.getFeatureColours();
FeaturesFile featuresFile = new FeaturesFile(
"examples/exampleFeatures.txt", DataSourceType.FILE);
- assertTrue("Test " + "Features file test"
- + "\nFailed to parse features file.",
+ assertTrue(
+ "Test " + "Features file test"
+ + "\nFailed to parse features file.",
featuresFile.parse(al.getDataset(), colours, true));
/*
Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
// GFF2 uses space as name/value separator in column 9
- String gffData = "METAL\tcc9900\n"
- + "GFF\n"
+ String gffData = "METAL\tcc9900\n" + "GFF\n"
+ "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
+ "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
FeaturesFile featuresFile = new FeaturesFile(gffData,
Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
// GFF3 uses '=' separator for name/value pairs in column 9
- // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in values
+ // 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,and another;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465;"
assertEquals("21", sf.getValueAsString("CSQ", "AF"));
assertEquals("benign,possibly_damaging",
sf.getValueAsString("CSQ", "POLYPHEN"));
- assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url decoded
+ assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url
+ // decoded
// todo change STRAND and !Phase into fields of SequenceFeature instead
assertEquals(".", sf.otherDetails.get("STRAND"));
assertEquals(0, sf.getStrand());
SequenceI seq2 = dataset.findName("seq2");
assertNotNull(seq1);
assertNotNull(seq2);
- assertFalse(
- "Failed to replace dummy seq1 with real sequence",
+ assertFalse("Failed to replace dummy seq1 with real sequence",
seq1 instanceof SequenceDummy
&& ((SequenceDummy) seq1).isDummy());
- assertFalse(
- "Failed to replace dummy seq2 with real sequence",
+ assertFalse("Failed to replace dummy seq2 with real sequence",
seq2 instanceof SequenceDummy
&& ((SequenceDummy) seq2).isDummy());
String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
assertFalse("dummy replacement buggy for seq2",
placeholderseq.equals(seq2.getSequenceAsString()));
assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
- assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
- .size());
+ assertEquals("Wrong number of features", 3,
+ seq1.getSequenceFeatures().size());
assertTrue(seq2.getSequenceFeatures().isEmpty());
- assertEquals(
- "Wrong number of features",
- 0,
- seq2.getSequenceFeatures() == null ? 0 : seq2
- .getSequenceFeatures().size());
- assertTrue(
- "Expected at least one CDNA/Protein mapping for seq1",
+ assertEquals("Wrong number of features", 0,
+ seq2.getSequenceFeatures() == null ? 0
+ : seq2.getSequenceFeatures().size());
+ assertTrue("Expected at least one CDNA/Protein mapping for seq1",
dataset.getCodonFrame(seq1) != null
&& dataset.getCodonFrame(seq1).size() > 0);
AlignmentI dataset = new Alignment(new SequenceI[] {});
FeaturesFile ffile = new FeaturesFile(simpleGffFile,
DataSourceType.FILE);
-
+
boolean parseResult = ffile.parse(dataset, null, false, false);
assertTrue("return result should be true", parseResult);
checkDatasetfromSimpleGff3(dataset);
@Test(groups = { "Functional" })
public void simpleGff3FileLoader() throws IOException
{
- AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
- simpleGffFile, DataSourceType.FILE);
+ AlignFrame af = new FileLoader(false)
+ .LoadFileWaitTillLoaded(simpleGffFile, DataSourceType.FILE);
assertTrue(
"Didn't read the alignment into an alignframe from Gff3 File",
af != null);
AlignmentI dataset = new Alignment(new SequenceI[] {});
FeaturesFile ffile = new FeaturesFile(simpleGffFile,
DataSourceType.FILE);
-
+
boolean parseResult = ffile.parse(dataset, null, false, true);
assertTrue("return result (relaxedID matching) should be true",
parseResult);
.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"
+ + "Pfam\tred\n" + "STARTGROUP\tuniprot\n"
+ "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
+ "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
* empty feature group to check handled correctly
*/
SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
- seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
- null));
- seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
- Float.NaN, null));
+ seq.addSequenceFeature(
+ new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f, null));
