+ 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.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.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.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);