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,
{
assertEquals("no sequences extracted from GFF3 file", 2,
dataset.getHeight());
-
+
SequenceI seq1 = dataset.findName("seq1");
SequenceI seq2 = dataset.findName("seq2");
assertNotNull(seq1);
"Expected at least one CDNA/Protein mapping for seq1",
dataset.getCodonFrame(seq1) != null
&& dataset.getCodonFrame(seq1).size() > 0);
-
+
}
@Test(groups = { "Functional" })
public void simpleGff3FileClass() throws IOException
{
AlignmentI dataset = new Alignment(new SequenceI[] {});
- FeaturesFile ffile = new FeaturesFile(simpleGffFile,
- FormatAdapter.FILE);
-
+ FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
+
boolean parseResult = ffile.parse(dataset, null, false, false);
assertTrue("return result should be true", parseResult);
checkDatasetfromSimpleGff3(dataset);
public void simpleGff3RelaxedIdMatching() throws IOException
{
AlignmentI dataset = new Alignment(new SequenceI[] {});
- FeaturesFile ffile = new FeaturesFile(simpleGffFile,
- FormatAdapter.FILE);
-
+ FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
+
boolean parseResult = ffile.parse(dataset, null, false, true);
assertTrue("return result (relaxedID matching) should be true",
parseResult);
* first with no features displayed
*/
FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
- Map<String, FeatureColourI> visible = fr
- .getDisplayedFeatureCols();
+ Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
String exported = featuresFile.printJalviewFormat(
al.getSequencesArray(), visible);
String expected = "No Features Visible";