/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.analysis;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertTrue;
-import jalview.analysis.AlignmentUtils.MappingResult;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+import org.junit.Test;
+
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.FormatAdapter;
import jalview.util.MapList;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
-
-import org.junit.Test;
-
public class AlignmentUtilsTests
{
// @formatter:off
a.setDataset(null);
return a;
}
+
/**
- * Test mapping of protein to cDNA.
+ * Test mapping of protein to cDNA, for the case where we have no sequence
+ * cross-references, so mappings are made first-served 1-1 where sequences
+ * translate.
*
* @throws IOException
*/
@Test
- public void testMapProteinToCdna() throws IOException
+ public void testMapProteinToCdna_noXrefs() throws IOException
{
- // protein: Human + Mouse, 3 residues
- AlignmentI protein = loadAlignment(
- ">Human\nKQY\n>Mouse\nAFP\n>Worm\nRST\n",
- "FASTA");
- // cDNA: Mouse, Human, Mouse, 9 bases
- // @formatter:off
- String dnaData =
- ">Mouse\nGAAATCCAG\n" +
- ">Human\nTTCGATTAC\n" +
- ">Mouse\nGTCGTTTGC\n" +
- ">Mouse\nGTCGTTTGCgac\n" + // not mapped - wrong length
- ">Fly\nGTCGTTTGC\n"; // not mapped - no name match
- // @formatter:on
- AlignmentI cdna1 = loadAlignment(
- dnaData,
- "FASTA");
- MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna1);
- assertEquals(mapped, MappingResult.Mapped);
-
- /*
- * Check two mappings (one for Mouse, one for Human)
- */
- assertEquals(2, protein.getCodonFrames().length);
- assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).length);
- assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).length);
-
- /*
- * Inspect mapping for Human protein
- */
- AlignedCodonFrame humanMapping = protein.getCodonFrame(protein
- .getSequenceAt(0))[0];
- assertEquals(1, humanMapping.getdnaSeqs().length);
- assertEquals(cdna1.getSequenceAt(1).getDatasetSequence(),
- humanMapping.getdnaSeqs()[0]);
- Mapping[] protMappings = humanMapping.getProtMappings();
+ List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
+ AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
+ protein.setDataset(null);
+
+ List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
+ dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
+ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
+ cdna.setDataset(null);
+
+ assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+
+ // 3 mappings made, each from 1 to 1 sequence
+ assertEquals(3, protein.getCodonFrames().size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
+
+ // V12345 mapped to A22222
+ AlignedCodonFrame acf = protein.getCodonFrame(
+ protein.getSequenceAt(0)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ Mapping[] protMappings = acf.getProtMappings();
assertEquals(1, protMappings.length);
MapList mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
assertTrue(Arrays.equals(new int[]
- { 1, 9 }, mapList.getFromRanges()));
- assertTrue(Arrays.equals(new int[]
- { 1, 3 }, mapList.getToRanges()));
-
- /*
- * Inspect mappings for Mouse protein
- */
- AlignedCodonFrame mouseMapping1 = protein.getCodonFrame(protein
- .getSequenceAt(1))[0];
- assertEquals(2, mouseMapping1.getdnaSeqs().length);
- assertEquals(cdna1.getSequenceAt(0).getDatasetSequence(),
- mouseMapping1.getdnaSeqs()[0]);
- assertEquals(cdna1.getSequenceAt(2).getDatasetSequence(),
- mouseMapping1.getdnaSeqs()[1]);
- protMappings = mouseMapping1.getProtMappings();
- assertEquals(2, protMappings.length);
- for (int i = 0; i < 2; i++)
- {
- mapList = protMappings[i].getMap();
- assertEquals(3, mapList.getFromRatio());
- assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[]
- { 1, 9 }, mapList.getFromRanges()));
- assertTrue(Arrays.equals(new int[]
- { 1, 3 }, mapList.getToRanges()));
- }
- }
-
- /**
- * Test mapping of protein to cDNA which may include start and/or stop codons.
