequence can
- * be 'realised' to a given real sequence
- */
- @Test(groups = { "Functional" })
- public void testIsRealisableWith()
- {
- SequenceI seq1 = new Sequence("Seq1", "tttaaaCCCGGGtttaaa");
- SequenceI seq2 = new Sequence("Seq2", "PG");
- SequenceI seq1proxy = new SequenceDummy("Seq1");
- seq1.createDatasetSequence();
- seq2.createDatasetSequence();
- MapList mapList = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
- 3, 1);
- AlignedCodonFrame acf = new AlignedCodonFrame();
- acf.addMap(seq1proxy, seq2, mapList);
-
- /*
- * Seq2 is mapped to SequenceDummy seq1proxy bases 4-9
- * This is 'realisable' from real sequence Seq1
- */
- assertTrue(acf.isRealisableWith(seq1));
-
- /*
- * test should fail if name doesn't match
- */
- seq1proxy.setName("Seq1a");
- assertFalse(acf.isRealisableWith(seq1));
- seq1proxy.setName("Seq1");
-
- SequenceI seq1ds = seq1.getDatasetSequence();
- seq1ds.setName("Seq1a");
- assertFalse(acf.isRealisableWith(seq1));
- seq1ds.setName("Seq1");
-
- /*
- * test should fail if no sequence overlap with mapping of bases 7-12
- * use artificial start/end values to test this
- */
- seq1ds.setStart(1);
- seq1ds.setEnd(6);
- // seq1 precedes mapped region:
- assertFalse(acf.isRealisableWith(seq1));
- seq1ds.setEnd(7);
- // seq1 includes first mapped base:
- assertTrue(acf.isRealisableWith(seq1));
- seq1ds.setStart(13);
- seq1ds.setEnd(18);
- // seq1 follows mapped region:
- assertFalse(acf.isRealisableWith(seq1));
- seq1ds.setStart(12);
- // seq1 includes last mapped base:
- assertTrue(acf.isRealisableWith(seq1));
- }
-
- /**
- * Tests for the method that converts mappings to a dummy sequence to mappings
- * to a compatible real sequence
- */
- @Test(groups = { "Functional" })
- public void testRealiseWith()
- {
- SequenceI seq1 = new Sequence("Seq1", "tttCAACCCGGGtttaaa");
- SequenceI seq2 = new Sequence("Seq2", "QPG");
- SequenceI seq2a = new Sequence("Seq2a", "QPG");
- SequenceI seq1proxy = new SequenceDummy("Seq1");
- seq1.createDatasetSequence();
- seq2.createDatasetSequence();
- seq2a.createDatasetSequence();
-
- /*
- * Make mappings from Seq2 and Seq2a peptides to dummy sequence Seq1
- */
- AlignedCodonFrame acf = new AlignedCodonFrame();
-
- // map PG to codons 7-12 (CCCGGG)
- MapList mapping1 = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
- 3, 1);
- acf.addMap(seq1proxy, seq2, mapping1);
- acf.addMap(seq1proxy, seq2a, mapping1);
-
- // map QP to codons 4-9 (CAACCC)
- MapList mapping2 = new MapList(new int[] { 4, 9 }, new int[] { 1, 2 },
- 3, 1);
- acf.addMap(seq1proxy, seq2, mapping2);
- acf.addMap(seq1proxy, seq2a, mapping2);
-
- /*
- * acf now has two mappings one from Seq1 to Seq2, one from Seq1 to Seq2a
- */
- assertEquals(2, acf.getdnaSeqs().length);
- assertSame(seq1proxy, acf.getdnaSeqs()[0]);
- assertSame(seq1proxy, acf.getdnaSeqs()[1]);
- assertEquals(2, acf.getProtMappings().length);
-
- // 'realise' these mappings with the compatible sequence seq1
- // two mappings should be updated:
- assertEquals(2, acf.realiseWith(seq1));
- assertSame(seq1.getDatasetSequence(), acf.getdnaSeqs()[0]);
- assertSame(seq1.getDatasetSequence(), acf.getdnaSeqs()[1]);
- }
-
- /**
- * Test the method that locates the mapped codon for a protein position.
- */
- @Test(groups = { "Functional" })
- public void testGetMappedRegion_eitherWay()
- {
- final Sequence seq1 = new Sequence("Seq1", "AAACCCGGGTTT");
- seq1.createDatasetSequence();
- final Sequence seq2 = new Sequence("Seq2", "KPGF");
- seq2.createDatasetSequence();
- final Sequence seq3 = new Sequence("Seq3", "QYKPGFSW");
- seq3.createDatasetSequence();
-
- /*
- * map Seq1 to all of Seq2 and part of Seq3
- */
- AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
- acf.addMap(seq1.getDatasetSequence(), seq2.getDatasetSequence(), map);
- map = new MapList(new int[] { 1, 12 }, new int[] { 3, 6 }, 3, 1);
- acf.addMap(seq1.getDatasetSequence(), seq3.getDatasetSequence(), map);
-
- /*
- * map part of Seq3 to Seq2
- */
- map = new MapList(new int[] { 3, 6 }, new int[] { 1, 4 }, 1, 1);
- acf.addMap(seq3.getDatasetSequence(), seq2.getDatasetSequence(), map);
-
- /*
- * original case - locate mapped codon for protein position
- */
- assertArrayEquals(new int[] { 4, 6 },
- acf.getMappedRegion(seq1, seq2, 2));
- assertArrayEquals(new int[] { 7, 9 },
- acf.getMappedRegion(seq1, seq3, 5));
- assertNull(acf.getMappedRegion(seq1, seq3, 1));
-
- /*
- * locate mapped protein for protein position
- */
- assertArrayEquals(new int[] { 4, 4 },
- acf.getMappedRegion(seq3, seq2, 2));
-
- /*
- * reverse location protein-to-protein
- */
- assertArrayEquals(new int[] { 2, 2 },
- acf.getMappedRegion(seq2, seq3, 4));
-
- /*
- * reverse location protein-from-nucleotide
- * any of codon [4, 5, 6] positions map to seq2/2
- */
- assertArrayEquals(new int[] { 2, 2 },
- acf.getMappedRegion(seq2, seq1, 4));
- assertArrayEquals(new int[] { 2, 2 },
- acf.getMappedRegion(seq2, seq1, 5));
- assertArrayEquals(new int[] { 2, 2 },
- acf.getMappedRegion(seq2, seq1, 6));
- }
-
- /**
- * Tests for addMap. See also tests for MapList.addMapList
- */
- @Test(groups = { "Functional" })
- public void testAddMap()
- {
- final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
- seq1.createDatasetSequence();
- final Sequence aseq1 = new Sequence("Seq1", "-V-L");
- aseq1.createDatasetSequence();
-
- AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
- 1, 2 }, 3, 1);
- acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- assertEquals(1, acf.getMappingsFromSequence(seq1).size());
- Mapping before = acf.getMappingsFromSequence(seq1).get(0);
-
- /*
- * add the same map again, verify it doesn't get duplicated
- */
- acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- assertEquals(1, acf.getMappingsFromSequence(seq1).size());
- assertSame(before, acf.getMappingsFromSequence(seq1).get(0));
- }
-}
git://source.jalview.org / jalview.git / blobdiff