X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=da73c50876a0da2b217dffb2aa88a955954783fe;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=f5f271d4bb14fa4062f75dd896244ac5553419b2;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index f5f271d..da73c50 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. @@ -57,21 +57,21 @@ public class AlignmentTest "//"; private static final String AA_SEQS_1 = - ">Seq1Name\n" + + ">Seq1Name/5-8\n" + "K-QY--L\n" + - ">Seq2Name\n" + + ">Seq2Name/12-15\n" + "-R-FP-W-\n"; private static final String CDNA_SEQS_1 = - ">Seq1Name\n" + + ">Seq1Name/100-111\n" + "AC-GG--CUC-CAA-CT\n" + - ">Seq2Name\n" + + ">Seq2Name/200-211\n" + "-CG-TTA--ACG---AAGT\n"; private static final String CDNA_SEQS_2 = - ">Seq1Name\n" + + ">Seq1Name/50-61\n" + "GCTCGUCGTACT\n" + - ">Seq2Name\n" + + ">Seq2Name/60-71\n" + "GGGTCAGGCAGT\n"; // @formatter:on @@ -176,11 +176,7 @@ public class AlignmentTest * Make mappings between sequences. The 'aligned cDNA' is playing the role * of what would normally be protein here. */ - AlignedCodonFrame acf = new AlignedCodonFrame(); - MapList ml = new MapList(new int[] { 1, 12 }, new int[] { 1, 12 }, 1, 1); - acf.addMap(al2.getSequenceAt(0), al1.getSequenceAt(0), ml); - acf.addMap(al2.getSequenceAt(1), al1.getSequenceAt(1), ml); - al1.addCodonFrame(acf); + makeMappings(al2, al1); ((Alignment) al2).alignAs(al1, false, true); assertEquals("GC-TC--GUC-GTA-CT", al2.getSequenceAt(0) @@ -200,11 +196,7 @@ public class AlignmentTest // see also AlignmentUtilsTests AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA"); AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA"); - AlignedCodonFrame acf = new AlignedCodonFrame(); - MapList ml = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1); - acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml); - acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml); - al2.addCodonFrame(acf); + makeMappings(al1, al2); ((Alignment) al2).alignAs(al1, false, true); assertEquals("K-Q-Y-L-", al2.getSequenceAt(0).getSequenceAsString()); @@ -212,6 +204,27 @@ public class AlignmentTest } /** + * Aligning protein from cDNA for a single sequence. This is the 'simple' case + * (as there is no need to compute codon 'alignments') but worth testing + * before tackling the multiple sequence case. + * + * @throws IOException + */ + @Test(groups = { "Functional" }) + public void testAlignAs_proteinAsCdna_singleSequence() throws IOException + { + /* + * simplest case remove all gaps + */ + verifyAlignAs(">protein\n-Q-K-\n", ">dna\nCAAaaa\n", "QK"); + + /* + * with sequence offsets + */ + verifyAlignAs(">protein/12-13\n-Q-K-\n", ">dna/20-25\nCAAaaa\n", "QK"); + } + + /** * Test aligning cdna as per protein alignment. * * @throws IOException @@ -224,11 +237,7 @@ public class AlignmentTest */ AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA"); AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA"); - AlignedCodonFrame acf = new AlignedCodonFrame(); - MapList ml = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1); - acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml); - acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml); - al2.addCodonFrame(acf); + makeMappings(al1, al2); /* * Realign DNA; currently keeping existing gaps in introns only @@ -241,6 +250,88 @@ public class AlignmentTest } /** + * Test aligning cdna as per protein - single sequences + * + * @throws