Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
FeaturesFile featuresFile = new FeaturesFile(
- "examples/exampleFeatures.txt", FormatAdapter.FILE);
+ "examples/exampleFeatures.txt", DataSourceType.FILE);
assertTrue("Test " + "Features file test"
+ "\nFailed to parse features file.",
featuresFile.parse(al.getDataset(), colours, true));
*/
SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
.getSequenceFeatures(); // FER_CAPAA
- assertEquals(7, sfs.length);
+ assertEquals(8, sfs.length);
SequenceFeature sf = sfs[0];
+ assertEquals("Pfam family%LINK%", sf.description);
+ assertEquals(0, sf.begin);
+ assertEquals(0, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("Pfam", sf.type);
+ assertEquals(1, sf.links.size());
+ assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
+ sf.links.get(0));
+
+ sf = sfs[1];
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(39, sf.begin);
assertEquals(39, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- sf = sfs[1];
+ sf = sfs[2];
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(44, sf.begin);
assertEquals(44, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- sf = sfs[2];
+ sf = sfs[3];
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(47, sf.begin);
assertEquals(47, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- sf = sfs[3];
+ sf = sfs[4];
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(77, sf.begin);
assertEquals(77, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- sf = sfs[4];
+ sf = sfs[5];
assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
sf.description);
- assertEquals("Pfam 8_8|http://pfam.sanger.ac.uk/family/PF00111",
- sf.links.get(0).toString());
+ assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
+ sf.links.get(0));
assertEquals(8, sf.begin);
assertEquals(83, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("Pfam", sf.type);
- sf = sfs[5];
+ sf = sfs[6];
assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
assertEquals(3, sf.begin);
assertEquals(93, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("Cath", sf.type);
- sf = sfs[6];
+ sf = sfs[7];
assertEquals(
"High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
sf.description);
assertEquals(
"PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
- sf.links.get(0).toString());
+ sf.links.get(0));
assertEquals(89, sf.begin);
assertEquals(89, sf.end);
assertEquals("netphos", sf.featureGroup);
+ "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,
- FormatAdapter.PASTE);
+ DataSourceType.PASTE);
assertTrue("Failed to parse features file",
featuresFile.parse(al.getDataset(), colours, true));
String ff = f.getPath();
FormatAdapter rf = new FormatAdapter();
- AlignmentI al = rf.readFile(ff, FormatAdapter.FILE,
- new IdentifyFile().identify(ff, FormatAdapter.FILE));
+ AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
+ new IdentifyFile().identify(ff, DataSourceType.FILE));
al.setDataset(null); // creates dataset sequences
assertNotNull("Couldn't read supplied alignment data.", al);
+ "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.\tID=$23";
FeaturesFile featuresFile = new FeaturesFile(gffData,
- FormatAdapter.PASTE);
+ DataSourceType.PASTE);
assertTrue("Failed to parse features file",
featuresFile.parse(al.getDataset(), colours, true));
String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
FeaturesFile featuresFile = new FeaturesFile(featureData,
- FormatAdapter.PASTE);
+ DataSourceType.PASTE);
assertTrue("Failed to parse features file",
featuresFile.parse(al.getDataset(), colours, true));
public void readGff3File() throws IOException
{
FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
- FormatAdapter.FILE);
+ DataSourceType.FILE);
Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
gffreader.addProperties(dataset);
checkDatasetfromSimpleGff3(dataset);
{
AlignmentI dataset = new Alignment(new SequenceI[] {});
FeaturesFile ffile = new FeaturesFile(simpleGffFile,
- FormatAdapter.FILE);
+ DataSourceType.FILE);
boolean parseResult = ffile.parse(dataset, null, false, false);
assertTrue("return result should be true", parseResult);
public void simpleGff3FileLoader() throws IOException
{
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
- simpleGffFile, FormatAdapter.FILE);
+ 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,
- FormatAdapter.FILE);
+ DataSourceType.FILE);
boolean parseResult = ffile.parse(dataset, null, false, true);
assertTrue("return result (relaxedID matching) should be true",
+ "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"
+ + "<html>Pfam domain<a href=\"http://pfam.xfam.org/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);
+ DataSourceType.PASTE);
featuresFile.parse(al.getDataset(), colours, false);
/*
+ "\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"
+ + "<html>Pfam domain<a href=\"http://pfam.xfam.org/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