X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;h=ca5bca35282b031b1ff98b5f6685ad4c64d725c8;hb=0a37e3b824b46b026916e124b42400590242d145;hp=d1c24d189231add9d327539066398267ff972909;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index d1c24d1..ca5bca3 100644
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -21,7 +21,6 @@
 package jalview.util;
 
 import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
@@ -32,14 +31,23 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 
 import java.util.List;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class DBRefUtilsTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * Test the method that selects DBRefEntry items whose source is in a supplied
    * list
@@ -74,9 +82,16 @@ public class DBRefUtilsTest
     assertSame(ref2, selected[0]);
     assertSame(ref3, selected[1]);
 
-    sources = new String[] { "Uniprot", "EMBLCDS" };
+    sources = new String[] { "EMBLCDS" };
     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]);
   }
 
   /**
@@ -99,39 +114,12 @@ public class DBRefUtilsTest
     assertEquals("UNIPROTKB/SWISS-CHEESE",
             DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
     assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
-  }
 
-  @Test(groups = { "Functional" })
-  public void testIsDasCoordinateSystem()
-  {
-    assertFalse(DBRefUtils.isDasCoordinateSystem(null, null));
-    assertFalse(DBRefUtils.isDasCoordinateSystem("pdbresnum", null));
-    assertFalse(DBRefUtils.isDasCoordinateSystem(null, new DBRefEntry(
-            "PDB", "v1", "a1")));
+    // these are not 'known' to Jalview
+    assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
+    assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
 
-    assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
-            new DBRefEntry("PDB", "v1", "a1")));
-    assertTrue(DBRefUtils.isDasCoordinateSystem("PDBRESNUM",
-            new DBRefEntry("PDB", "v1", "a1")));
-    // "pdb" is converted to upper-case in DBRefEntry constructor
-    assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
-            new DBRefEntry("pdb", "v1", "a1")));
-    assertFalse(DBRefUtils.isDasCoordinateSystem("pdb", new DBRefEntry(
-            "pdb", "v1", "a1")));
-
-    assertTrue(DBRefUtils.isDasCoordinateSystem("UNIPROT", new DBRefEntry(
-            "Uniprot", "v1", "a1")));
-    assertTrue(DBRefUtils.isDasCoordinateSystem("Uniprot", new DBRefEntry(
-            "UNIPROT", "v1", "a1")));
-    assertFalse(DBRefUtils.isDasCoordinateSystem("UNIPROTKB",
-            new DBRefEntry("pdb", "v1", "a1")));
-
-    assertTrue(DBRefUtils.isDasCoordinateSystem("EMBL", new DBRefEntry(
-            "EMBL", "v1", "a1")));
-    assertTrue(DBRefUtils.isDasCoordinateSystem("embl", new DBRefEntry(
-            "embl", "v1", "a1")));
   }
-
   /**
    * Test 'parsing' a DBRef - non PDB case
    */
@@ -147,6 +135,11 @@ public class DBRefUtilsTest
     assertEquals("1.2", ref.getVersion());
     assertEquals("a7890", ref.getAccessionId());
     assertTrue(seq.getAllPDBEntries().isEmpty());
+    SequenceI seq2 = new Sequence("Seq2", "ABCD");
+    // Check that whitespace doesn't confuse parseToDbRef
+    DBRefEntry ref2 = DBRefUtils.parseToDbRef(seq2, "EMBL", "1.2",
+            " a7890");
+    assertEquals(ref, ref2);
   }
 
   /**