IOException + */ + @Test(groups = { "Functional" }) + public void testAlignAs_cdnaAsProtein_singleSequence() throws IOException + { + /* + * simple case insert one gap + */ + verifyAlignAs(">dna\nCAAaaa\n", ">protein\nQ-K\n", "CAA---aaa"); + + /* + * simple case but with sequence offsets + */ + verifyAlignAs(">dna/5-10\nCAAaaa\n", ">protein/20-21\nQ-K\n", + "CAA---aaa"); + + /* + * insert gaps as per protein, drop gaps within codons + */ + verifyAlignAs(">dna/10-18\nCA-Aa-aa--AGA\n", ">aa/6-8\n-Q-K--R\n", + "---CAA---aaa------AGA"); + } + + /** + * Helper method that makes mappings and then aligns the first alignment as + * the second + * + * @param fromSeqs + * @param toSeqs + * @param expected + * @throws IOException + */ + public void verifyAlignAs(String fromSeqs, String toSeqs, String expected) + throws IOException + { + /* + * Load alignments and add mappings from nucleotide to protein (or from + * first to second if both the same type) + */ + AlignmentI al1 = loadAlignment(fromSeqs, "FASTA"); + AlignmentI al2 = loadAlignment(toSeqs, "FASTA"); + makeMappings(al1, al2); + + /* + * Realign DNA; currently keeping existing gaps in introns only + */ + ((Alignment) al1).alignAs(al2, false, true); + assertEquals(expected, al1.getSequenceAt(0).getSequenceAsString()); + } + + /** + * Helper method to make mappings from protein to dna sequences, and add the + * mappings to the protein alignment + * + * @param alFrom + * @param alTo + */ + public void makeMappings(AlignmentI alFrom, AlignmentI alTo) + { + AlignmentI prot = !alFrom.isNucleotide() ? alFrom : alTo; + AlignmentI nuc = alFrom == prot ? alTo : alFrom; + + int ratio = (alFrom.isNucleotide() == alTo.isNucleotide() ? 1 : 3); + + AlignedCodonFrame acf = new AlignedCodonFrame(); + + for (int i = 0; i < nuc.getHeight(); i++) + { + SequenceI seqFrom = nuc.getSequenceAt(i); + SequenceI seqTo = prot.getSequenceAt(i); + MapList ml = new MapList(new int[] { seqFrom.getStart(), + seqFrom.getEnd() }, + new int[] { seqTo.getStart(), seqTo.getEnd() }, ratio, 1); + acf.addMap(seqFrom, seqTo, ml); + } + + prot.addCodonFrame(acf); + } + + /** * Test aligning dna as per protein alignment, for the case where there are * introns (i.e. some dna sites have no mapping from a peptide). * @@ -254,18 +345,19 @@ public class AlignmentTest */ String dna1 = "A-Aa-gG-GCC-cT-TT"; String dna2 = "c--CCGgg-TT--T-AA-A"; - AlignmentI al1 = loadAlignment(">Seq1\n" + dna1 + "\n>Seq2\n" + dna2 - + "\n", "FASTA"); - AlignmentI al2 = loadAlignment(">Seq1\n-P--YK\n>Seq2\nG-T--F\n", - "FASTA"); + AlignmentI al1 = loadAlignment(">Seq1/6-17\n" + dna1 + + "\n>Seq2/20-31\n" + dna2 + "\n", "FASTA"); + AlignmentI al2 = loadAlignment( + ">Seq1/7-9\n-P--YK\n>Seq2/11-13\nG-T--F\n", "FASTA"); AlignedCodonFrame acf = new AlignedCodonFrame(); // Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT // Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA - MapList ml1 = new MapList(new int[] { 1, 2, 5, 8, 10, 12 }, new int[] { - 1, 3 }, 3, 1); + // TODO sequence offsets + MapList ml1 = new MapList(new int[] { 6, 7, 10, 13, 15, 17 }, new int[] + { 7, 9 }, 3, 1); acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1); - MapList ml2 = new MapList(new int[] { 2, 4, 7, 12 }, - new int[] { 1, 3 }, 3, 1); + MapList ml2 = new MapList(new int[] { 21, 23, 26, 31 }, new int[] { 11, + 13 }, 3, 1); acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2); al2.addCodonFrame(acf);