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 static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
-import jalview.datamodel.AlignedCodonFrame;
+import jalview.api.FeatureRenderer;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import java.awt.Color;
import java.io.File;
import java.io.IOException;
-import java.util.Iterator;
import java.util.Map;
-import java.util.Set;
import org.testng.annotations.Test;
.getSequenceFeatures();
assertEquals(1, sfs.length);
SequenceFeature sf = sfs[0];
- assertEquals("Iron-sulfur; 2Fe-2S", sf.description);
+ assertEquals("Iron-sulfur,2Fe-2S", sf.description);
assertEquals(44, sf.begin);
assertEquals(45, sf.end);
assertEquals("uniprot", sf.featureGroup);
String gffData = "##gff-version 3\n"
+ "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
+ "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
- + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.";
+ + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
FeaturesFile featuresFile = new FeaturesFile(gffData,
FormatAdapter.PASTE);
assertTrue("Failed to parse features file",
assertEquals(1, sfs.length);
SequenceFeature sf = sfs[0];
// description parsed from Note attribute
- assertEquals("Iron-sulfur (2Fe-2S); another note", sf.description);
+ assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
assertEquals(39, sf.begin);
assertEquals(39, sf.end);
assertEquals("uniprot", sf.featureGroup);
sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
assertEquals(1, sfs.length);
sf = sfs[0];
- assertEquals("uniprot", sf.description);
+ // ID used for description if available
+ assertEquals("$23", sf.description);
assertEquals(55, sf.begin);
assertEquals(130, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("no sequences extracted from GFF3 file", 2,
dataset.getHeight());
- SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
- .findName("seq2");
+ SequenceI seq1 = dataset.findName("seq1");
+ SequenceI seq2 = dataset.findName("seq2");
assertNotNull(seq1);
assertNotNull(seq2);
assertFalse(
assertTrue(
"Didn't read the alignment into an alignframe from Gff3 File",
af != null);
- // FIXME codon mappings are on the alignment but not on the dataset
- checkDatasetfromSimpleGff3(af.getViewport().getAlignment()/* .getDataset() */);
+ checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
}
@Test(groups = { "Functional" })
checkDatasetfromSimpleGff3(dataset);
}
- /**
- * Tests loading exonerate GFF2 output, including 'similarity' alignment
- * feature, on to sequences
- */
@Test(groups = { "Functional" })
- public void testExonerateImport()
+ public void testPrintJalviewFormat() throws Exception
{
- FileLoader loader = new FileLoader(false);
- AlignFrame af = loader.LoadFileWaitTillLoaded(
- "examples/testdata/exonerateseqs.fa",
- FormatAdapter.FILE);
-
- af.loadJalviewDataFile("examples/testdata/exonerateoutput.gff",
- FormatAdapter.FILE, null, null);
-
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ Map<String, Object> colours = af.getFeatureRenderer()
+ .getFeatureColours();
+ String features = "METAL\tcc9900\n"
+ + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
+ + "Pfam\tred\n"
+ + "STARTGROUP\tuniprot\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
+ + "<html>Pfam domain<a href=\"http://pfam.sanger.ac.uk/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
+ + "ENDGROUP\tuniprot\n";
+ FeaturesFile featuresFile = new FeaturesFile(features,
+ FormatAdapter.PASTE);
+ featuresFile.parse(al.getDataset(), colours, false);
+
+ /*
+ * first with no features displayed
+ */
+ FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
+ Map<String, Object> visible = fr
+ .getDisplayedFeatureCols();
+ String exported = featuresFile.printJalviewFormat(
+ al.getSequencesArray(), visible);
+ String expected = "No Features Visible";
+ assertEquals(expected, exported);
+
+ /*
+ * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
+ */
+ fr.setVisible("METAL");
+ fr.setVisible("GAMMA-TURN");
+ visible = fr.getDisplayedFeatureCols();
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
+ visible);
+ expected = "METAL\tcc9900\n"
+ + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
+ + "\nSTARTGROUP\tuniprot\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+ + "ENDGROUP\tuniprot\n";
+ assertEquals(expected, exported);
+
+ /*
+ * now set Pfam visible
+ */
+ fr.setVisible("Pfam");
+ visible = fr.getDisplayedFeatureCols();
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
+ visible);
/*
- * verify one mapping to a dummy sequence, one to a real one
+ * note the order of feature types is uncontrolled - derives from
+ * FeaturesDisplayed.featuresDisplayed which is a HashSet
*/
- Set<AlignedCodonFrame> mappings = af
- .getViewport().getAlignment().getDataset().getCodonFrames();
- assertEquals(2, mappings.size());
- Iterator<AlignedCodonFrame> iter = mappings.iterator();
-
- // first mapping is to dummy sequence
- AlignedCodonFrame mapping = iter.next();
- Mapping[] mapList = mapping.getProtMappings();
- assertEquals(1, mapList.length);
- assertTrue(mapList[0].getTo() instanceof SequenceDummy);
- assertEquals("DDB_G0269124", mapList[0].getTo().getName());
-
- // second mapping is to a sequence in the alignment
- mapping = iter.next();
- mapList = mapping.getProtMappings();
- assertEquals(1, mapList.length);
- SequenceI proteinSeq = af.getViewport().getAlignment()
- .findName("DDB_G0280897");
- assertSame(proteinSeq.getDatasetSequence(), mapList[0].getTo());
- assertEquals(1, mapping.getdnaToProt().length);
-
- // 143 in protein should map to codon [11270, 11269, 11268] in dna
- int[] mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
- assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-
- // 182 in protein should map to codon [11153, 11152, 11151] in dna
- mappedRegion = mapList[0].getMap().locateInFrom(182, 182);
- assertArrayEquals(new int[] { 11153, 11151 }, mappedRegion);
-
- // and the reverse mapping:
- mappedRegion = mapList[0].getMap().locateInTo(11151, 11153);
- assertArrayEquals(new int[] { 182, 182 }, mappedRegion);
-
- // 11150 in dna should _not_ map to protein
- mappedRegion = mapList[0].getMap().locateInTo(11150, 11150);
- assertNull(mappedRegion);
-
- // similarly 183 in protein should _not_ map to dna
- mappedRegion = mapList[0].getMap().locateInFrom(183, 183);
- assertNull(mappedRegion);
+ expected = "METAL\tcc9900\n"
+ + "Pfam\tff0000\n"
+ + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
+ + "\nSTARTGROUP\tuniprot\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+ + "<html>Pfam domain<a href=\"http://pfam.sanger.ac.uk/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
+ + "ENDGROUP\tuniprot\n";
+ assertEquals(expected, exported);
}
}
git://source.jalview.org / jalview.git / blobdiff