*/
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 static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.assertNull;
+import org.testng.annotations.Test;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
-
-import org.junit.Test;
+import java.util.Set;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResults.Match;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
import jalview.util.MapList;
+import jalview.util.MappingUtils;
public class AlignmentUtilsTests
{
"GGGTCAGGCAGT\n";
// @formatter:on
- public static Sequence ts=new Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
+ // public static Sequence ts=new
+ // Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
+ public static Sequence ts = new Sequence("short",
+ "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
@Test
- public void testExpandFlanks()
+ public void testExpandContext()
{
AlignmentI al = new Alignment(new Sequence[] {});
- for (int i=4;i<14;i+=3)
+ for (int i = 4; i < 14; i += 2)
{
SequenceI s1=ts.deriveSequence().getSubSequence(i, i+7);
al.addSequence(s1);
System.out.println(new AppletFormatAdapter().formatSequences("Clustal", al, true));
for (int flnk=-1;flnk<25; flnk++)
{
- AlignmentI exp;
- System.out.println("\nFlank size: "+flnk);
- System.out.println(new AppletFormatAdapter().formatSequences("Clustal", exp=AlignmentUtils.expandContext(al, flnk), true));
- if (flnk==-1) {
- for (SequenceI sq:exp.getSequences())
+ AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
+ System.out.println("\nFlank size: " + flnk);
+ System.out.println(new AppletFormatAdapter().formatSequences(
+ "Clustal", exp, true));
+ if (flnk == -1)
{
+ /*
+ * Full expansion to complete sequences
+ */
+ for (SequenceI sq : exp.getSequences())
+ {
String ung = sq.getSequenceAsString().replaceAll("-+", "");
- assertTrue("Flanking sequence not the same as original dataset sequence.\n"+ung+"\n"+sq.getDatasetSequence().getSequenceAsString(),ung.equalsIgnoreCase(sq.getDatasetSequence().getSequenceAsString()));
+ final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
+ + ung
+ + "\n"
+ + sq.getDatasetSequence().getSequenceAsString();
+ assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
+ .getSequenceAsString()));
+ }
}
+ else if (flnk == 24)
+ {
+ /*
+ * Last sequence is fully expanded, others have leading gaps to match
+ */
+ assertTrue(exp.getSequenceAt(4).getSequenceAsString()
+ .startsWith("abc"));
+ assertTrue(exp.getSequenceAt(3).getSequenceAsString()
+ .startsWith("--abc"));
+ assertTrue(exp.getSequenceAt(2).getSequenceAsString()
+ .startsWith("----abc"));
+ assertTrue(exp.getSequenceAt(1).getSequenceAsString()
+ .startsWith("------abc"));
+ assertTrue(exp.getSequenceAt(0).getSequenceAsString()
+ .startsWith("--------abc"));
}
}
- }
+ }
+
+ /**
+ * Test that annotations are correctly adjusted by expandContext
+ */
+ @Test
+ public void testExpandContext_annotation()
+ {
+ AlignmentI al = new Alignment(new Sequence[]
+ {});
+ SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
+ // subsequence DEF:
+ SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
+ al.addSequence(seq1);
+
+ /*
+ * Annotate DEF with 4/5/6 respectively
+ */
+ Annotation[] anns = new Annotation[]
+ { new Annotation(4), new Annotation(5), new Annotation(6) };
+ AlignmentAnnotation ann = new AlignmentAnnotation("SS",
+ "secondary structure", anns);
+ seq1.addAlignmentAnnotation(ann);
+
+ /*
+ * The annotations array should match aligned positions
+ */
+ assertEquals(3, ann.annotations.length);
+ assertEquals(4, ann.annotations[0].value, 0.001);
+ assertEquals(5, ann.annotations[1].value, 0.001);
+ assertEquals(6, ann.annotations[2].value, 0.001);
+
+ /*
+ * Check annotation to sequence position mappings before expanding the
+ * sequence; these are set up in Sequence.addAlignmentAnnotation ->
+ * Annotation.setSequenceRef -> createSequenceMappings
+ */
+ assertNull(ann.getAnnotationForPosition(1));
+ assertNull(ann.getAnnotationForPosition(2));
+ assertNull(ann.getAnnotationForPosition(3));
+ assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
+ assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
+ assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
+ assertNull(ann.getAnnotationForPosition(7));
+ assertNull(ann.getAnnotationForPosition(8));
+ assertNull(ann.getAnnotationForPosition(9));
+
+ /*
+ * Expand the subsequence to the full sequence abcDEFghi
+ */
+ AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
+ assertEquals("abcDEFghi", expanded.getSequenceAt(0)
+ .getSequenceAsString());
+
+ /*
+ * Confirm the alignment and sequence have the same SS annotation,
