+/*
+ * 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.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+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.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
/**
* Unit tests for Alignment datamodel.
"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;
- private Alignment 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.
*/
- @Before
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws IOException
{
- al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
- AppletFormatAdapter.PASTE, "STH");
- for (int i = 0; i < al.getSequencesArray().length; ++i)
+ al = loadAlignment(TEST_DATA, "STH");
+ int i = 0;
+ for (AlignmentAnnotation ann : al.getAlignmentAnnotation())
{
- al.getSequenceAt(i).setDatasetSequence(
- al.getSequenceAt(i).createDatasetSequence());
- al.addAnnotation(al.getSequenceAt(i).getAnnotation()[0]);
- al.getSequenceAt(i).getAnnotation()[0].setCalcId("CalcIdFor"
- + al.getSequenceAt(i).getName());
+ ann.setCalcId("CalcIdFor" + al.getSequenceAt(i).getName());
+ i++;
}
}
/**
* Test method that returns annotations that match on calcId.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testFindAnnotation_byCalcId()
{
Iterable<AlignmentAnnotation> anns = al
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<AlignedCodonFrame> 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<int[]> hiddenCols = new ArrayList<int[]>();
+
+ 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]);
+ }
}
git://source.jalview.org / jalview.git / blobdiff