*/
package jalview.analysis;
+import static org.testng.Assert.assertNotEquals;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.analysis.AlignmentUtils.DnaVariant;
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.Mapping;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SeqDistanceContactMatrix;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.gff.SequenceOntologyI;
+import jalview.util.Comparison;
import jalview.util.MapList;
import jalview.util.MappingUtils;
-import jalview.ws.params.InvalidArgumentException;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
public class AlignmentUtilsTests
{
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure",
+ new Annotation[] {});
+ AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
+ "jnetpred", new Annotation[] {});
+ AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
+ new Annotation[] {});
+ AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
+ new Annotation[] {});
+
+ AlignmentAnnotation[] anns1 = new AlignmentAnnotation[] { ann1, ann3,
+ ann4 };
+
+ AlignmentAnnotation[] anns2 = new AlignmentAnnotation[] { ann2, ann3,
+ ann4 };
+
+ AlignmentAnnotation[] anns3 = new AlignmentAnnotation[] { ann3, ann4 };
+
+ AlignmentAnnotation[] anns4 = new AlignmentAnnotation[0];
+
+ AlignmentAnnotation[] anns5 = new AlignmentAnnotation[] { ann1, ann2,
+ ann3, ann4 };
}
@Test(groups = { "Functional" })
* the given protein. That is, given a transcript-to-peptide mapping, find the
* cds-to-peptide mapping that relates to both, and return the CDS sequence.
*/
- @Test
+ @Test(groups = "Functional")
public void testFindCdsForProtein()
{
List<AlignedCodonFrame> mappings = new ArrayList<>();
* cds-to-peptide mapping that relates to both, and return the CDS sequence.
* This test is for the case where transcript and CDS are the same length.
*/
- @Test
+ @Test(groups = "Functional")
public void testFindCdsForProtein_noUTR()
{
List<AlignedCodonFrame> mappings = new ArrayList<>();
dnaToPeptide);
assertSame(seq, cds1.getDatasetSequence());
}
+
+ @Test(groups = "Functional")
+ public void testAddReferenceAnnotations()
+ {
+ SequenceI longseq = new Sequence("longA", "ASDASDASDASDAASDASDASDASDA");
+ Annotation[] aa = new Annotation[longseq.getLength()];
+
+ for (int p = 0; p < aa.length; p++)
+ {
+ aa[p] = new Annotation("P", "pos " + (p + 1), (char) 0,
+ (float) p + 1);
+ }
+ AlignmentAnnotation refAnnot = new AlignmentAnnotation("LongSeqAnnot",
+ "Annotations", aa);
+ refAnnot.setCalcId("Test");
+ longseq.addAlignmentAnnotation(refAnnot);
+ verifyExpectedSequenceAnnotation(refAnnot);
+
+ Alignment ourAl = new Alignment(
+ new SequenceI[]
+ { longseq.getSubSequence(5, 10),
+ longseq.getSubSequence(7, 12) });
+ ourAl.createDatasetAlignment();
+
+ // transfer annotation
+ SortedMap<String, String> tipEntries = new TreeMap<>();
+ Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+
+ AlignmentUtils.findAddableReferenceAnnotations(ourAl.getSequences(),
+ tipEntries, candidates, ourAl);
+ AlignmentUtils.addReferenceAnnotations(candidates, ourAl, null);
+
+ assertNotNull(ourAl.getAlignmentAnnotation());
+ assertEquals(ourAl.getAlignmentAnnotation().length, 2);
+
+ for (AlignmentAnnotation alan : ourAl.getAlignmentAnnotation())
+ {
+ verifyExpectedSequenceAnnotation(alan);
+ }
+ // Everything above works for 2.11.3 and 2.11.2.x.