+ * referencing the expanded sequence
+ */
+ ann = expanded.getSequenceAt(0).getAnnotation()[0];
+ assertSame(ann, expanded.getAlignmentAnnotation()[0]);
+ assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
+
+ /*
+ * The annotations array should have null values except for annotated
+ * positions
+ */
+ assertNull(ann.annotations[0]);
+ assertNull(ann.annotations[1]);
+ assertNull(ann.annotations[2]);
+ assertEquals(4, ann.annotations[3].value, 0.001);
+ assertEquals(5, ann.annotations[4].value, 0.001);
+ assertEquals(6, ann.annotations[5].value, 0.001);
+ assertNull(ann.annotations[6]);
+ assertNull(ann.annotations[7]);
+ assertNull(ann.annotations[8]);
+
+ /*
+ * sequence position mappings should be unchanged
+ */
+ assertNull(ann.getAnnotationForPosition(1));
+ assertNull(ann.getAnnotationForPosition(2));
+ assertNull(ann.getAnnotationForPosition(3));
+ assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
+ assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
+ assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
+ assertNull(ann.getAnnotationForPosition(7));
+ assertNull(ann.getAnnotationForPosition(8));
+ assertNull(ann.getAnnotationForPosition(9));
+ }
/**
* Test method that returns a map of lists of sequences by sequence name.
assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
}
+
+ /**
+ * Test the method that extracts the exon-only part of a dna alignment.
+ */
+ @Test
+ public void testMakeExonAlignment()
+ {
+ SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
+ SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
+ SequenceI pep1 = new Sequence("pep1", "GF");
+ SequenceI pep2 = new Sequence("pep2", "GFP");
+ dna1.createDatasetSequence();
+ dna2.createDatasetSequence();
+ pep1.createDatasetSequence();
+ pep2.createDatasetSequence();
+
+ Set<AlignedCodonFrame> mappings = new HashSet<AlignedCodonFrame>();
+ MapList map = new MapList(new int[]
+ { 4, 6, 10, 12 }, new int[]
+ { 1, 2 }, 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
+ mappings.add(acf);
+ map = new MapList(new int[]
+ { 1, 3, 7, 9, 13, 15 }, new int[]
+ { 1, 3 }, 3, 1);
+ acf = new AlignedCodonFrame();
+ acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
+ mappings.add(acf);
+
+ AlignmentI exons = AlignmentUtils.makeExonAlignment(new SequenceI[]
+ { dna1, dna2 }, mappings);
+ assertEquals(2, exons.getSequences().size());
+ assertEquals("GGGTTT", exons.getSequenceAt(0).getSequenceAsString());
+ assertEquals("GGGTTTCCC", exons.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * Verify updated mappings
+ */
+ assertEquals(2, mappings.size());
+
+ /*
+ * Mapping from pep1 to GGGTTT in first new exon sequence
+ */
+ List<AlignedCodonFrame> pep1Mapping = MappingUtils
+ .findMappingsForSequence(pep1, mappings);
+ assertEquals(1, pep1Mapping.size());
+ // map G to GGG
+ SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
+ assertEquals(1, sr.getResults().size());
+ Match m = sr.getResults().get(0);
+ assertEquals(exons.getSequenceAt(0).getDatasetSequence(),
+ m.getSequence());
+ assertEquals(1, m.getStart());
+ assertEquals(3, m.getEnd());
+ // map F to TTT
+ sr = MappingUtils.buildSearchResults(pep1, 2, mappings);
+ m = sr.getResults().get(0);
+ assertEquals(exons.getSequenceAt(0).getDatasetSequence(),
+ m.getSequence());
+ assertEquals(4, m.getStart());
+ assertEquals(6, m.getEnd());
+
+ /*
+ * Mapping from pep2 to GGGTTTCCC in second new exon sequence
+ */
+ List<AlignedCodonFrame> pep2Mapping = MappingUtils
+ .findMappingsForSequence(pep2, mappings);
+ assertEquals(1, pep2Mapping.size());
+ // map G to GGG
+ sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
+ assertEquals(1, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertEquals(exons.getSequenceAt(1).getDatasetSequence(),
+ m.getSequence());
+ assertEquals(1, m.getStart());
+ assertEquals(3, m.getEnd());
+ // map F to TTT
+ sr = MappingUtils.buildSearchResults(pep2, 2, mappings);
+ m = sr.getResults().get(0);
+ assertEquals(exons.getSequenceAt(1).getDatasetSequence(),
+ m.getSequence());
+ assertEquals(4, m.getStart());
+ assertEquals(6, m.getEnd());
+ // map P to CCC
+ sr = MappingUtils.buildSearchResults(pep2, 3, mappings);
+ m = sr.getResults().get(0);
+ assertEquals(exons.getSequenceAt(1).getDatasetSequence(),
+ m.getSequence());
+ assertEquals(7, m.getStart());
+ assertEquals(9, m.getEnd());
+ }
+
+ /**
+ * Test the method that makes an exon-only sequence from a DNA sequence and
+ * its product mapping. Test includes the expected case that the DNA sequence
+ * already has a protein product (Uniprot translation) which in turn has an
+ * x-ref to the EMBLCDS record.
