+
+ @Test(groups = { "Functional" })
+ public void testOutputFeatureFilters()
+ {
+ FeaturesFile ff = new FeaturesFile();
+ StringBuilder sb = new StringBuilder();
+ Map<String, FeatureColourI> visible = new HashMap<>();
+ visible.put("pfam", new FeatureColour(Color.red));
+ Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
+
+ // with no filters, nothing is output
+ ff.outputFeatureFilters(sb, visible, featureFilters);
+ assertEquals("", sb.toString());
+
+ // with filter for not visible features only, nothing is output
+ FeatureMatcherSet filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byLabel(Condition.Present, null));
+ featureFilters.put("foobar", filter);
+ ff.outputFeatureFilters(sb, visible, featureFilters);
+ assertEquals("", sb.toString());
+
+ // with filters for visible feature types
+ FeatureMatcherSet filter2 = new FeatureMatcherSet();
+ filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
+ "PolyPhen"));
+ filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
+ featureFilters.put("pfam", filter2);
+ visible.put("foobar", new FeatureColour(Color.blue));
+ ff.outputFeatureFilters(sb, visible, featureFilters);
+ String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
+ assertEquals(expected, sb.toString());
+ }
+
+ /**
+ * Output as GFF should not include features which are not visible due to
+ * colour threshold or feature filter settings
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testPrintGffFormat_withFilters() throws Exception
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
+ null);
+ sf1.setValue("clin_sig", "Likely Pathogenic");
+ sf1.setValue("AF", "24");
+ al.getSequenceAt(0).addSequenceFeature(sf1);
+ SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
+ null);
+ 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";
+
+ fr.setVisible("METAL");
+ fr.setColour("METAL", new FeatureColour(Color.PINK));
+ String exported = featuresFile.printGffFormat(al.getSequencesArray(),
+ fr, false, false);
+ String 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);
+
+ /*
+ * now threshold to Score > 1.1 - should exclude sf2
+ */
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
+ Color.white, 0f, 2f);
+ fc.setAboveThreshold(true);
+ fc.setThreshold(1.1f);
+ fr.setColour("METAL", fc);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false, false);
+ expected = gffHeader
+ + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n";
+ assertEquals(expected, exported);
+
+ /*
+ * remove threshold and check sf2 is exported
+ */
+ fc.setAboveThreshold(false);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false, false);
+ 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);
+
+ /*
+ * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
+ */
+ FeatureMatcherSetI filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
+ "clin_sig"));
+ fr.setFeatureFilter("METAL", filter);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false, false);
+ expected = gffHeader
+ + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
+ assertEquals(expected, exported);
+ }
+
+ /**
+ * Output as Jalview should not include features which are not visible due to
+ * colour threshold or feature filter settings
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testPrintJalviewFormat_withFilters() throws Exception
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
+ "grp1");
+ sf1.setValue("clin_sig", "Likely Pathogenic");
+ sf1.setValue("AF", "24");
+ al.getSequenceAt(0).addSequenceFeature(sf1);
+ SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
+ "grp2");
+ 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 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)
+ */
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
+ Color.white, 0f, 2f);
+ fc.setAboveThreshold(true);
+ fc.setThreshold(1.1f);
+ fr.setColour("METAL", fc);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false, false);
+ expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
+ + "STARTGROUP\tgrp1\n"
+ + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
+ + "ENDGROUP\tgrp1\n";
+ assertEquals(expected, exported);
+
+ /*
+ * remove threshold and check sf2 is exported
+ */
+ fc.setAboveThreshold(false);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false, false);
+ expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
+ + "STARTGROUP\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);
+
+ /*
+ * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
+ */
+ FeatureMatcherSetI filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
+ "clin_sig"));
+ fr.setFeatureFilter("METAL", filter);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false, false);
+ expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+ expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
+ + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
+ + "STARTGROUP\tgrp2\n"
+ + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
+ + "ENDGROUP\tgrp2\n";
+ assertEquals(expected, exported);
+ }