/*
* 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 .
* 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.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
import jalview.util.MapList;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
/**
* Unit tests for Alignment datamodel.
*
* @author gmcarstairs
*
*/
public class AlignmentTest
{
// @formatter:off
private static final String TEST_DATA =
"# STOCKHOLM 1.0\n" +
"#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
"#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
"#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
"D.melanogaster.1 G.AGCC.CU...AUGAUCGA\n" +
"#=GR D.melanogaster.1 SS ................((((\n" +
"D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
"#=GR D.melanogaster.2 SS ................((((\n" +
"D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
"#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" +
"//";
private static final String AA_SEQS_1 =
">Seq1Name/5-8\n" +
"K-QY--L\n" +
">Seq2Name/12-15\n" +
"-R-FP-W-\n";
private static final String CDNA_SEQS_1 =
">Seq1Name/100-111\n" +
"AC-GG--CUC-CAA-CT\n" +
">Seq2Name/200-211\n" +
"-CG-TTA--ACG---AAGT\n";
private static final String CDNA_SEQS_2 =
">Seq1Name/50-61\n" +
"GCTCGUCGTACT\n" +
">Seq2Name/60-71\n" +
"GGGTCAGGCAGT\n";
// @formatter:on
private AlignmentI al;
/**
* Helper method to load an alignment and ensure dataset sequences are set up.
*
* @param data
* @param format
* TODO
* @return
* @throws IOException
*/
protected AlignmentI loadAlignment(final String data, String format)
throws IOException
{
AlignmentI a = new FormatAdapter().readFile(data,
AppletFormatAdapter.PASTE, format);
a.setDataset(null);
return a;
}
/*
* Read in Stockholm format test data including secondary structure
* annotations.
*/
@BeforeMethod(alwaysRun = true)
public void setUp() throws IOException
{
al = loadAlignment(TEST_DATA, "STH");
int i = 0;
for (AlignmentAnnotation ann : al.getAlignmentAnnotation())
{
ann.setCalcId("CalcIdFor" + al.getSequenceAt(i).getName());
i++;
}
}
/**
* Test method that returns annotations that match on calcId.
*/
@Test(groups = { "Functional" })
public void testFindAnnotation_byCalcId()
{
Iterable anns = al
.findAnnotation("CalcIdForD.melanogaster.2");
Iterator iter = anns.iterator();
assertTrue(iter.hasNext());
AlignmentAnnotation ann = iter.next();
assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
assertFalse(iter.hasNext());
}
@Test(groups = { "Functional" })
public void testDeleteAllAnnotations_includingAutocalculated()
{
AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
"Consensus", 0.5);
aa.autoCalculated = true;
al.addAnnotation(aa);
AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
assertEquals("Wrong number of annotations before deleting", 4,
anns.length);
al.deleteAllAnnotations(true);
assertEquals("Not all deleted", 0, al.getAlignmentAnnotation().length);
}
@Test(groups = { "Functional" })
public void testDeleteAllAnnotations_excludingAutocalculated()
{
AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
"Consensus", 0.5);
aa.autoCalculated = true;
al.addAnnotation(aa);
AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
assertEquals("Wrong number of annotations before deleting", 4,
anns.length);
al.deleteAllAnnotations(false);
assertEquals("Not just one annotation left", 1,
al.getAlignmentAnnotation().length);
}
/**
* Tests for realigning as per a supplied alignment: Dna as Dna.
*
* Note: AlignedCodonFrame's state variables are named for protein-to-cDNA
* mapping, but can be exploited for a general 'sequence-to-sequence' mapping
* as here.
*
* @throws IOException
*/
@Test(groups = { "Functional" })
public void testAlignAs_dnaAsDna() throws IOException
{
// aligned cDNA:
AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
// unaligned cDNA:
AlignmentI al2 = loadAlignment(CDNA_SEQS_2, "FASTA");
/*
* Make mappings between sequences. The 'aligned cDNA' is playing the role
* of what would normally be protein here.
*/
makeMappings(al1, al2);
((Alignment) al2).alignAs(al1, false, true);
assertEquals("GC-TC--GUC-GTACT", al2.getSequenceAt(0)
.getSequenceAsString());
assertEquals("-GG-GTC--AGG--CAGT", al2.getSequenceAt(1)
.getSequenceAsString());
}
/**
* Aligning protein from cDNA.
