import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.gui.JvOptionPane;
+import java.util.ArrayList;
+import java.util.List;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
+
public class SequenceFeatureTest
{
@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>Type</td><td>variant</td><td></td></tr>"
- + "<tr><td>Start/end</td><td>22</td><td></td></tr>"
+ 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());
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
// contact feature
sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
null);
- expected = "<br><table><tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>"
- + "<tr><td>Start/end</td><td>28:31</td><td></td></tr>"
+ 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());
+ 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>Type</td><td>variant</td><td></td></tr>"
- + "<tr><td>Start/end</td><td>22-33</td><td></td></tr>"
+ 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());
+ 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>Type</td><td>Pfam</td><td></td></tr>"
- + "<tr><td>Start/end</td><td>8-83</td><td></td></tr>"
+ 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());
+ 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));
}
}