X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;fp=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;h=b187b67f65f32f23095c81acfe5453ceb6289dc6;hb=be77f1e015d9b97391e23541850f37ea03b41b9b;hp=0ee438893bbafd3dfdf1a8253f6692cd9e174fe9;hpb=ceaa7e68d47ff6a236c7445bd99c9e8d8bd7558e;p=jalview.git
diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index 0ee4388..b187b67 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;
@@ -66,6 +67,7 @@ public class UniprotTest
+ "ML"
+ "ML"
+ "M"
+ + "LLMVM"
+ "MHAPL VSKDL"
+ "";
@@ -101,7 +103,7 @@ public class UniprotTest
* Check sequence features
*/
Vector features = entry.getFeature();
- assertEquals(6, features.size());
+ assertEquals(7, features.size());
UniprotFeature sf = features.get(0);
assertEquals("signal peptide", sf.getType());
assertNull(sf.getDescription());
@@ -141,6 +143,16 @@ public class UniprotTest
assertEquals(41, sf.getPosition());
assertEquals(41, sf.getBegin());
assertEquals(41, sf.getEnd());
+
+ sf = features.get(6);
+ assertEquals("sequence variant", sf.getType());
+ 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");
/*
* Check cross-references
*/
@@ -221,10 +233,14 @@ public class UniprotTest
uf.setPosition(23);
uf.setOriginal("K");
- uf.setVariation("y");
+ Vector vars = new Vector();
+ vars.add("y");
+ uf.setVariation(vars);
assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
- uf.setVariation("z"); // unknown variant - fails gracefully
+ vars.clear();
+ vars.add("z"); // unknown variant - fails gracefully
+ uf.setVariation(vars);
assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
uf.setVariation(null); // variant missing - is ignored