+ // now simulate copy/paste to new alignment
+ SequenceI[] newSeqAl = new SequenceI[2];
+ // copy sequences but no annotation
+ newSeqAl[0] = new Sequence(ourAl.getSequenceAt(0),
+ ourAl.getSequenceAt(0).getAnnotation());
+ newSeqAl[1] = new Sequence(ourAl.getSequenceAt(1),
+ ourAl.getSequenceAt(1).getAnnotation());
+
+ Alignment newAl = new Alignment(newSeqAl);
+ // delete annotation
+ for (SequenceI sq : newAl.getSequences())
+ {
+ sq.setAlignmentAnnotation(new AlignmentAnnotation[0]);
+ }
+ // JAL-4182 scenario test
+ SequenceGroup sg = new SequenceGroup(Arrays.asList(newSeqAl));
+ sg.setStartRes(0);
+ sg.setEndRes(newAl.getWidth());
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0],
+ newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1],
+ newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
+ for (AlignmentAnnotation alan : newAl.getAlignmentAnnotation())
+ {
+ verifyExpectedSequenceAnnotation(alan);
+ }
+ }
+
+ /**
+ * helper - tests annotation is mapped to position it was originally created
+ * for
+ *
+ * @param alan
+ */
+ private void verifyExpectedSequenceAnnotation(AlignmentAnnotation alan)
+ {
+ for (int c = 0; c < alan.annotations.length; c++)
+ {
+ Annotation a = alan.annotations[c];
+ if (a != null)
+ {
+ assertEquals("Misaligned annotation at " + c,
+ (float) alan.sequenceRef.findPosition(c), a.value);
+ }
+ else
+ {
+ assertTrue("Unexpected Null at position " + c,
+ c >= alan.sequenceRef.getLength()
+ || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
+ }
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testAddReferenceContactMap()
+ {
+ SequenceI sq = new Sequence("a", "SSSQ");
+ ContactMatrixI cm = new SeqDistanceContactMatrix(4);
+ AlignmentAnnotation cm_aan = sq.addContactList(cm);
+ cm_aan.description = cm_aan.description + " cm1";
+ SequenceI dssq = sq.createDatasetSequence();
+
+ // remove annotation on our non-dataset sequence
+ sq.removeAlignmentAnnotation(sq.getAnnotation()[0]);
+ // test transfer
+ Alignment al = new Alignment(new SequenceI[] { sq });
+ SortedMap<String, String> tipEntries = new TreeMap<>();
+ Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+
+ AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
+ tipEntries, candidates, al);
+ AlignmentUtils.addReferenceAnnotations(candidates, al, null);
+ assertTrue("No contact map annotation transferred",
+ al.getAlignmentAnnotation() != null
+ && al.getAlignmentAnnotation().length == 1);
+ AlignmentAnnotation alan = al.findAnnotations(sq, null, cm_aan.label)
+ .iterator().next();
+ ContactMatrixI t_cm = al.getContactMatrixFor(alan);
+ assertNotNull("No contact map for the transferred annotation row.",
+ t_cm);
+ assertTrue(t_cm instanceof SeqDistanceContactMatrix);
+ assertTrue(((SeqDistanceContactMatrix) t_cm).hasReferenceSeq());
+
+ ContactListI cl = al.getContactListFor(alan, 1);
+ assertNotNull(
+ "No contact matrix recovered after reference annotation transfer",
+ cl);
+ // semantics of sequence associated contact list is slightly tricky - column
+ // 3 in alignment should have data
+ cl = al.getContactListFor(alan, 3);
+ assertNotNull(
+ "Contact matrix should have data for last position in sequence",
+ cl);
+
+ ContactMatrixI cm2 = new SeqDistanceContactMatrix(4);
+ dssq.addContactList(cm2);
+ tipEntries = new TreeMap<>();
+ candidates = new LinkedHashMap<>();
+
+ AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
+ tipEntries, candidates, al);
+ AlignmentUtils.addReferenceAnnotations(candidates, al, null);
+ assertTrue("Expected two contact map annotation transferred",
+ al.getAlignmentAnnotation() != null
+ && al.getAlignmentAnnotation().length == 2);
+
+ }
+
+ @Test(
+ groups = "Functional",
+ dataProvider = "SecondaryStructureAnnotations")
+ public void testSecondaryStructurePresentAndSources(
+ AlignmentAnnotation[] annotations, boolean expectedSSPresent,
+ ArrayList<String> expectedSSSources)
+ {
+ Assert.assertEquals(expectedSSPresent,
+ AlignmentUtils.isSecondaryStructurePresent(annotations));
+ Assert.assertEquals(expectedSSSources,
+ AlignmentUtils.getSecondaryStructureSources(annotations));
+ }
+
+ @DataProvider(name = "SecondaryStructureAnnotations")
+ public static Object[][] provideSecondaryStructureAnnotations()
+ {
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure",
+ new Annotation[] {});
+ AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
+ "jnetpred", new Annotation[] {});
+ AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
+ new Annotation[] {});
+ AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
+ new Annotation[] {});
+
+ List<String> ssSources1 = new ArrayList<>(
+ Arrays.asList("3D Structures"));
+ List<String> ssSources2 = new ArrayList<>(Arrays.asList("JPred"));
+ List<String> ssSources3 = new ArrayList<>(
+ Arrays.asList("3D Structures", "JPred"));
+ List<String> ssSources4 = new ArrayList<>();
+
+ return new Object[][] {
+ { new AlignmentAnnotation[]
+ { ann1, ann3, ann4 }, true, ssSources1 },
+ { new AlignmentAnnotation[]
+ { ann2, ann3, ann4 }, true, ssSources2 },
+ { new AlignmentAnnotation[]
+ { ann3, ann4 }, false, ssSources4 },
+ { new AlignmentAnnotation[] {}, false, ssSources4 },
+ { new AlignmentAnnotation[]
+ { ann1, ann2, ann3, ann4 }, true, ssSources3 } };
