X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;h=0ef3c2553d40b474601b12f0d65d6326d07fd021;hb=9fdb65ed10ce0b70bed3b61fb50704bba294b243;hp=96935cea0a87cc58f8a85f8777fb3b8713e9e5c0;hpb=65675b2d016736f8ca4dfb2493863c4d53cec591;p=jalview.git

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index 96935ce..0ef3c25 100644
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -32,14 +32,23 @@ 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 +83,16 @@ 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]);
   }
 
   /**
@@ -99,6 +115,11 @@ public class DBRefUtilsTest
     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" })
@@ -158,6 +179,9 @@ public class DBRefUtilsTest
     SequenceI seq = new Sequence("Seq1", "ABCD");
     DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
             "1WRI A; 7-80;");
+    // TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
+    // PDB ref in Stockholm
+
     DBRefEntry[] refs = seq.getDBRefs();
     assertEquals(1, refs.length);
     assertSame(ref, refs[0]);
@@ -194,8 +218,7 @@ public class DBRefUtilsTest
         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));
@@ -228,8 +251,7 @@ public class DBRefUtilsTest
     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));
@@ -242,7 +264,7 @@ public class DBRefUtilsTest
   @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
@@ -252,9 +274,8 @@ 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[] 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));
@@ -270,7 +291,7 @@ public class DBRefUtilsTest
   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
@@ -281,10 +302,9 @@ 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)));
-  
+
     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));