- *
- * @throws IOException
- */
- @Test
- public void testMapProteinToCdna_stopStartCodons() throws IOException
- {
- // protein: Human + Mouse, 3 residues
- AlignmentI protein = loadAlignment(
- ">Human\nKQY\n>Mouse\nAFP\n>Worm\nRST\n", "FASTA");
- // @formatter:off
- String dnaData =
- ">Mouse\natgGAAATCCAG\n" + // Mouse with start codon
- ">Human\nTTCGATtactaa\n" + // Human with stop codon TAA
- ">Mouse\nGTCGTTTGctaG\n" + // Mouse with stop codon TAG
- ">Human\nGTCGTTTgctGa\n" + // Human with stop codon TGA
- ">Mouse\nATGGTCGTTTGCtag\n"; // Mouse with start and stop codons
- // @formatter:on
- AlignmentI cdna1 = loadAlignment(
- dnaData,
- "FASTA");
- MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna1);
- assertEquals(mapped, MappingResult.Mapped);
-
- /*
- * Check two mappings (one for Mouse, one for Human)
- */
- assertEquals(2, protein.getCodonFrames().length);
- assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).length);
- assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).length);
-
- /*
- * Inspect mapping for Human protein - should map to 2nd and 4th cDNA seqs
- */
- AlignedCodonFrame humanMapping = protein.getCodonFrame(protein
- .getSequenceAt(0))[0];
- assertEquals(2, humanMapping.getdnaSeqs().length);
- assertEquals(cdna1.getSequenceAt(1).getDatasetSequence(),
- humanMapping.getdnaSeqs()[0]);
- assertEquals(cdna1.getSequenceAt(3).getDatasetSequence(),
- humanMapping.getdnaSeqs()[1]);
- Mapping[] protMappings = humanMapping.getProtMappings();
- // two mappings, both to cDNA with stop codon
- assertEquals(2, protMappings.length);
- MapList mapList = protMappings[0].getMap();
- assertEquals(3, mapList.getFromRatio());
- assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[]
- { 1, 9 }, mapList.getFromRanges()));
- assertTrue(Arrays.equals(new int[]
- { 1, 3 }, mapList.getToRanges()));
- mapList = protMappings[1].getMap();
- assertEquals(3, mapList.getFromRatio());
- assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[]
- { 1, 9 }, mapList.getFromRanges()));
- assertTrue(Arrays.equals(new int[]
- { 1, 3 }, mapList.getToRanges()));
-
- /*
- * Inspect mapping for Mouse protein - should map to 1st/3rd/5th cDNA seqs
- */
- AlignedCodonFrame mouseMapping = protein.getCodonFrame(protein
- .getSequenceAt(1))[0];
- assertEquals(3, mouseMapping.getdnaSeqs().length);
- assertEquals(cdna1.getSequenceAt(0).getDatasetSequence(),
- mouseMapping.getdnaSeqs()[0]);
- assertEquals(cdna1.getSequenceAt(2).getDatasetSequence(),
- mouseMapping.getdnaSeqs()[1]);
- assertEquals(cdna1.getSequenceAt(4).getDatasetSequence(),
- mouseMapping.getdnaSeqs()[2]);
-
- // three mappings
- protMappings = mouseMapping.getProtMappings();
- assertEquals(3, protMappings.length);
-
- // first mapping to cDNA with start codon
- mapList = protMappings[0].getMap();
- assertEquals(3, mapList.getFromRatio());
- assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[]
- { 4, 12 }, mapList.getFromRanges()));
+ { 1, 9 }, mapList.getFromRanges().get(0)));
+ assertEquals(1, mapList.getFromRanges().size());
assertTrue(Arrays.equals(new int[]
- { 1, 3 }, mapList.getToRanges()));
-
- // second mapping to cDNA with stop codon
- mapList = protMappings[1].getMap();
- assertEquals(3, mapList.getFromRatio());
- assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[]
- { 1, 9 }, mapList.getFromRanges()));
- assertTrue(Arrays.equals(new int[]
- { 1, 3 }, mapList.getToRanges()));
-
- // third mapping to cDNA with start and stop codon
- mapList = protMappings[2].getMap();
- assertEquals(3, mapList.getFromRatio());
- assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[]
- { 4, 12 }, mapList.getFromRanges()));
- assertTrue(Arrays.equals(new int[]
- { 1, 3 }, mapList.getToRanges()));
+ { 1, 3 }, mapList.getToRanges().get(0)));
+ assertEquals(1, mapList.getToRanges().size());
+