+ */
+ @Test
+ public void testMakeExonSequences()
+ {
+ SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
+ SequenceI pep1 = new Sequence("pep1", "GF");
+ dna1.createDatasetSequence();
+ pep1.createDatasetSequence();
+ pep1.getDatasetSequence().addDBRef(
+ new DBRefEntry("EMBLCDS", "2", "A12345"));
+
+ /*
+ * Make the mapping from dna to protein. The protein sequence has a DBRef to
+ * EMBLCDS|A12345.
+ */
+ Set<AlignedCodonFrame> mappings = new HashSet<AlignedCodonFrame>();
+ MapList map = new MapList(new int[]
+ { 4, 6, 10, 12 }, new int[]
+ { 1, 2 }, 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
+ mappings.add(acf);
+
+ AlignedCodonFrame newMapping = new AlignedCodonFrame();
+ List<SequenceI> exons = AlignmentUtils.makeExonSequences(dna1, acf,
+ newMapping);
+ assertEquals(1, exons.size());
+ SequenceI exon = exons.get(0);
+
+ assertEquals("GGGTTT", exon.getSequenceAsString());
+ assertEquals("dna1|A12345", exon.getName());
+ assertEquals(1, exon.getDBRef().length);
+ DBRefEntry cdsRef = exon.getDBRef()[0];
+ assertEquals("EMBLCDS", cdsRef.getSource());
+ assertEquals("2", cdsRef.getVersion());
+ assertEquals("A12345", cdsRef.getAccessionId());
+ }
+
+ /**
+ * Test the method that makes an exon-only alignment from a DNA sequence and
+ * its product mappings, for the case where there are multiple exon mappings
+ * to different protein products.
+ */
+ @Test
+ public void testMakeExonAlignment_multipleProteins()
+ {
+ SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
+ SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
+ SequenceI pep2 = new Sequence("pep2", "KP"); // aaaccc
+ SequenceI pep3 = new Sequence("pep3", "KF"); // aaaTTT
+ dna1.createDatasetSequence();
+ pep1.createDatasetSequence();
+ pep2.createDatasetSequence();
+ pep3.createDatasetSequence();
+ pep1.getDatasetSequence().addDBRef(
+ new DBRefEntry("EMBLCDS", "2", "A12345"));
+ pep2.getDatasetSequence().addDBRef(
+ new DBRefEntry("EMBLCDS", "3", "A12346"));
+ pep3.getDatasetSequence().addDBRef(
+ new DBRefEntry("EMBLCDS", "4", "A12347"));
+
+ /*
+ * Make the mappings from dna to protein. Using LinkedHashset is a
+ * convenience so results are in the input order. There is no assertion that
+ * the generated exon sequences are in any particular order.