+ seq.addSequenceFeature(
+ new SequenceFeature("Pfam", "desc2", 4, 9, Float.NaN, null));
seq = al.getSequenceAt(2); // FER1_SOLLC
- seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
- Float.NaN, ""));
- seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
- -2.6f, ""));
+ seq.addSequenceFeature(
+ new SequenceFeature("Pfam", "desc3", 0, 0, Float.NaN, ""));
+ seq.addSequenceFeature(
+ new SequenceFeature("Pfam", "desc4", 5, 8, -2.6f, ""));
/*
* first with no features displayed, exclude non-positional features
/*
* features are output within group, ordered by sequence and type
*/
- expected = "METAL\tcc9900\n"
- + "Pfam\tff0000\n"
+ expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
+ "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+ "\nSTARTGROUP\tuniprot\n"
+ "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
fr, false, false);
String gffHeader = "##gff-version 2\n";
assertEquals(gffHeader, exported);
- exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
- true, false);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, true,
+ false);
assertEquals(gffHeader, exported);
/*
new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
al.getSequenceAt(0).addSequenceFeature(
new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
- al.getSequenceAt(1)
- .addSequenceFeature(
- new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
- "s3dm"));
+ al.getSequenceAt(1).addSequenceFeature(new SequenceFeature("GAMMA-TURN",
+ "Turn", 36, 38, 2.1f, "s3dm"));
SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
"Uniprot");
sf.setStrand("+");
*/
fr.setGroupVisibility("Uniprot", true);
fr.setGroupVisibility("s3dm", false);
- exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
- true, false);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, true,
+ false);
String expected = gffHeader
+ "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
assertEquals(expected, exported);
exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
false, false);
// Pfam feature columns include strand(+), phase(2), attributes
- expected = gffHeader
- + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
- // CSQ output as CSQ=att1=value1,att2=value2
- // note all commas are encoded here which is wrong - it should be
- // SIFT=benign,mostly benign,cloudy%2C with meatballs
+ expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ // CSQ output as CSQ=att1=value1,att2=value2
+ // note all commas are encoded here which is wrong - it should be
+ // SIFT=benign,mostly benign,cloudy%2C with meatballs
+ "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white;"
+ "CSQ=SIFT=benign%2Cmostly benign%2Ccloudy%2C with meatballs,consequence=missense_variant\n"
+ "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
sf2.setValue("clin_sig", "Benign");
sf2.setValue("AF", "46");
al.getSequenceAt(0).addSequenceFeature(sf2);
-
+
FeaturesFile featuresFile = new FeaturesFile();
FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
final String gffHeader = "##gff-version 2\n";
sf2.setValue("clin_sig", "Benign");
sf2.setValue("AF", "46");
al.getSequenceAt(0).addSequenceFeature(sf2);
-
+
FeaturesFile featuresFile = new FeaturesFile();
FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
fr.findAllFeatures(true);
-
+
fr.setVisible("METAL");
fr.setColour("METAL", new FeatureColour(Color.PINK));
- String exported = featuresFile.printJalviewFormat(
- al.getSequencesArray(),
- fr, false, false);
+ String exported = featuresFile
+ .printJalviewFormat(al.getSequencesArray(), fr, false, false);
String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
+ "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
+ "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
+ "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
+ "ENDGROUP\tgrp2\n";
assertEquals(expected, exported);
-
+
/*
* now threshold to Score > 1.1 - should exclude sf2
* (and there should be no empty STARTGROUP/ENDGROUP output)
+ "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
+ "ENDGROUP\tgrp1\n";
assertEquals(expected, exported);
-
+
/*
* remove threshold and check sf2 is exported
*/
+ "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
+ "ENDGROUP\tgrp2\n";
assertEquals(expected, exported);
-
+
/*
* filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
*/
git://source.jalview.org / jalview.git / blobdiff