+ // V12346 mapped to A33333
+ acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+
+ // V12347 mapped to A11111
+ acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+
+ // no mapping involving the 'extra' A44444
+ assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
}
/**
@Test
public void testAlignSequenceAs_withMapping_noIntrons()
{
- /*
- * Simple case: no gaps in dna
- */
- SequenceI dna = new Sequence("Seq1", "GGGAAA");
- dna.createDatasetSequence();
- SequenceI protein = new Sequence("Seq1", "-A-L-");
- protein.createDatasetSequence();
- AlignedCodonFrame acf = new AlignedCodonFrame();
MapList map = new MapList(new int[]
{ 1, 6 }, new int[]
{ 1, 2 }, 3, 1);
- acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
/*
* No existing gaps in dna:
*/
- AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
- false);
- assertEquals("---GGG---AAA", dna.getSequenceAsString());
+ checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
+ "---GGG---AAA");
/*
* Now introduce gaps in dna but ignore them when realigning.
*/
- dna.setSequence("-G-G-G-A-A-A-");
- AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
- false);
- assertEquals("---GGG---AAA", dna.getSequenceAsString());
+ checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
+ "---GGG---AAA");
/*
* Now include gaps in dna when realigning. First retaining 'mapped' gaps
* only, i.e. those within the exon region.
*/
- dna.setSequence("-G-G--G-A--A-A-");
- AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', true,
- false);
- assertEquals("---G-G--G---A--A-A", dna.getSequenceAsString());
+ checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
+ "---G-G--G---A--A-A");
/*
* Include all gaps in dna when realigning (within and without the exon
* region). The leading gap, and the gaps between codons, are subsumed by
* the protein alignment gap.
*/
- dna.setSequence("-G-GG--AA-A-");
- AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', true,
- true);
- assertEquals("---G-GG---AA-A-", dna.getSequenceAsString());
+ checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", true, true, map,
+ "---G-GG---AA-A-");
/*
* Include only unmapped gaps in dna when realigning (outside the exon
* region). The leading gap, and the gaps between codons, are subsumed by
* the protein alignment gap.
*/
- dna.setSequence("-G-GG--AA-A-");
- AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
- true);
- assertEquals("---GGG---AAA-", dna.getSequenceAsString());
+ checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
+ "---GGG---AAA-");
}
/**
public void testAlignSequenceAs_withMapping_withIntrons()
{
/*
- * Simple case: no gaps in dna
- */
- SequenceI dna = new Sequence("Seq1", "GGGAAACCCTTTGGG");
- dna.createDatasetSequence();
- SequenceI protein = new Sequence("Seq1", "-A-L-");
- protein.createDatasetSequence();
- AlignedCodonFrame acf = new AlignedCodonFrame();
-
- /*
* Exons at codon 2 (AAA) and 4 (TTT)
*/
MapList map = new MapList(new int[]
{ 4, 6, 10, 12 }, new int[]
{ 1, 2 }, 3, 1);
- acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
/*
- * Align dna as "-A-L-". The protein 'gaps' follow the introns, i.e are
- * placed immediately before the mapped codons.
+ * Simple case: no gaps in dna
*/
- AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
- false);
- assertEquals("GGG---AAACCC---TTTGGG", dna.getSequenceAsString());
+ checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
+ "GGG---AAACCCTTTGGG");
/*
* Add gaps to dna - but ignore when realigning.
*/
- dna.setSequence("-G-G-G--A--A---AC-CC-T-TT-GG-G-");
- AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
- false);
- assertEquals("GGG---AAACCC---TTTGGG", dna.getSequenceAsString());
+ checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
+ false, false, map, "GGG---AAACCCTTTGGG");
/*
* Add gaps to dna - include within exons only when realigning.
