+ "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
+ "<feature type=\"sequence variant\" description=\"Foo\"><variation>L</variation><variation>LMV</variation><original>M</original><location><position position=\"42\"/></location></feature>"
+ "<feature type=\"sequence variant\" description=\"Foo\"><variation>LL</variation><variation>LMV</variation><original>ML</original><location><begin position=\"42\"/><end position=\"43\"/></location></feature>"
+ + "<feature type=\"sequence variant\" description=\"Foo Too\"><variation>LL</variation><variation>LMVK</variation><original>MLML</original><location><begin position=\"42\"/><end position=\"45\"/></location></feature>"
+ "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
+ "</uniprot>";
* Check sequence features
*/
Vector<UniprotFeature> features = entry.getFeature();
- assertEquals(8, features.size());
+ assertEquals(9, features.size());
UniprotFeature sf = features.get(0);
assertEquals("signal peptide", sf.getType());
assertNull(sf.getDescription());
assertEquals(42, sf.getBegin());
assertEquals(43, sf.getEnd());
Assert.assertEquals(Uniprot.getDescription(sf),
- "p.MetLeu42LeuLeu" + "\n" + "p.MetLeu42LeuMetVal Foo"); /*
- * Check cross-references
- */
+ "p.MetLeu42LeuLeu" + "\n" + "p.MetLeu42LeuMetVal Foo");
+
+ sf = features.get(8);
+ assertEquals(42, sf.getBegin());
+ assertEquals(45, sf.getEnd());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "p.MLML42LeuLeu" + "\n" + "p.MLML42LMVK Foo Too");
+
+ /*
+ * Check cross-references
+ */
Vector<PDBEntry> xrefs = entry.getDbReference();
assertEquals(3, xrefs.size());
uf.setPosition(23);
uf.setOriginal("K");
- Vector<String> vars = new Vector();
+ Vector<String> vars = new Vector<>();
vars.add("y");
uf.setVariation(vars);
assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
+ vars.add("W");
+ assertEquals("p.Lys23Tyr\np.Lys23Trp Hello",
+ Uniprot.getDescription(uf));
+
+ /*
+ * indel cases
+ * up to 3 bases (original or variant) are shown using 3 letter code
+ */
+ vars.clear();
+ vars.add("KWE");
+ uf.setOriginal("KLS");
+ assertEquals(
+ "p.LysLeuSer23LysTrpGlu Hello",
+ Uniprot.getDescription(uf));
+
+ // adding a fourth original base switches to single letter code
+ uf.setOriginal("KLST");
+ assertEquals("p.KLST23LysTrpGlu Hello",
+ Uniprot.getDescription(uf));
+
+ // adding a fourth variant switches to a condensed representation
+ vars.clear();
+ vars.add("KWES");
+ assertEquals("p.KLST23KWES Hello", Uniprot.getDescription(uf));
+
vars.clear();
vars.add("z"); // unknown variant - fails gracefully
- uf.setVariation(vars);
+ uf.setOriginal("K");
assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
uf.setVariation(null); // variant missing - is ignored