/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.util.MapList;
import jalview.util.MappingUtils;
import java.util.Map;
import java.util.TreeMap;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignmentUtilsTests
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
public static Sequence ts = new Sequence("short",
"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
al.addSequence(s1);
}
- System.out.println(new AppletFormatAdapter().formatSequences("Clustal",
+ System.out.println(new AppletFormatAdapter().formatSequences(
+ FileFormat.Clustal,
al, true));
for (int flnk = -1; flnk < 25; flnk++)
{
AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
System.out.println("\nFlank size: " + flnk);
System.out.println(new AppletFormatAdapter().formatSequences(
- "Clustal", exp, true));
+ FileFormat.Clustal, exp, true));
if (flnk == -1)
{
/*
{
final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
+ ">Seq1Name\nABCD\n";
- AlignmentI al = loadAlignment(data, "FASTA");
+ AlignmentI al = loadAlignment(data, FileFormat.Fasta);
Map<String, List<SequenceI>> map = AlignmentUtils
.getSequencesByName(al);
assertEquals(2, map.keySet().size());
* @return
* @throws IOException
*/
- protected AlignmentI loadAlignment(final String data, String format)
+ protected AlignmentI loadAlignment(final String data, FileFormatI format)
throws IOException
{
AlignmentI a = new FormatAdapter().readFile(data,
- AppletFormatAdapter.PASTE, format);
+ DataSourceType.PASTE, format);
a.setDataset(null);
return a;
}
assertEquals(1, mappings.size());
// map G to GGG
- SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
+ SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
assertEquals(1, sr.getResults().size());
- Match m = sr.getResults().get(0);
+ SearchResultMatchI m = sr.getResults().get(0);
assertSame(cds1Dss, m.getSequence());
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
/*
* check cds2 acquired a variant feature in position 5
*/
- SequenceFeature[] sfs = cds2Dss.getSequenceFeatures();
+ List<SequenceFeature> sfs = cds2Dss.getSequenceFeatures();
assertNotNull(sfs);
- assertEquals(1, sfs.length);
- assertEquals("variant", sfs[0].type);
- assertEquals(5, sfs[0].begin);
- assertEquals(5, sfs[0].end);
+ assertEquals(1, sfs.size());
+ assertEquals("variant", sfs.get(0).type);
+ assertEquals(5, sfs.get(0).begin);
+ assertEquals(5, sfs.get(0).end);
}
/**
* that partially overlap 5' or 3' (start or end) of target sequence
*/
AlignmentUtils.transferFeatures(dna, cds, map, null);
- SequenceFeature[] sfs = cds.getSequenceFeatures();
- assertEquals(6, sfs.length);
+ List<SequenceFeature> sfs = cds.getSequenceFeatures();
+ assertEquals(6, sfs.size());
- SequenceFeature sf = sfs[0];
+ SequenceFeature sf = sfs.get(0);
assertEquals("type2", sf.getType());
assertEquals("desc2", sf.getDescription());
assertEquals(2f, sf.getScore());
assertEquals(1, sf.getBegin());
assertEquals(1, sf.getEnd());
- sf = sfs[1];
+ sf = sfs.get(1);
assertEquals("type3", sf.getType());
assertEquals("desc3", sf.getDescription());
assertEquals(3f, sf.getScore());
assertEquals(1, sf.getBegin());
assertEquals(3, sf.getEnd());
- sf = sfs[2];
+ sf = sfs.get(2);
assertEquals("type4", sf.getType());
assertEquals(2, sf.getBegin());
assertEquals(5, sf.getEnd());
- sf = sfs[3];
+ sf = sfs.get(3);
assertEquals("type5", sf.getType());
assertEquals(1, sf.getBegin());
assertEquals(6, sf.getEnd());
- sf = sfs[4];
+ sf = sfs.get(4);
assertEquals("type8", sf.getType());
assertEquals(6, sf.getBegin());
assertEquals(6, sf.getEnd());
- sf = sfs[5];
+ sf = sfs.get(5);
assertEquals("type9", sf.getType());
assertEquals(6, sf.getBegin());
assertEquals(6, sf.getEnd());
// desc4 and desc8 are the 'omit these' varargs
AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
- SequenceFeature[] sfs = cds.getSequenceFeatures();
- assertEquals(1, sfs.length);
+ List<SequenceFeature> sfs = cds.getSequenceFeatures();
+ assertEquals(1, sfs.size());
- SequenceFeature sf = sfs[0];
+ SequenceFeature sf = sfs.get(0);
assertEquals("type5", sf.getType());
assertEquals(1, sf.getBegin());
assertEquals(6, sf.getEnd());
// "type5" is the 'select this type' argument
AlignmentUtils.transferFeatures(dna, cds, map, "type5");
- SequenceFeature[] sfs = cds.getSequenceFeatures();
- assertEquals(1, sfs.length);
+ List<SequenceFeature> sfs = cds.getSequenceFeatures();
+ assertEquals(1, sfs.size());
- SequenceFeature sf = sfs[0];
