+ FeatureSettingsBean[] data = new FeatureSettingsBean[1];
+ data[0] = new FeatureSettingsBean("Cath", fc, null, false);
+ fr.setFeaturePriority(data);
+ assertEquals(fr.getColour(sf1), Color.red);
+ data[0] = new FeatureSettingsBean("Cath", fc, null, true);
+ fr.setFeaturePriority(data);
+ assertEquals(fr.getColour(sf1), Color.red);
+
+ /*
+ * hide feature group, then unhide
+ */
+ fr.setGroupVisibility("group1", false);
+ assertNull(fr.getColour(sf1));
+ fr.setGroupVisibility("group1", true);
+ assertEquals(fr.getColour(sf1), Color.red);
+
+ /*
+ * graduated colour by score, no threshold, no score
+ *
+ */
+ FeatureColourI gc = new FeatureColour(Color.red, Color.yellow,
+ Color.red, Color.green, 1f, 11f);
+ fr.getFeatureColours().put("Cath", gc);
+ assertEquals(fr.getColour(sf1), Color.green);
+
+ /*
+ * graduated colour by score, no threshold, with score value
+ */
+ SequenceFeature sf2 = new SequenceFeature("Cath", "", 6, 8, 6f,
+ "group1");
+ // score 6 is half way from yellow(255, 255, 0) to red(255, 0, 0)
+ Color expected = new Color(255, 128, 0);
+ assertEquals(fr.getColour(sf2), expected);
+
+ /*
+ * above threshold, score is above threshold - no change
+ */
+ gc.setAboveThreshold(true);
+ gc.setThreshold(5f);
+ assertEquals(fr.getColour(sf2), expected);
+
+ /*
+ * threshold is min-max; now score 6 is 1/6 of the way from 5 to 11
+ * or from yellow(255, 255, 0) to red(255, 0, 0)
+ */
+ gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
+ 5f, 11f);
+ fr.getFeatureColours().put("Cath", gc);
+ gc.setAutoScaled(false); // this does little other than save a checkbox setting!
+ assertEquals(fr.getColour(sf2), new Color(255, 213, 0));
+
+ /*
+ * feature score is below threshold - no colour
+ */
+ gc.setAboveThreshold(true);
+ gc.setThreshold(7f);
+ assertNull(fr.getColour(sf2));
+
+ /*
+ * feature score is above threshold - no colour
+ */
+ gc.setBelowThreshold(true);
+ gc.setThreshold(3f);
+ assertNull(fr.getColour(sf2));
+
+ /*
+ * colour by feature attribute value
+ * first with no value held
+ */
+ gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
+ 1f, 11f);
+ fr.getFeatureColours().put("Cath", gc);
+ gc.setAttributeName("AF");
+ assertEquals(fr.getColour(sf2), Color.green);
+
+ // with non-numeric attribute value
+ sf2.setValue("AF", "Five");
+ assertEquals(fr.getColour(sf2), Color.green);
+
+ // with numeric attribute value
+ sf2.setValue("AF", "6");
+ assertEquals(fr.getColour(sf2), expected);
+
+ // with numeric value outwith threshold
+ gc.setAboveThreshold(true);
+ gc.setThreshold(10f);
+ assertNull(fr.getColour(sf2));
+
+ // with filter on AF < 4
+ gc.setAboveThreshold(false);
+ assertEquals(fr.getColour(sf2), expected);
+ FeatureMatcherSetI filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.LT, "4.0", "AF"));
+ fr.setFeatureFilter("Cath", filter);
+ assertNull(fr.getColour(sf2));
+
+ // with filter on 'Consequence contains missense'
+ filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Contains, "missense",
+ "Consequence"));
+ fr.setFeatureFilter("Cath", filter);
+ // if feature has no Consequence attribute, no colour
+ assertNull(fr.getColour(sf2));
+ // if attribute does not match filter, no colour
+ sf2.setValue("Consequence", "Synonymous");
+ assertNull(fr.getColour(sf2));
+ // attribute matches filter
+ sf2.setValue("Consequence", "Missense variant");
+ assertEquals(fr.getColour(sf2), expected);
+
+ // with filter on CSQ:Feature contains "ENST01234"
+ filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Matches, "ENST01234",
+ "CSQ", "Feature"));
+ fr.setFeatureFilter("Cath", filter);
+ // if feature has no CSQ data, no colour
+ assertNull(fr.getColour(sf2));
+ // if CSQ data does not include Feature, no colour
+ Map<String, String> csqData = new HashMap<>();
+ csqData.put("BIOTYPE", "Transcript");
+ sf2.setValue("CSQ", csqData);
+ assertNull(fr.getColour(sf2));
+ // if attribute does not match filter, no colour
+ csqData.put("Feature", "ENST9876");
+ assertNull(fr.getColour(sf2));
+ // attribute matches filter
+ csqData.put("Feature", "ENST01234");
+ assertEquals(fr.getColour(sf2), expected);
+ }
+
+ @Test(groups = "Functional")
+ public void testIsVisible()
+ {
+ String seqData = ">s1\nMLQGIFPRS\n";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+ DataSourceType.PASTE);
+ AlignViewportI av = af.getViewport();
+ FeatureRenderer fr = new FeatureRenderer(av);
+ SequenceI seq = av.getAlignment().getSequenceAt(0);
+ SequenceFeature sf = new SequenceFeature("METAL", "Desc", 10, 10, 1f,
+ "Group");
+ sf.setValue("AC", "11");
+ sf.setValue("CLIN_SIG", "Likely Pathogenic");
+ seq.addSequenceFeature(sf);
+
+ assertFalse(fr.isVisible(null));
+
+ /*
+ * initial state FeatureRenderer hasn't 'found' feature
+ * and so its feature type has not yet been set visible
+ */
+ assertFalse(fr.getDisplayedFeatureCols().containsKey("METAL"));
+ assertFalse(fr.isVisible(sf));
+
+ fr.findAllFeatures(true);
+ assertTrue(fr.isVisible(sf));
+
+ /*
+ * feature group not visible
+ */
+ fr.setGroupVisibility("Group", false);
+ assertFalse(fr.isVisible(sf));
+ fr.setGroupVisibility("Group", true);
+ assertTrue(fr.isVisible(sf));
+
+ /*
+ * feature score outwith colour threshold (score > 2)
+ */
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
+ Color.white, 0, 10);
+ fc.setAboveThreshold(true);
+ fc.setThreshold(2f);
+ fr.setColour("METAL", fc);
+ assertFalse(fr.isVisible(sf)); // score 1 is not above threshold 2
+ fc.setBelowThreshold(true);
+ assertTrue(fr.isVisible(sf)); // score 1 is below threshold 2
+
+ /*
+ * colour with threshold on attribute AC (value is 11)
+ */
+ fc.setAttributeName("AC");
+ assertFalse(fr.isVisible(sf)); // value 11 is not below threshold 2
+ fc.setAboveThreshold(true);
+ assertTrue(fr.isVisible(sf)); // value 11 is above threshold 2
+
+ fc.setAttributeName("AF"); // attribute AF is absent in sf
+ assertTrue(fr.isVisible(sf)); // feature is not excluded by threshold
+
+ FeatureMatcherSetI filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Contains, "pathogenic",
+ "CLIN_SIG"));
+ fr.setFeatureFilter("METAL", filter);
+ assertTrue(fr.isVisible(sf)); // feature matches filter
+ filter.and(FeatureMatcher.byScore(Condition.LE, "0.4"));
+ assertFalse(fr.isVisible(sf)); // feature doesn't match filter