*
* @throws IOException
*/
@Test(groups = { "Functional" })
public void testAlignAs_proteinAsCdna() throws IOException
{
// see also AlignmentUtilsTests
AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
makeMappings(al1, al2);
// Fudge - alignProteinAsCdna expects mappings to be on protein
al2.getCodonFrames().addAll(al1.getCodonFrames());
((Alignment) al2).alignAs(al1, false, true);
assertEquals("K-Q-Y-L-", al2.getSequenceAt(0).getSequenceAsString());
assertEquals("-R-F-P-W", al2.getSequenceAt(1).getSequenceAsString());
}
/**
* Test aligning cdna as per protein alignment.
*
* @throws IOException
*/
@Test(groups = { "Functional" }, enabled = false)
// TODO review / update this test after redesign of alignAs method
public void testAlignAs_cdnaAsProtein() throws IOException
{
/*
* Load alignments and add mappings for cDNA to protein
*/
AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
makeMappings(al1, al2);
/*
* Realign DNA; currently keeping existing gaps in introns only
*/
((Alignment) al1).alignAs(al2, false, true);
assertEquals("ACG---GCUCCA------ACT", al1.getSequenceAt(0)
.getSequenceAsString());
assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1)
.getSequenceAsString());
}
/**
* Test aligning cdna as per protein - single sequences
*
* @throws IOException
*/
@Test(groups = { "Functional" }, enabled = false)
// TODO review / update this test after redesign of alignAs method
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 between sequences, and add the mappings to
* the 'mapped from' alignment
*
* @param alFrom
* @param alTo
*/
public void makeMappings(AlignmentI alFrom, AlignmentI alTo)
{
int ratio = (alFrom.isNucleotide() == alTo.isNucleotide() ? 1 : 3);
AlignedCodonFrame acf = new AlignedCodonFrame();
for (int i = 0; i < alFrom.getHeight(); i++)
{
SequenceI seqFrom = alFrom.getSequenceAt(i);
SequenceI seqTo = alTo.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);
}
alFrom.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).
*
* @throws IOException
*/
@Test(groups = { "Functional" }, enabled = false)
// TODO review / update this test after redesign of alignAs method
public void testAlignAs_dnaAsProtein_withIntrons() throws IOException
{
/*
* Load alignments and add mappings for cDNA to protein
*/
String dna1 = "A-Aa-gG-GCC-cT-TT";
String dna2 = "c--CCGgg-TT--T-AA-A";
AlignmentI al1 = loadAlignment(">Dna1/6-17\n" + dna1
+ "\n>Dna2/20-31\n" + dna2 + "\n", "FASTA");
AlignmentI al2 = loadAlignment(
">Pep1/7-9\n-P--YK\n>Pep2/11-13\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[] { 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[] { 21, 23, 26, 31 }, new int[] { 11,
13 }, 3, 1);
acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2);
al2.addCodonFrame(acf);
/*
* Align ignoring gaps in dna introns and exons
*/
((Alignment) al1).alignAs(al2, false, false);
assertEquals("---AAagG------GCCcTTT", al1.getSequenceAt(0)
.getSequenceAsString());
// note 1 gap in protein corresponds to 'gg-' in DNA (3 positions)
assertEquals("cCCGgg-TTT------AAA", al1.getSequenceAt(1)
.getSequenceAsString());
/*
* Reset and realign, preserving gaps in dna introns and exons
*/
al1.getSequenceAt(0).setSequence(dna1);
al1.getSequenceAt(1).setSequence(dna2);
((Alignment) al1).alignAs(al2, true, true);
// String dna1 = "A-Aa-gG-GCC-cT-TT";
// String dna2 = "c--CCGgg-TT--T-AA-A";
// assumption: we include 'the greater of' protein/dna gap lengths, not both
assertEquals("---A-Aa-gG------GCC-cT-TT", al1.getSequenceAt(0)
.getSequenceAsString());
assertEquals("c--CCGgg-TT--T------AA-A", al1.getSequenceAt(1)
.getSequenceAsString());
}
@Test(groups = "Functional")
public void testCopyConstructor() throws IOException
{
AlignmentI protein = loadAlignment(AA_SEQS_1, FormatAdapter.PASTE);
// create sequence and alignment datasets
protein.setDataset(null);
AlignedCodonFrame acf = new AlignedCodonFrame();
List acfList = Arrays.asList(new AlignedCodonFrame[]
{ acf });
protein.getDataset().setCodonFrames(acfList);
AlignmentI copy = new Alignment(protein);
/*
* copy has different aligned sequences but the same dataset sequences
*/
assertFalse(copy.getSequenceAt(0) == protein.getSequenceAt(0));
assertFalse(copy.getSequenceAt(1) == protein.getSequenceAt(1));
assertSame(copy.getSequenceAt(0).getDatasetSequence(), protein
.getSequenceAt(0).getDatasetSequence());
assertSame(copy.getSequenceAt(1).getDatasetSequence(), protein
.getSequenceAt(1).getDatasetSequence());
// TODO should the copy constructor copy the dataset?