+ }
+
+ @Test(dataProvider = "SecondaryStructureAnnotationColours")
+ public void testSecondaryStructureAnnotationColour(char symbol,
+ Color expectedColor)
+ {
+ Color actualColor = AlignmentUtils
+ .getSecondaryStructureAnnotationColour(symbol);
+ Assert.assertEquals(actualColor, expectedColor);
+ }
+
+ @DataProvider(name = "SecondaryStructureAnnotationColours")
+ public static Object[][] provideSecondaryStructureAnnotationColours()
+ {
+ return new Object[][] { { 'C', Color.gray }, { 'E', Color.green },
+ { 'H', Color.red },
+ { '-', Color.gray } };
+ }
+
+ @Test(dataProvider = "SSAnnotationPresence")
+ public void testIsSSAnnotationPresent(
+ Map<SequenceI, List<AlignmentAnnotation>> annotations,
+ boolean expectedPresence)
+ {
+ boolean actualPresence = AlignmentUtils
+ .isSSAnnotationPresent(annotations);
+ Assert.assertEquals(actualPresence, expectedPresence);
+ }
+
+ @DataProvider(name = "SSAnnotationPresence")
+ public static Object[][] provideSSAnnotationPresence()
+ {
+ Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
+ SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
+ List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
+ annotationsList1.add(new AlignmentAnnotation("Secondary Structure",
+ "Secondary Structure", new Annotation[] {}));
+ annotations1.put(seq1, annotationsList1); // Annotation present secondary
+ // structure for seq1
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
+ SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
+ List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
+ annotationsList2.add(new AlignmentAnnotation("Other Annotation",
+ "Other Annotation", new Annotation[] {}));
+ annotations2.put(seq2, annotationsList2); // Annotation not related to any
+ // of secondary structure for seq2
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
+ // Empty annotation map
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
+ SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
+ List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
+ annotationsList4.add(new AlignmentAnnotation("jnetpred", "jnetpred",
+ new Annotation[] {}));
+ annotations4.put(seq4, annotationsList4); // Annotation present from JPred
+ // for seq4
+
+ return new Object[][] { { annotations1, true }, // Annotations present
+ // secondary structure
+ // present
+ { annotations2, false }, // No annotations related to any of the
+ // secondary structure present
+ { annotations3, false }, // Empty annotation map
+ { annotations4, true }, // Annotations present from JPred secondary
+ // structure present
+ };
+ }
+
+ @Test
+ public void testGetSSSourceFromAnnotationDescription(
+ AlignmentAnnotation[] annotations, String expectedSSSource)
+ {
+ List<String> actualSSSource = AlignmentUtils
+ .extractSSSourceInAlignmentAnnotation(annotations);
+ Assert.assertEquals(actualSSSource, expectedSSSource);
+ }
+
+ @DataProvider(name = "SSSourceFromAnnotationDescription")
+ public static Object[][] provideSSSourceFromAnnotationDescription()
+ {
+ Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
+ SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
+ List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
+ annotationsList1.add(new AlignmentAnnotation("jnetpred", "JPred Output",
+ new Annotation[] {}));
+ annotations1.put(seq1, annotationsList1); // Annotation present from JPred
+ // for seq1
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
+ SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
+ List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
+ annotationsList2.add(new AlignmentAnnotation("Secondary Structure",
+ "Secondary Structure for af-q43517-f1A", new Annotation[] {}));
+ annotations2.put(seq2, annotationsList2); // Annotation present secondary
+ // structure from Alphafold for
+ // seq2
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
+ // Empty annotation map
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
+ SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
+ List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
+ annotationsList4.add(new AlignmentAnnotation("Secondary Structure",
+ "Secondary Structure for 4zhpA", new Annotation[] {}));
+ annotations4.put(seq4, annotationsList4); // Annotation present secondary
+ // structure from pdb for seq4
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations5 = new HashMap<>();
+ SequenceI seq5 = new Sequence("Seq5", "ASD---ASD---AS-", 37, 44);
+ List<AlignmentAnnotation> annotationsList5 = new ArrayList<>();
+ annotationsList5.add(new AlignmentAnnotation("Secondary Structure",
+ "Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P",
+ new Annotation[] {}));
+ annotations5.put(seq5, annotationsList5); // Annotation present secondary
+ // structure from Swiss model for
+ // seq5
+
+ // JPred Output - JPred
+ // Secondary Structure for af-q43517-f1A - Alphafold
+ // Secondary Structure for 4zhpA - Experimental
+ // Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P -
+ // Swiss Model
+
+ return new Object[][] { { annotations1, "JPred" },
+ { annotations2, "Alphafold" },
+ { annotations3, null },
+ { annotations4, "PDB" },
+ { annotations5, "Swiss Model" } };
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff