JAL-1645 source formatting and organise imports

[jalview.git] / test / jalview / datamodel / AlignedCodonIteratorTest.java

diff --git a/test/jalview/datamodel/AlignedCodonIteratorTest.java b/test/jalview/datamodel/AlignedCodonIteratorTest.java
index d9c7e12..dd30b60 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonIteratorTest.java
+++ b/test/jalview/datamodel/AlignedCodonIteratorTest.java
@@ -21,16 +21,16 @@ public class AlignedCodonIteratorTest
   /**
    * Test normal case for iterating over aligned codons.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testNext()
   {
     SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc");
     from.createDatasetSequence();
     SequenceI to = new Sequence("Seq1", "-PQ-R-");
     to.createDatasetSequence();
-    MapList map = new MapList(new int[]
-    { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[]
-    { 1, 3 }, 3, 1);
+    MapList map = new MapList(
+            new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 },
+            new int[] { 1, 3 }, 3, 1);
     Mapping m = new Mapping(to.getDatasetSequence(), map);
 
     Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
@@ -49,16 +49,16 @@ public class AlignedCodonIteratorTest
   /**
    * Test weird case where the mapping skips over a peptide.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testNext_unmappedPeptide()
   {
     SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc");
     from.createDatasetSequence();
     SequenceI to = new Sequence("Seq1", "-PQ-TR-");
     to.createDatasetSequence();
-    MapList map = new MapList(new int[]
-    { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[]
-    { 1, 2, 4, 4 }, 3, 1);
+    MapList map = new MapList(
+            new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[] { 1,
+                2, 4, 4 }, 3, 1);
     Mapping m = new Mapping(to.getDatasetSequence(), map);
 
     Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
@@ -73,20 +73,19 @@ public class AlignedCodonIteratorTest
     assertEquals("R", codon.product);
     assertFalse(codons.hasNext());
   }
-  
+
   /**
    * Test for exception thrown for an incomplete codon.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testNext_incompleteCodon()
   {
     SequenceI from = new Sequence("Seq1", "-CgC-C-cCgTt");
     from.createDatasetSequence();
     SequenceI to = new Sequence("Seq1", "-PQ-R-");
     to.createDatasetSequence();
-    MapList map = new MapList(new int[]
-    { 1, 1, 3, 4, 6, 6, 8, 8 }, new int[]
-    { 1, 3 }, 3, 1);
+    MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 8 },
+            new int[] { 1, 3 }, 3, 1);
     Mapping m = new Mapping(to.getDatasetSequence(), map);
 
     Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
@@ -106,18 +105,16 @@ public class AlignedCodonIteratorTest
   /**
    * Test normal case for iterating over aligned codons.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testAnother()
   {
     SequenceI from = new Sequence("Seq1", "TGCCATTACCAG-");
     from.createDatasetSequence();
     SequenceI to = new Sequence("Seq1", "CHYQ");
     to.createDatasetSequence();
-    MapList map = new MapList(new int[]
-    { 1, 12 }, new int[]
-    { 1, 4 }, 3, 1);
+    MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
     Mapping m = new Mapping(to.getDatasetSequence(), map);
-  
+
     Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
     AlignedCodon codon = codons.next();
     assertEquals("[0, 1, 2]", codon.toString());