X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;h=060c3032f2abf456765a2d516c359c59843773c8;hb=2a86b2b3d7b5e8ad3f23d7895637cbfb24685fac;hp=b70e5811642536bff2d2084e9e8dafa734609d12;hpb=0cddb5c5bf43803985172d28a09597563ec4ae7b;p=jalview.git
diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index b70e581..060c303 100644
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -35,6 +35,7 @@ import java.io.Reader;
import java.io.StringReader;
import java.util.Vector;
+import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@@ -67,6 +68,8 @@ public class UniprotTest
+ "ML"
+ "M"
+ "LLMVM"
+ + "LLLMVML"
+ + "LLLMVKMLML"
+ "MHAPL VSKDL"
+ "";
@@ -102,7 +105,7 @@ public class UniprotTest
* Check sequence features
*/
Vector features = entry.getFeature();
- assertEquals(7, features.size());
+ assertEquals(9, features.size());
UniprotFeature sf = features.get(0);
assertEquals("signal peptide", sf.getType());
assertNull(sf.getDescription());
@@ -124,33 +127,50 @@ public class UniprotTest
sf = features.get(3);
assertEquals("sequence variant", sf.getType());
- assertEquals("Variation: 'L' Original: 'M'", sf.getDescription());
+ assertNull(sf.getDescription());
assertEquals(41, sf.getPosition());
assertEquals(41, sf.getBegin());
assertEquals(41, sf.getEnd());
sf = features.get(4);
assertEquals("sequence variant", sf.getType());
- assertEquals("Pathogenic Variation: 'L' Original: 'M'",
- sf.getDescription());
+ assertEquals("Pathogenic", sf.getDescription());
assertEquals(41, sf.getPosition());
assertEquals(41, sf.getBegin());
assertEquals(41, sf.getEnd());
sf = features.get(5);
assertEquals("sequence variant", sf.getType());
- assertEquals("Pathogenic Original: 'M'", sf.getDescription());
+ assertEquals("Pathogenic", sf.getDescription());
assertEquals(41, sf.getPosition());
assertEquals(41, sf.getBegin());
assertEquals(41, sf.getEnd());
sf = features.get(6);
assertEquals("sequence variant", sf.getType());
- assertEquals("Foo Variation: 'L', Variation: 'LMV' Original: 'M'",
+ assertEquals("Foo",
sf.getDescription());
assertEquals(42, sf.getPosition());
assertEquals(42, sf.getBegin());
assertEquals(42, sf.getEnd());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "p.Met42Leu" + "
"
+ + "p.Met42LeuMetVal Foo");
+
+ sf = features.get(7);
+ assertEquals(42, sf.getBegin());
+ assertEquals(43, sf.getEnd());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "p.MetLeu42LeuLeu" + "
"
+ + "p.MetLeu42LeuMetVal Foo");
+
+ sf = features.get(8);
+ assertEquals(42, sf.getBegin());
+ assertEquals(45, sf.getEnd());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "p.MLML42LeuLeu" + "
"
+ + "p.MLML42LMVK Foo Too");
+
/*
* Check cross-references
*/
@@ -219,4 +239,53 @@ public class UniprotTest
assertEquals(expectedDescription,
Uniprot.getUniprotEntryDescription(entry));
}
+
+ @Test(groups = { "Functional" })
+ public void testGetDescription()
+ {
+ UniprotFeature uf = new UniprotFeature();
+ assertEquals("", Uniprot.getDescription(uf));
+
+ uf.setDescription("Hello");
+ assertEquals("Hello", Uniprot.getDescription(uf));
+
+ uf.setPosition(23);
+ uf.setOriginal("K");
+ Vector vars = new Vector<>();
+ vars.add("y");
+ uf.setVariation(vars);
+ assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
+
+ // multiple variants generate an html description over more than one line
+ vars.add("W");
+ assertEquals("p.Lys23Tyr
p.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 single letter code
+ vars.clear();
+ vars.add("KWES");
+ assertEquals("p.KLST23KWES Hello", Uniprot.getDescription(uf));
+
+ vars.clear();
+ vars.add("z"); // unknown variant - fails gracefully
+ uf.setOriginal("K");
+ assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
+
+ uf.setVariation(null); // variant missing - is ignored
+ assertEquals("Hello", Uniprot.getDescription(uf));
+ }
}