JAL-1645 source formatting and organise imports

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

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index af5fd1e..c270029 100644 (file)
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -22,7 +22,7 @@ public class DBRefUtilsTest
    * Test the method that selects DBRefEntry items whose source is in a supplied
    * list
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testSelectRefs()
   {
     assertNull(DBRefUtils.selectRefs(null, null));
@@ -32,10 +32,8 @@ 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 };
-    String[] sources = new String[]
-    { "EMBL", "UNIPROT" };
+    DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3 };
+    String[] sources = new String[] { "EMBL", "UNIPROT" };
 
     DBRefEntry[] selected = DBRefUtils.selectRefs(dbrefs, sources);
     assertEquals(3, selected.length);
@@ -43,21 +41,18 @@ public class DBRefUtilsTest
     assertSame(ref2, selected[1]);
     assertSame(ref3, selected[2]);
 
-    sources = new String[]
-    { "EMBL" };
+    sources = new String[] { "EMBL" };
     selected = DBRefUtils.selectRefs(dbrefs, sources);
     assertEquals(1, selected.length);
     assertSame(ref1, selected[0]);
 
-    sources = new String[]
-    { "UNIPROT" };
+    sources = new String[] { "UNIPROT" };
     selected = DBRefUtils.selectRefs(dbrefs, sources);
     assertEquals(2, selected.length);
     assertSame(ref2, selected[0]);
     assertSame(ref3, selected[1]);
 
-    sources = new String[]
-    { "Uniprot", "EMBLCDS" };
+    sources = new String[] { "Uniprot", "EMBLCDS" };
     selected = DBRefUtils.selectRefs(dbrefs, sources);
     assertNull(selected);
   }
@@ -66,7 +61,7 @@ public class DBRefUtilsTest
    * Test the method that converts (currently three) database names to a
    * canonical name (not case-sensitive)
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testGetCanonicalName()
   {
     assertNull(DBRefUtils.getCanonicalName(null));
@@ -83,7 +78,7 @@ public class DBRefUtilsTest
             DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testIsDasCoordinateSystem()
   {
     assertFalse(DBRefUtils.isDasCoordinateSystem(null, null));
@@ -106,8 +101,7 @@ public class DBRefUtilsTest
     assertTrue(DBRefUtils.isDasCoordinateSystem("Uniprot", new DBRefEntry(
             "UNIPROT", "v1", "a1")));
     assertFalse(DBRefUtils.isDasCoordinateSystem("UNIPROTKB",
-            new DBRefEntry(
-            "pdb", "v1", "a1")));
+            new DBRefEntry("pdb", "v1", "a1")));
 
     assertTrue(DBRefUtils.isDasCoordinateSystem("EMBL", new DBRefEntry(
             "EMBL", "v1", "a1")));
@@ -118,7 +112,7 @@ public class DBRefUtilsTest
   /**
    * Test 'parsing' a DBRef - non PDB case
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testParseToDbRef()
   {
     SequenceI seq = new Sequence("Seq1", "ABCD");
@@ -135,7 +129,7 @@ public class DBRefUtilsTest
   /**
    * Test 'parsing' a DBRef - Stockholm PDB format
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testParseToDbRef_PDB()
   {
     SequenceI seq = new Sequence("Seq1", "ABCD");
@@ -160,7 +154,7 @@ public class DBRefUtilsTest
    * Test the method that searches for matches references - case when we are
    * matching a reference with no mappings
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testSearchRefs_noMapping()
   {
     DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
@@ -173,12 +167,11 @@ public class DBRefUtilsTest
     DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
     // ref5 matches although it has a mapping - ignored
     DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
-    ref5.setMap(new Mapping(new MapList(new int[]
-    { 1, 1 }, new int[]
-    { 1, 1 }, 1, 1)));
+    ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
+        1 }, 1, 1)));
 
-    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[]
-    { ref1, ref2, ref3, ref4, ref5 }, target);
+    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
+        ref2, ref3, ref4, ref5 }, target);
     assertEquals(3, matches.length);
     assertSame(ref1, matches[0]);
     assertSame(ref2, matches[1]);
@@ -189,32 +182,29 @@ public class DBRefUtilsTest
    * Test the method that searches for matches references - case when we are
    * matching a reference with a mapping
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testSearchRefs_withMapping()
   {
     DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
-    final Mapping map1 = new Mapping(new MapList(new int[]
-    { 1, 1 }, new int[]
-    { 1, 1 }, 1, 1));
+    final Mapping map1 = new Mapping(new MapList(new int[] { 1, 1 },
+            new int[] { 1, 1 }, 1, 1));
     target.setMap(map1);
 
     // these all match target iff mappings match
     DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
     DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
-    final Mapping map2 = new Mapping(new MapList(new int[]
-    { 1, 1 }, new int[]
-    { 1, 1 }, 1, 1));
+    final Mapping map2 = new Mapping(new MapList(new int[] { 1, 1 },
+            new int[] { 1, 1 }, 1, 1));
     ref2.setMap(map2);
 
     // different map: no match
     DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
-    final Mapping map3 = new Mapping(new MapList(new int[]
-    { 1, 1 }, new int[]
-    { 1, 1 }, 2, 2));
+    final Mapping map3 = new Mapping(new MapList(new int[] { 1, 1 },
+            new int[] { 1, 1 }, 2, 2));
     ref3.setMap(map3);
 
-    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[]
-    { ref1, ref2, ref3 }, target);
+    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
+        ref2, ref3 }, target);
     assertEquals(2, matches.length);
     assertSame(ref1, matches[0]);
     assertSame(ref2, matches[1]);