X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;h=c7f216e7cd33ce0ef185ebc559ff44f71bc3ed04;hb=11f6e7a63cc627f5dffb0dd382343bd99d15121c;hp=2d4be719173e0d9b1822a4e0efad3565401b8975;hpb=e957648a02a9e25795a92a4f39a5e3c1e7adb230;p=jalview.git
diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index 2d4be71..c7f216e 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;
@@ -63,6 +64,11 @@ public class UniprotTest
+ ""
+ ""
+ ""
+ + "ML"
+ + "ML"
+ + "M"
+ + "LLMVM"
+ + "LLLMVML"
+ "MHAPL VSKDL"
+ "";
@@ -98,7 +104,7 @@ public class UniprotTest
* Check sequence features
*/
Vector features = entry.getFeature();
- assertEquals(3, features.size());
+ assertEquals(8, features.size());
UniprotFeature sf = features.get(0);
assertEquals("signal peptide", sf.getType());
assertNull(sf.getDescription());
@@ -118,9 +124,44 @@ public class UniprotTest
assertEquals(21, sf.getBegin());
assertEquals(247, sf.getEnd());
- /*
- * Check cross-references
- */
+ sf = features.get(3);
+ assertEquals("sequence variant", sf.getType());
+ 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", 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", 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",
+ sf.getDescription());
+ assertEquals(42, sf.getPosition());
+ assertEquals(42, sf.getBegin());
+ assertEquals(42, sf.getEnd());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "p.Met42Leu" + "\n" + "p.Met42LeuMetVal Foo");
+
+ sf = features.get(7);
+ assertEquals(42, sf.getBegin());
+ assertEquals(43, sf.getEnd());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "p.MetLeu42LeuLeu" + "\n" + "p.MetLeu42LeuMetVal Foo"); /*
+ * Check cross-references
+ */
Vector xrefs = entry.getDbReference();
assertEquals(3, xrefs.size());
@@ -163,11 +204,11 @@ public class UniprotTest
new StringReader(UNIPROT_XML)).get(0);
/*
- * name formatted as source | accession ids | names
- * source database converted to Jalview canonical name
+ * name formatted with Uniprot Entry name
*/
- String expectedName = "UNIPROT|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
- assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
+ String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
+ assertEquals(expectedName,
+ Uniprot.getUniprotEntryId(entry));
}
/**
@@ -186,4 +227,29 @@ 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));
+
+ 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
+ assertEquals("Hello", Uniprot.getDescription(uf));
+ }
}