Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

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

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index d1c24d1..d3e6221 100644 (file)
--- 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 +31,24 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
 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;
 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
@@ -54,29 +63,36 @@ 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[] { "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.size());
+    assertSame(ref1, selected.get(0));
+    assertSame(ref2, selected.get(1));
+    assertSame(ref3, selected.get(2));
   }
 
   /**
@@ -99,39 +115,12 @@ 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")));
-
-    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")));
+    // these are not 'known' to Jalview
+    assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
+    assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
 
-    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
    */
@@ -140,9 +129,9 @@ 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());
@@ -161,9 +150,9 @@ 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
@@ -196,8 +185,9 @@ 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));
@@ -229,8 +219,9 @@ 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));
@@ -254,7 +245,8 @@ 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));
@@ -282,8 +274,9 @@ 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));