AlignFrame af = new AlignFrame(al, 500, 500);
Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
- // GFF3 uses '=' separator for name/value pairs in colum 9
+ // GFF3 uses '=' separator for name/value pairs in column 9
+ // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in values
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"
+ + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465\n"
+ "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
FeaturesFile featuresFile = new FeaturesFile(gffData,
DataSourceType.PASTE);
assertEquals(39, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- assertEquals(
- "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
- sf.getValue("ATTRIBUTES"));
+ assertEquals(4, sf.otherDetails.size());
+ assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465",
+ sf.otherDetails.get("evidence"));
+ assertEquals("Iron-sulfur (2Fe-2S),another note",
+ sf.otherDetails.get("Note"));
+ assertEquals(".", sf.otherDetails.get("STRAND"));
+ assertEquals(".", sf.otherDetails.get("!Phase"));
// verify feature on FER1_SOLLC1
sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
"s3dm"));
SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
"Uniprot");
- sf.setAttributes("x=y;black=white");
sf.setStrand("+");
sf.setPhase("2");
+ sf.setValue("x", "y");
+ sf.setValue("black", "white");
al.getSequenceAt(1).addSequenceFeature(sf);
/*
String exported = featuresFile.printGffFormat(al.getSequencesArray(),
fr, false, false);
String expected = gffHeader
- + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
- + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+ + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
+ + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
assertEquals(expected, exported);
/*
fr.setColour("METAL", fc);
exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
false, false);
- expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
+ expected = gffHeader
+ + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n";
assertEquals(expected, exported);
/*
fc.setAboveThreshold(false);
exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
false, false);
- expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
- + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+ expected = gffHeader
+ + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
+ + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
assertEquals(expected, exported);
/*
fr.setFeatureFilter("METAL", filter);
exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
false, false);
- expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+ expected = gffHeader
+ + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
assertEquals(expected, exported);
}