+
+ private void checkDatasetfromSimpleGff3(AlignmentI dataset)
+ {
+ assertEquals("no sequences extracted from GFF3 file", 2,
+ dataset.getHeight());
+
+ SequenceI seq1 = dataset.findName("seq1");
+ SequenceI seq2 = dataset.findName("seq2");
+ assertNotNull(seq1);
+ assertNotNull(seq2);
+ assertFalse(
+ "Failed to replace dummy seq1 with real sequence",
+ seq1 instanceof SequenceDummy
+ && ((SequenceDummy) seq1).isDummy());
+ 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 seq1",
+ placeholderseq.equals(seq1.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().length);
+ assertNull(seq2.getSequenceFeatures());
+ assertEquals(
+ "Wrong number of features",
+ 0,
+ seq2.getSequenceFeatures() == null ? 0 : seq2
+ .getSequenceFeatures().length);
+ assertTrue(
+ "Expected at least one CDNA/Protein mapping for seq1",
+ dataset.getCodonFrame(seq1) != null
+ && dataset.getCodonFrame(seq1).size() > 0);
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void readGff3File() throws IOException
+ {
+ FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
+ FormatAdapter.FILE);
+ Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
+ gffreader.addProperties(dataset);
+ checkDatasetfromSimpleGff3(dataset);
+ }
+
+ @Test(groups = { "Functional" })
+ public void simpleGff3FileClass() throws IOException
+ {
+ AlignmentI dataset = new Alignment(new SequenceI[] {});
+ FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.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, FormatAdapter.FILE);
+ assertTrue(
+ "Didn't read the alignment into an alignframe from Gff3 File",
+ af != null);
+ checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
+ }
+
+ @Test(groups = { "Functional" })
+ public void simpleGff3RelaxedIdMatching() throws IOException
+ {
+ AlignmentI dataset = new Alignment(new SequenceI[] {});
+ FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
+
+ boolean parseResult = ffile.parse(dataset, null, false, true);
+ assertTrue("return result (relaxedID matching) should be true",
+ parseResult);
+ checkDatasetfromSimpleGff3(dataset);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testPrintJalviewFormat() throws Exception
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ Map<String, FeatureColourI> 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.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);
+ featuresFile.parse(al.getDataset(), colours, false);
+
+ /*
+ * first with no features displayed
+ */
+ FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
+ Map<String, FeatureColourI> 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);
+ /*
+ * note the order of feature types is uncontrolled - derives from
+ * FeaturesDisplayed.featuresDisplayed which is a HashSet
+ */
+ 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.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);
+ }