+
+ @Test(groups = { "Functional" })
+ public void testGetDetailsReport()
+ {
+ SequenceI seq = new Sequence("TestSeq", "PLRFQMD");
+ String seqName = seq.getName();
+
+ // single locus, no group, no score
+ SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22,
+ null);
+ String expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22</td></tr>"
+ + "<tr><td>Type</td><td>variant</td><td></td></tr>"
+ + "<tr><td>Description</td><td>G,C</td><td></td></tr></table>";
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+
+ // contact feature
+ sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
+ null);
+ expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>28:31</td></tr>"
+ + "<tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>"
+ + "<tr><td>Description</td><td>a description</td><td></td></tr></table>";
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+
+ sf = new SequenceFeature("variant", "G,C", 22, 33, 12.5f, "group");
+ sf.setValue("Parent", "ENSG001");
+ sf.setValue("Child", "ENSP002");
+ expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22-33</td></tr>"
+ + "<tr><td>Type</td><td>variant</td><td></td></tr>"
+ + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
+ + "<tr><td>Score</td><td>12.5</td><td></td></tr>"
+ + "<tr><td>Group</td><td>group</td><td></td></tr>"
+ + "<tr><td>Child</td><td></td><td>ENSP002</td></tr>"
+ + "<tr><td>Parent</td><td></td><td>ENSG001</td></tr></table>";
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+
+ /*
+ * feature with embedded html link in description
+ */
+ String desc = "<html>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></html>";
+ sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot");
+ expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>8-83</td></tr>"
+ + "<tr><td>Type</td><td>Pfam</td><td></td></tr>"
+ + "<tr><td>Description</td><td>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></td><td></td></tr>"
+ + "<tr><td>Group</td><td>Uniprot</td><td></td></tr></table>";
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+ }
+
+ /**
+ * Feature details report for a virtual feature should include original and
+ * mapped locations, and also derived peptide consequence if it can be
+ * determined
+ */
+ @Test(groups = { "Functional" })
+ public void testGetDetailsReport_virtualFeature()
+ {
+ SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
+ SequenceI seq = new Sequence("TestSeq/8-14", "PLRFQMD");
+ MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
+ 3, 1);
+ Mapping mapping = new Mapping(seq, map);
+ List<SequenceFeature> features = new ArrayList<>();
+ // vary ttg (Leu) to ttc (Phe)
+ SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
+ null);
+ sf.setValue("alleles", "G,C"); // needed to compute peptide consequence!
+ features.add(sf);
+
+ MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
+
+ String expected = "<br><table><tr><td>Location</td><td>Cds</td><td>106</td></tr>"
+ + "<tr><td>Peptide Location</td><td>TestSeq</td><td>9</td></tr>"
+ + "<tr><td>Type</td><td>variant</td><td></td></tr>"
+ + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
+ + "<tr><td>Consequence</td><td><i>Translated by Jalview</i></td><td>p.Leu9Phe</td></tr>"
+ + "<tr><td>alleles</td><td></td><td>G,C</td></tr>" + "</table>";
+
+ assertEquals(expected, sf.getDetailsReport(seq.getName(), mf));
+
+ /*
+ * exon feature extending beyond mapped range; mapped location should be
+ * restricted to peptide mapped range limit i.e. 10-13
+ */
+ SequenceFeature sf2 = new SequenceFeature("exon", "exon 1", 109, 230,
+ null);
+ features.add(sf2);
+ expected = "<br><table><tr><td>Location</td><td>Cds</td><td>109-230</td></tr>"
+ + "<tr><td>Peptide Location</td><td>TestSeq</td><td>10-13</td></tr>"
+ + "<tr><td>Type</td><td>exon</td><td></td></tr>"
+ + "<tr><td>Description</td><td>exon 1</td><td></td></tr>"
+ + "</table>";
+ assertEquals(expected, sf2.getDetailsReport(seq.getName(), mf));
+ }