*/
- dna.setSequence("-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
- AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', true,
- false);
- assertEquals("GGG---A--A---ACCC---T-TTGGG", dna.getSequenceAsString());
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
+ true, false, map, "GGG---A--A---ACCCT-TTGGG");
/*
* Include gaps outside exons only when realigning.
*/
- dna.setSequence("-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
- AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
- true);
- assertEquals("-G-G-G---AAA-C-CC---TTT-GG-G-", dna.getSequenceAsString());
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
+ false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
+
+ /*
+ * Include gaps following first intron if we are 'preserving mapped gaps'
+ */
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
+ true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
/*
* Include all gaps in dna when realigning.
*/
- dna.setSequence("-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
- AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', true,
- true);
- assertEquals("-G-G-G---A--A---A-C-CC---T-TT-GG-G-",
- dna.getSequenceAsString());
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
+ true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
}
/**
@Test
public void testAlignSequenceAs_withMapping_withUnmappedProtein()
{
- SequenceI dna = new Sequence("Seq1", "GGGAAACCCTTTGGG");
+
+ /*
+ * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
+ */
+ final MapList map = new MapList(new int[]
+ { 4, 6, 10, 12 }, new int[]
+ { 1, 1, 3, 3 }, 3, 1);
+
+
+ /*
+ * Expect alignment does nothing (aborts realignment). Change this test
+ * first if different behaviour wanted.
+ */
+ checkAlignSequenceAs("GGGAAACCCTTTGGG", "-A-L-P-", false,
+ false, map, "GGGAAACCCTTTGGG");
+ }
+
+ /**
+ * Helper method that performs and verifies the method under test.
+ *
+ * @param dnaSeq
+ * @param proteinSeq
+ * @param preserveMappedGaps
+ * @param preserveUnmappedGaps
+ * @param map
+ * @param expected
+ */
+ protected void checkAlignSequenceAs(final String dnaSeq,
+ final String proteinSeq, final boolean preserveMappedGaps,
+ final boolean preserveUnmappedGaps, MapList map,
+ final String expected)
+ {
+ SequenceI dna = new Sequence("Seq1", dnaSeq);
dna.createDatasetSequence();
- SequenceI protein = new Sequence("Seq1", "-A-L-P-");
+ SequenceI protein = new Sequence("Seq1", proteinSeq);
protein.createDatasetSequence();
AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
+
+ AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-',
+ preserveMappedGaps, preserveUnmappedGaps);
+ assertEquals(expected, dna.getSequenceAsString());
+ }
+
+ /**
+ * Test for the alignSequenceAs method where we preserve gaps in introns only.
+ */
+ @Test
+ public void testAlignSequenceAs_keepIntronGapsOnly()
+ {
/*
- * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
+ * Intron GGGAAA followed by exon CCCTTT
*/
MapList map = new MapList(new int[]
- { 4, 6, 10, 12 }, new int[]
- { 1, 1, 3, 3 }, 3, 1);
+ { 7, 12 }, new int[]
+ { 1, 2 }, 3, 1);
+
+ checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL",
+ false, true, map, "GG-G-AA-ACCCTTT");
+ }
+
+ /**
+ * Test for the method that generates an aligned translated sequence from one
+ * mapping.
+ */
+ @Test
+ public void testGetAlignedTranslation_dnaLikeProtein()
+ {
+ // dna alignment will be replaced
+ SequenceI dna = new Sequence("Seq1", "T-G-CC-A--T-TAC-CAG-");
+ dna.createDatasetSequence();
+ // protein alignment will be 'applied' to dna
+ SequenceI protein = new Sequence("Seq1", "-CH-Y--Q-");
+ protein.createDatasetSequence();
+ MapList map = new MapList(new int[]
+ { 1, 12 }, new int[]
+ { 1, 4 }, 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
+ final SequenceI aligned = AlignmentUtils
+ .getAlignedTranslation(protein, '-', acf);
+ assertEquals("---TGCCAT---TAC------CAG---", aligned.getSequenceAsString());
+ assertSame(aligned.getDatasetSequence(), dna.getDatasetSequence());
+ }
+
+ /**
+ * Test the method that realigns protein to match mapped codon alignment.