// or make a new one referring to the same dataset sequences??
assertNull(copy.getDataset());
// assertArrayEquals(copy.getDataset().getSequencesArray(), protein
// .getDataset().getSequencesArray());
}
/**
* Test behaviour of createDataset
*
* @throws IOException
*/
@Test(groups = "Functional")
public void testCreateDatasetAlignment() throws IOException
{
AlignmentI protein = new FormatAdapter().readFile(AA_SEQS_1,
AppletFormatAdapter.PASTE, "FASTA");
/*
* create a dataset sequence on first sequence
* leave the second without one
*/
protein.getSequenceAt(0).createDatasetSequence();
assertNotNull(protein.getSequenceAt(0).getDatasetSequence());
assertNull(protein.getSequenceAt(1).getDatasetSequence());
/*
* add a mapping to the alignment
*/
AlignedCodonFrame acf = new AlignedCodonFrame();
protein.addCodonFrame(acf);
assertNull(protein.getDataset());
assertTrue(protein.getCodonFrames().contains(acf));
/*
* create the alignment dataset
* note this creates sequence datasets where missing
* as a side-effect (in this case, on seq2
*/
// TODO promote this method to AlignmentI
((Alignment) protein).createDatasetAlignment();
// TODO this method should return AlignmentI not Alignment !!
Alignment ds = protein.getDataset();
// side-effect: dataset created on second sequence
assertNotNull(protein.getSequenceAt(1).getDatasetSequence());
// dataset alignment has references to dataset sequences
assertEquals(ds.getSequenceAt(0), protein.getSequenceAt(0)
.getDatasetSequence());
assertEquals(ds.getSequenceAt(1), protein.getSequenceAt(1)
.getDatasetSequence());
// codon frames should have been moved to the dataset
// getCodonFrames() should delegate to the dataset:
assertTrue(protein.getCodonFrames().contains(acf));
// prove the codon frames are indeed on the dataset:
assertTrue(ds.getCodonFrames().contains(acf));
}
@Test(groups = "Functional")
public void testAddCodonFrame()
{
AlignmentI align = new Alignment(new SequenceI[] {});
AlignedCodonFrame acf = new AlignedCodonFrame();
align.addCodonFrame(acf);
assertEquals(1, align.getCodonFrames().size());
assertTrue(align.getCodonFrames().contains(acf));
// can't add the same object twice:
align.addCodonFrame(acf);
assertEquals(1, align.getCodonFrames().size());
// create dataset alignment - mappings move to dataset
((Alignment) align).createDatasetAlignment();
assertSame(align.getCodonFrames(), align.getDataset().getCodonFrames());
assertEquals(1, align.getCodonFrames().size());
AlignedCodonFrame acf2 = new AlignedCodonFrame();
align.addCodonFrame(acf2);
assertTrue(align.getDataset().getCodonFrames().contains(acf));
}
@Test(groups = "Functional")
public void getVisibleStartAndEndIndexTest()
{
Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
AlignmentI align = new Alignment(new SequenceI[] { seq });
ArrayList hiddenCols = new ArrayList();
int[] startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
assertEquals(0, startEnd[0]);
assertEquals(25, startEnd[1]);
hiddenCols.add(new int[] { 0, 0 });
startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
assertEquals(1, startEnd[0]);
assertEquals(25, startEnd[1]);
hiddenCols.add(new int[] { 6, 9 });
hiddenCols.add(new int[] { 11, 12 });
startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
assertEquals(1, startEnd[0]);
assertEquals(25, startEnd[1]);
hiddenCols.add(new int[] { 24, 25 });
startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
System.out.println(startEnd[0] + " : " + startEnd[1]);
assertEquals(1, startEnd[0]);
assertEquals(23, startEnd[1]);
}
}