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Merge branch 'develop' into releases/Release_2_10_Branch
[jalview.git]
/
test
/
jalview
/
util
/
DBRefUtilsTest.java
diff --git
a/test/jalview/util/DBRefUtilsTest.java
b/test/jalview/util/DBRefUtilsTest.java
index
5e0683e
..
1c68a71
100644
(file)
--- a/
test/jalview/util/DBRefUtilsTest.java
+++ b/
test/jalview/util/DBRefUtilsTest.java
@@
-74,9
+74,16
@@
public class DBRefUtilsTest
assertSame(ref2, selected[0]);
assertSame(ref3, selected[1]);
assertSame(ref2, selected[0]);
assertSame(ref3, selected[1]);
- sources = new String[] { "Uniprot", "EMBLCDS" };
+ sources = new String[] { "EMBLCDS" };
selected = DBRefUtils.selectRefs(dbrefs, sources);
assertNull(selected);
selected = DBRefUtils.selectRefs(dbrefs, sources);
assertNull(selected);
+
+ sources = new String[] { "embl", "uniprot" };
+ selected = DBRefUtils.selectRefs(dbrefs, sources);
+ assertEquals(3, selected.length);
+ assertSame(ref1, selected[0]);
+ assertSame(ref2, selected[1]);
+ assertSame(ref3, selected[2]);
}
/**
}
/**
@@
-99,6
+106,11
@@
public class DBRefUtilsTest
assertEquals("UNIPROTKB/SWISS-CHEESE",
DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
assertEquals("UNIPROTKB/SWISS-CHEESE",
DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
+
+ // these are not 'known' to Jalview
+ assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
+ assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
+
}
@Test(groups = { "Functional" })
}
@Test(groups = { "Functional" })
@@
-197,8
+209,7
@@
public class DBRefUtilsTest
1 }, 1, 1)));
List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
1 }, 1, 1)));
List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
- ref1,
- ref2, ref3, ref4, ref5 }, target);
+ ref1, ref2, ref3, ref4, ref5 }, target);
assertEquals(3, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
assertEquals(3, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
@@
-231,8
+242,7
@@
public class DBRefUtilsTest
ref3.setMap(map3);
List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
ref3.setMap(map3);
List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
- ref1,
- ref2, ref3 }, target);
+ ref1, ref2, ref3 }, target);
assertEquals(2, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
assertEquals(2, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
@@
-245,7
+255,7
@@
public class DBRefUtilsTest
@Test(groups = { "Functional" })
public void testSearchRefs_accessionid()
{
@Test(groups = { "Functional" })
public void testSearchRefs_accessionid()
{
-
+
DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
// constructor does not upper-case accession id
DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
// constructor does not upper-case accession id
@@
-255,9
+265,8
@@
public class DBRefUtilsTest
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
-
- DBRefEntry[] dbrefs = new DBRefEntry[] { ref1,
- ref2, ref3, ref4, ref5 };
+
+ DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5 };
List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
assertEquals(3, matches.size());
assertSame(ref1, matches.get(0));
List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
assertEquals(3, matches.size());
assertSame(ref1, matches.get(0));
@@
-273,7
+282,7
@@
public class DBRefUtilsTest
public void testSearchRefs_wildcardAccessionid()
{
DBRefEntry target = new DBRefEntry("EMBL", "2", null);
public void testSearchRefs_wildcardAccessionid()
{
DBRefEntry target = new DBRefEntry("EMBL", "2", null);
-
+
DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
// constructor changes embl to EMBL
DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
// constructor changes embl to EMBL
DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
@@
-284,10
+293,9
@@
public class DBRefUtilsTest
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
-
+
List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
- ref1,
- ref2, ref3, ref4, ref5 }, target);
+ ref1, ref2, ref3, ref4, ref5 }, target);
assertEquals(4, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
assertEquals(4, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));