Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalvi...

[jalview.git] / test / jalview / util / DBRefUtilsTest.java

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index 0368d1e..f92e454 100644 (file)
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -33,6 +33,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
 
+import java.util.Arrays;
 import java.util.List;
 
 import org.testng.annotations.BeforeClass;
@@ -62,25 +63,25 @@ public class DBRefUtilsTest
     DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
     // Source is converted to upper-case by this constructor!
     DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
-    DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3 };
+    List<DBRefEntry> dbrefs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3 });
     String[] sources = new String[] { "EMBL", "UNIPROT" };
 
-    DBRefEntry[] selected = DBRefUtils.selectRefs(dbrefs, sources);
-    assertEquals(3, selected.length);
-    assertSame(ref1, selected[0]);
-    assertSame(ref2, selected[1]);
-    assertSame(ref3, selected[2]);
+    List<DBRefEntry> selected = DBRefUtils.selectRefs(dbrefs, sources);
+    assertEquals(3, selected.size());
+    assertSame(ref1, selected.get(0));
+    assertSame(ref2, selected.get(1));
+    assertSame(ref3, selected.get(2));
 
     sources = new String[] { "EMBL" };
     selected = DBRefUtils.selectRefs(dbrefs, sources);
-    assertEquals(1, selected.length);
-    assertSame(ref1, selected[0]);
+    assertEquals(1, selected.size());
+    assertSame(ref1, selected.get(0));
 
     sources = new String[] { "UNIPROT" };
     selected = DBRefUtils.selectRefs(dbrefs, sources);
-    assertEquals(2, selected.length);
-    assertSame(ref2, selected[0]);
-    assertSame(ref3, selected[1]);
+    assertEquals(2, selected.size());
+    assertSame(ref2, selected.get(0));
+    assertSame(ref3, selected.get(1));
 
     sources = new String[] { "EMBLCDS" };
     selected = DBRefUtils.selectRefs(dbrefs, sources);
@@ -88,10 +89,10 @@ public class DBRefUtilsTest
 
     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]);
+    assertEquals(3, selected.size());
+    assertSame(ref1, selected.get(0));
+    assertSame(ref2, selected.get(1));
+    assertSame(ref3, selected.get(2));
   }
 
   /**
@@ -128,13 +129,18 @@ public class DBRefUtilsTest
   {
     SequenceI seq = new Sequence("Seq1", "ABCD");
     DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
-    DBRefEntry[] refs = seq.getDBRefs();
-    assertEquals(1, refs.length);
-    assertSame(ref, refs[0]);
+    List<DBRefEntry> refs = seq.getDBRefs();
+    assertEquals(1, refs.size());
+    assertSame(ref, refs.get(0));
     assertEquals("EMBL", ref.getSource());
     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);
   }
 
   /**
@@ -149,9 +155,9 @@ public class DBRefUtilsTest
     // 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]);
+    List<DBRefEntry> refs = seq.getDBRefs();
+    assertEquals(1, refs.size());
+    assertSame(ref, refs.get(0));
     assertEquals("PDB", ref.getSource());
     assertEquals("1.2", ref.getVersion());
     // DBRef id is pdbId + chain code
@@ -184,8 +190,9 @@ public class DBRefUtilsTest
     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);
+    List<DBRefEntry> matches = DBRefUtils.searchRefs(
+               Arrays.asList(new DBRefEntry[] {
+        ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL);
     assertEquals(3, matches.size());
     assertSame(ref1, matches.get(0));
     assertSame(ref2, matches.get(1));
@@ -217,8 +224,9 @@ public class DBRefUtilsTest
             new int[] { 1, 1 }, 2, 2));
     ref3.setMap(map3);
 
-    List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
-        ref1, ref2, ref3 }, target);
+    List<DBRefEntry> matches = DBRefUtils.searchRefs(
+               Arrays.asList(new DBRefEntry[] {
+        ref1, ref2, ref3 }), target, DBRefUtils.SEARCH_MODE_FULL);
     assertEquals(2, matches.size());
     assertSame(ref1, matches.get(0));
     assertSame(ref2, matches.get(1));
@@ -242,7 +250,8 @@ public class DBRefUtilsTest
     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 };
+    List<DBRefEntry> dbrefs = Arrays.asList(new DBRefEntry[] {
+                ref1, ref2, ref3, ref4, ref5 });
     List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
     assertEquals(3, matches.size());
     assertSame(ref1, matches.get(0));
@@ -270,8 +279,9 @@ public class DBRefUtilsTest
     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);
+    List<DBRefEntry> matches = DBRefUtils.searchRefs(
+               Arrays.asList(new DBRefEntry[] {
+        ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL);
     assertEquals(4, matches.size());
     assertSame(ref1, matches.get(0));
     assertSame(ref2, matches.get(1));