+ */
+ Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+ // map ...GGG...TTT to GF
+ MapList map = new MapList(new int[]
+ { 4, 6, 10, 12 }, new int[]
+ { 1, 2 }, 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
+ mappings.add(acf);
+
+ // map aaa...ccc to KP
+ map = new MapList(new int[]
+ { 1, 3, 7, 9 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
+ mappings.add(acf);
+
+ // map aaa......TTT to KF
+ map = new MapList(new int[]
+ { 1, 3, 10, 12 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
+ mappings.add(acf);
+
+ /*
+ * Create the Exon alignment; also replaces the dna-to-protein mappings with
+ * exon-to-protein and exon-to-dna mappings
+ */
+ AlignmentI exal = AlignmentUtils.makeExonAlignment(new SequenceI[]
+ { dna1 }, mappings);
+
+ /*
+ * Verify we have 3 exon sequences, mapped to pep1/2/3 respectively
+ */
+ List<SequenceI> exons = exal.getSequences();
+ assertEquals(3, exons.size());
+
+ SequenceI exon = exons.get(0);
+ assertEquals("GGGTTT", exon.getSequenceAsString());
+ assertEquals("dna1|A12345", exon.getName());
+ assertEquals(1, exon.getDBRef().length);
+ DBRefEntry cdsRef = exon.getDBRef()[0];
+ assertEquals("EMBLCDS", cdsRef.getSource());
+ assertEquals("2", cdsRef.getVersion());
+ assertEquals("A12345", cdsRef.getAccessionId());
+
+ exon = exons.get(1);
+ assertEquals("aaaccc", exon.getSequenceAsString());
+ assertEquals("dna1|A12346", exon.getName());
+ assertEquals(1, exon.getDBRef().length);
+ cdsRef = exon.getDBRef()[0];
+ assertEquals("EMBLCDS", cdsRef.getSource());
+ assertEquals("3", cdsRef.getVersion());
+ assertEquals("A12346", cdsRef.getAccessionId());
+
+ exon = exons.get(2);
+ assertEquals("aaaTTT", exon.getSequenceAsString());
+ assertEquals("dna1|A12347", exon.getName());
+ assertEquals(1, exon.getDBRef().length);
+ cdsRef = exon.getDBRef()[0];
+ assertEquals("EMBLCDS", cdsRef.getSource());
+ assertEquals("4", cdsRef.getVersion());
+ assertEquals("A12347", cdsRef.getAccessionId());
+
+ /*
+ * Verify there are mappings from each exon sequence to its protein product
+ * and also to its dna source
+ */
+ Iterator<AlignedCodonFrame> newMappingsIterator = mappings.iterator();
+
+ // mappings for dna1 - exon1 - pep1
+ AlignedCodonFrame exonMapping = newMappingsIterator.next();
+ List<Mapping> dnaMappings = exonMapping.getMappingsForSequence(dna1);
+ assertEquals(1, dnaMappings.size());
+ assertSame(exons.get(0).getDatasetSequence(), dnaMappings.get(0)
+ .getTo());
+ assertEquals("G(1) in CDS should map to G(4) in DNA", 4, dnaMappings
+ .get(0).getMap().getToPosition(1));
+ List<Mapping> peptideMappings = exonMapping
+ .getMappingsForSequence(pep1);
+ assertEquals(1, peptideMappings.size());
+ assertSame(pep1.getDatasetSequence(), peptideMappings.get(0).getTo());
+
+ // mappings for dna1 - exon2 - pep2
+ exonMapping = newMappingsIterator.next();
+ dnaMappings = exonMapping.getMappingsForSequence(dna1);
+ assertEquals(1, dnaMappings.size());
+ assertSame(exons.get(1).getDatasetSequence(), dnaMappings.get(0)
+ .getTo());
+ assertEquals("c(4) in CDS should map to c(7) in DNA", 7, dnaMappings
+ .get(0).getMap().getToPosition(4));
+ peptideMappings = exonMapping.getMappingsForSequence(pep2);
+ assertEquals(1, peptideMappings.size());
+ assertSame(pep2.getDatasetSequence(), peptideMappings.get(0).getTo());
+
+ // mappings for dna1 - exon3 - pep3
+ exonMapping = newMappingsIterator.next();
+ dnaMappings = exonMapping.getMappingsForSequence(dna1);
+ assertEquals(1, dnaMappings.size());
+ assertSame(exons.get(2).getDatasetSequence(), dnaMappings.get(0)
+ .getTo());
+ assertEquals("T(4) in CDS should map to T(10) in DNA", 10, dnaMappings
+ .get(0).getMap().getToPosition(4));
+ peptideMappings = exonMapping.getMappingsForSequence(pep3);
+ assertEquals(1, peptideMappings.size());
+ assertSame(pep3.getDatasetSequence(), peptideMappings.get(0).getTo());
+ }
}
git://source.jalview.org / jalview.git / blobdiff