+ SequenceFeature sf = sfs.get(0);
assertEquals("type5", sf.getType());
assertEquals(1, sf.getBegin());
assertEquals(6, sf.getEnd());
List<AlignedCodonFrame> pep1CdsMappings = MappingUtils
.findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
assertEquals(1, pep1CdsMappings.size());
- SearchResults sr = MappingUtils.buildSearchResults(pep1, 1,
+ SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1,
pep1CdsMappings);
assertEquals(1, sr.getResults().size());
- Match m = sr.getResults().get(0);
+ SearchResultMatchI m = sr.getResults().get(0);
assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
* var6 P -> H COSMIC
* var6 P -> R COSMIC
*/
- SequenceFeature[] sfs = peptide.getSequenceFeatures();
- assertEquals(5, sfs.length);
+ List<SequenceFeature> sfs = peptide.getSequenceFeatures();
+ SequenceFeatures.sortFeatures(sfs, true);
+ assertEquals(5, sfs.size());
- SequenceFeature sf = sfs[0];
+ /*
+ * features are sorted by start position ascending, but in no
+ * particular order where start positions match; asserts here
+ * simply match the data returned (the order is not important)
+ */
+ SequenceFeature sf = sfs.get(0);
assertEquals(1, sf.getBegin());
assertEquals(1, sf.getEnd());
- assertEquals("p.Lys1Glu", sf.getDescription());
- assertEquals("var1.125A>G", sf.getValue("ID"));
- assertNull(sf.getValue("clinical_significance"));
- assertEquals("ID=var1.125A>G", sf.getAttributes());
+ assertEquals("p.Lys1Asn", sf.getDescription());
+ assertEquals("var4", sf.getValue("ID"));
+ assertEquals("Benign", sf.getValue("clinical_significance"));
+ assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes());
assertEquals(1, sf.links.size());
- // link to variation is urlencoded
assertEquals(
- "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
+ "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
sf.links.get(0));
assertEquals(ensembl, sf.getFeatureGroup());
- sf = sfs[1];
+ sf = sfs.get(1);
assertEquals(1, sf.getBegin());
assertEquals(1, sf.getEnd());
assertEquals("p.Lys1Gln", sf.getDescription());
sf.links.get(0));
assertEquals(dbSnp, sf.getFeatureGroup());
- sf = sfs[2];
+ sf = sfs.get(2);
assertEquals(1, sf.getBegin());
assertEquals(1, sf.getEnd());
- assertEquals("p.Lys1Asn", sf.getDescription());
- assertEquals("var4", sf.getValue("ID"));
- assertEquals("Benign", sf.getValue("clinical_significance"));
- assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes());
+ assertEquals("p.Lys1Glu", sf.getDescription());
+ assertEquals("var1.125A>G", sf.getValue("ID"));
+ assertNull(sf.getValue("clinical_significance"));
+ assertEquals("ID=var1.125A>G", sf.getAttributes());
assertEquals(1, sf.links.size());
+ // link to variation is urlencoded
assertEquals(
- "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
+ "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
sf.links.get(0));
assertEquals(ensembl, sf.getFeatureGroup());
- // var5 generates two distinct protein variant features
- sf = sfs[3];
+ sf = sfs.get(3);
assertEquals(3, sf.getBegin());
assertEquals(3, sf.getEnd());
- assertEquals("p.Pro3His", sf.getDescription());
+ assertEquals("p.Pro3Arg", sf.getDescription());
assertEquals("var6", sf.getValue("ID"));
assertEquals("Good", sf.getValue("clinical_significance"));
assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
- "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+ "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
sf.links.get(0));
assertEquals(cosmic, sf.getFeatureGroup());
- sf = sfs[4];
+ // var5 generates two distinct protein variant features
+ sf = sfs.get(4);
assertEquals(3, sf.getBegin());
assertEquals(3, sf.getEnd());
- assertEquals("p.Pro3Arg", sf.getDescription());
+ assertEquals("p.Pro3His", sf.getDescription());
assertEquals("var6", sf.getValue("ID"));
assertEquals("Good", sf.getValue("clinical_significance"));
assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
- "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+ "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
sf.links.get(0));
assertEquals(cosmic, sf.getFeatureGroup());
}
assertEquals(1, mappings.size());
// map G to GGG
- SearchResults sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
+ SearchResultsI sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
assertEquals(1, sr.getResults().size());
- Match m = sr.getResults().get(0);
+ SearchResultMatchI m = sr.getResults().get(0);
assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());