+ */
+ @Test
+ public void testAlignProteinAsDna()
+ {
+ // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
+ SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
+ // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
+ SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
+ // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
+ SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
+ AlignmentI dna = new Alignment(new SequenceI[]
+ { dna1, dna2, dna3 });
+ dna.setDataset(null);
+
+ // protein alignment will be realigned like dna
+ SequenceI prot1 = new Sequence("Seq1", "CHYQ");
+ SequenceI prot2 = new Sequence("Seq2", "CHYQ");
+ SequenceI prot3 = new Sequence("Seq3", "CHYQ");
+ AlignmentI protein = new Alignment(new SequenceI[]
+ { prot1, prot2, prot3 });
+ protein.setDataset(null);
+
+ MapList map = new MapList(new int[]
+ { 1, 12 }, new int[]
+ { 1, 4 }, 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
+ acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
+ acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
+ protein.setCodonFrames(Collections.singleton(acf));
+
/*
- * Align dna as "-A-L-P-". Currently, does nothing (aborts realignment).
- * Change this test first if different behaviour wanted.
+ * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9]
+ * [8,9,10] [10,11,12] [11,12,13]
*/
- AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
+ AlignmentUtils.alignProteinAsDna(protein, dna);
+ assertEquals("C-H--Y-Q-", prot1.getSequenceAsString());
+ assertEquals("-C--H-Y-Q", prot2.getSequenceAsString());
+ assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
+ }
+
+ /**
+ * Test the method that tests whether a CDNA sequence translates to a protein
+ * sequence
+ */
+ @Test
+ public void testTranslatesAs()
+ {
+ assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
+ "FPKG".toCharArray()));
+ // with start codon
+ assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
+ 3, "FPKG".toCharArray()));
+ // with stop codon1
+ assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
+ 0, "FPKG".toCharArray()));
+ // with stop codon2
+ assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
+ 0, "FPKG".toCharArray()));
+ // with stop codon3
+ assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
+ 0, "FPKG".toCharArray()));
+ // with start and stop codon1
+ assertTrue(AlignmentUtils.translatesAs(
+ "atgtttcccaaaggtaa".toCharArray(), 3, "FPKG".toCharArray()));
+ // with start and stop codon2
+ assertTrue(AlignmentUtils.translatesAs(
+ "atgtttcccaaaggtag".toCharArray(), 3, "FPKG".toCharArray()));
+ // with start and stop codon3
+ assertTrue(AlignmentUtils.translatesAs(
+ "atgtttcccaaaggtga".toCharArray(), 3, "FPKG".toCharArray()));
+
+ // wrong protein
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
+ 0,
+ "FPMG".toCharArray()));
+ }
+
+ /**
+ * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
+ * stop codons in addition to the protein coding sequence.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapProteinToCdna_withStartAndStopCodons()
+ throws IOException
+ {
+ List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
+ AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
+ protein.setDataset(null);
+
+ List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ // start + SAR:
+ dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
+ // = EIQ + stop
+ dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
+ // = start +EIQ + stop
+ dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
+ dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
+ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
+ cdna.setDataset(null);
+
+ assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+
+ // 3 mappings made, each from 1 to 1 sequence
+ assertEquals(3, protein.getCodonFrames().size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
+
+ // V12345 mapped from A22222
+ AlignedCodonFrame acf = protein.getCodonFrame(
+ protein.getSequenceAt(0)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ Mapping[] protMappings = acf.getProtMappings();
+ assertEquals(1, protMappings.length);
+ MapList mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges().get(0)));
+ assertEquals(1, mapList.getFromRanges().size());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
+ assertEquals(1, mapList.getToRanges().size());
+
+ // V12346 mapped from A33333 starting position 4
+ acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ protMappings = acf.getProtMappings();
+ assertEquals(1, protMappings.length);
+ mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 4, 12 }, mapList.getFromRanges().get(0)));
+ assertEquals(1, mapList.getFromRanges().size());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
+ assertEquals(1, mapList.getToRanges().size());
+
+ // V12347 mapped to A11111 starting position 4
+ acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ protMappings = acf.getProtMappings();
+ assertEquals(1, protMappings.length);
+ mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 4, 12 }, mapList.getFromRanges().get(0)));
+ assertEquals(1, mapList.getFromRanges().size());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
+ assertEquals(1, mapList.getToRanges().size());
+
+ // no mapping involving the 'extra' A44444
+ assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
+ }
+
+ /**
+ * Test mapping of protein to cDNA, for the case where we have some sequence
+ * cross-references. Verify that 1-to-many mappings are made where
+ * cross-references exist and sequences are mappable.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapProteinToCdna_withXrefs() throws IOException
+ {
+ List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
+ AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
+ protein.setDataset(null);
+
+ List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
+ dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
+ dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ
+ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5]));
+ cdna.setDataset(null);
+
+ // Xref A22222 to V12345 (should get mapped)
+ dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
+ // Xref V12345 to A44444 (should get mapped)
+ protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
+ // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
+ dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
+ // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
+ // it should get paired up with the unmapped A33333
+ // A11111 should be mapped to V12347
+ // A55555 is spare and has no xref so is not mapped
+
+ assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+
+ // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
+ assertEquals(3, protein.getCodonFrames().size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
+
+ // one mapping for each of the first 4 cDNA sequences
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size());
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size());
+
+ // V12345 mapped to A22222 and A44444
+ AlignedCodonFrame acf = protein.getCodonFrame(
+ protein.getSequenceAt(0)).get(0);
+ assertEquals(2, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ assertEquals(cdna.getSequenceAt(3).getDatasetSequence(),
+ acf.getdnaSeqs()[1]);
+
+ // V12346 mapped to A33333
+ acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+
+ // V12347 mapped to A11111
+ acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+
+ // no mapping involving the 'extra' A55555
+ assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty());
+ }
+
+ /**
+ * Test mapping of protein to cDNA, for the case where we have some sequence
+ * cross-references. Verify that once we have made an xref mapping we don't
+ * also map un-xrefd sequeces.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapProteinToCdna_prioritiseXrefs() throws IOException
+ {
+ List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
+ AlignmentI protein = new Alignment(
+ protseqs.toArray(new SequenceI[protseqs.size()]));
+ protein.setDataset(null);
+
+ List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
+ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs
+ .size()]));
+ cdna.setDataset(null);
+
+ // Xref A22222 to V12345 (should get mapped)
+ // A11111 should then be mapped to the unmapped V12346
+ dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
+
+ assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+
+ // 2 protein mappings made
+ assertEquals(2, protein.getCodonFrames().size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
+
+ // one mapping for each of the cDNA sequences
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
+
+ // V12345 mapped to A22222
+ AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
+ .get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+
+ // V12346 mapped to A11111
+ acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ }
+
+ /**
+ * Test the method that shows or hides sequence annotations by type(s) and
+ * selection group.
+ */
+ @Test
+ public void testShowOrHideSequenceAnnotations()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "AAA");
+ SequenceI seq2 = new Sequence("Seq2", "BBB");
+ SequenceI seq3 = new Sequence("Seq3", "CCC");
+ Annotation[] anns = new Annotation[]
+ { new Annotation(2f) };
+ AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
+ anns);
+ ann1.setSequenceRef(seq1);
+ AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
+ anns);
+ ann2.setSequenceRef(seq2);
+ AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
+ anns);
+ AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
+ ann4.setSequenceRef(seq1);
+ AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns);
+ ann5.setSequenceRef(seq2);
+ AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns);
+ AlignmentI al = new Alignment(new SequenceI[] {seq1, seq2, seq3});
+ al.addAnnotation(ann1); // Structure for Seq1
+ al.addAnnotation(ann2); // Structure for Seq2
+ al.addAnnotation(ann3); // Structure for no sequence
+ al.addAnnotation(ann4); // Temp for seq1
+ al.addAnnotation(ann5); // Temp for seq2
+ al.addAnnotation(ann6); // Temp for no sequence
+ List<String> types = new ArrayList<String>();
+ List<SequenceI> scope = new ArrayList<SequenceI>();
+
+ /*
+ * Set all sequence related Structure to hidden (ann1, ann2)
+ */
+ types.add("Structure");
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
false);
- assertEquals("GGGAAACCCTTTGGG", dna.getSequenceAsString());
+ assertFalse(ann1.visible);
+ assertFalse(ann2.visible);
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertTrue(ann4.visible); // not Structure, not affected
+ assertTrue(ann5.visible); // "
+ assertTrue(ann6.visible); // not sequence-related, not affected
+
+ /*
+ * Set Temp in {seq1, seq3} to hidden
+ */
+ types.clear();
+ types.add("Temp");
+ scope.add(seq1);
+ scope.add(seq3);
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
+ false);
+ assertFalse(ann1.visible); // unchanged
+ assertFalse(ann2.visible); // unchanged
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertFalse(ann4.visible); // Temp for seq1 hidden
+ assertTrue(ann5.visible); // not in scope, not affected
+ assertTrue(ann6.visible); // not sequence-related, not affected
+
+ /*
+ * Set Temp in all sequences to hidden
+ */
+ types.clear();
+ types.add("Temp");
+ scope.add(seq1);
+ scope.add(seq3);
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
+ false);
+ assertFalse(ann1.visible); // unchanged
+ assertFalse(ann2.visible); // unchanged
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertFalse(ann4.visible); // Temp for seq1 hidden
+ assertFalse(ann5.visible); // Temp for seq2 hidden
+ assertTrue(ann6.visible); // not sequence-related, not affected
+
+ /*
+ * Set all types in {seq1, seq3} to visible
+ */
+ types.clear();
+ scope.clear();
+ scope.add(seq1);
+ scope.add(seq3);
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
+ true);
+ assertTrue(ann1.visible); // Structure for seq1 set visible
+ assertFalse(ann2.visible); // not in scope, unchanged
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertTrue(ann4.visible); // Temp for seq1 set visible
+ assertFalse(ann5.visible); // not in scope, unchanged
+ assertTrue(ann6.visible); // not sequence-related, not affected
+
+ /*
+ * Set all types in all scope to hidden
+ */
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
+ false);
+ assertFalse(ann1.visible);
+ assertFalse(ann2.visible);
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertFalse(ann4.visible);
+ assertFalse(ann5.visible);
+ assertTrue(ann6.visible); // not sequence-related, not affected
+ }
+
+ /**
+ * Tests for the method that checks if one sequence cross-references another
+ */
+ @Test
+ public void testHasCrossRef()
+ {
+ assertFalse(AlignmentUtils.hasCrossRef(null, null));
+ SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
+ assertFalse(AlignmentUtils.hasCrossRef(seq1, null));
+ assertFalse(AlignmentUtils.hasCrossRef(null, seq1));
+ SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
+ assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
+
+ // different ref
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193"));
+ assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
+
+ // case-insensitive; version number is ignored
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192"));
+ assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
+
+ // right case!
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
+ assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
+ // test is one-way only
+ assertFalse(AlignmentUtils.hasCrossRef(seq2, seq1));
+ }
+
+ /**
+ * Tests for the method that checks if either sequence cross-references the
+ * other
+ */
+ @Test
+ public void testHaveCrossRef()
+ {
+ assertFalse(AlignmentUtils.hasCrossRef(null, null));
+ SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
+ assertFalse(AlignmentUtils.haveCrossRef(seq1, null));
+ assertFalse(AlignmentUtils.haveCrossRef(null, seq1));
+ SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
+ assertFalse(AlignmentUtils.haveCrossRef(seq1, seq2));
+
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
+ assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
+ // next is true for haveCrossRef, false for hasCrossRef
+ assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
+
+ // now the other way round
+ seq1.setDBRef(null);
+ seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
+ assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
+ assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
+
+ // now both ways
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
+ assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
+ assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
}
}
git://source.jalview.org / jalview.git / blobdiff