JAL-1645 source formatting and organise imports

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

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index 35d92d3..23aa889 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/test/jalview/datamodel/AlignedCodonFrameTest.java
@@ -15,11 +15,10 @@ public class AlignedCodonFrameTest
   /**
    * Test the method that locates the first aligned sequence that has a mapping.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testFindAlignedSequence()
   {
-    AlignmentI cdna = new Alignment(new SequenceI[]
-    {});
+    AlignmentI cdna = new Alignment(new SequenceI[] {});
     final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
     seq1.createDatasetSequence();
     cdna.addSequence(seq1);
@@ -27,8 +26,7 @@ public class AlignedCodonFrameTest
     seq2.createDatasetSequence();
     cdna.addSequence(seq2);
 
-    AlignmentI aa = new Alignment(new SequenceI[]
-    {});
+    AlignmentI aa = new Alignment(new SequenceI[] {});
     final Sequence aseq1 = new Sequence("Seq1", "-P-R");
     aseq1.createDatasetSequence();
     aa.addSequence(aseq1);
@@ -43,27 +41,23 @@ public class AlignedCodonFrameTest
 
     assertNull(acf.findAlignedSequence(seq1, aa));
 
-    MapList map = new MapList(new int[]
-    { 1, 6 }, new int[]
-    { 1, 2 }, 3, 1);
+    MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
     acf.addMap(seq1.getDatasetSequence(), aseq2.getDatasetSequence(), map);
 
     /*
      * DNA seq1 maps to AA seq2
      */
-    assertEquals(aa.getSequenceAt(1),
- acf.findAlignedSequence(cdna
+    assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(cdna
             .getSequenceAt(0).getDatasetSequence(), aa));
 
-    assertEquals(cdna.getSequenceAt(0),
- acf.findAlignedSequence(aa
+    assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(aa
             .getSequenceAt(1).getDatasetSequence(), cdna));
   }
 
   /**
    * Test the method that locates the mapped codon for a protein position.
    */
-    @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testGetMappedRegion()
   {
     // introns lower case, exons upper case
@@ -87,13 +81,11 @@ public class AlignedCodonFrameTest
     /*
      * Set up the mappings for the exons (upper-case bases)
      */
-    MapList map = new MapList(new int[]
-    { 2, 4, 6, 6, 8, 9 }, new int[]
-    { 1, 2 }, 3, 1);
+    MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
+        1, 2 }, 3, 1);
     acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
-    map = new MapList(new int[]
-    { 1, 2, 4, 5, 7, 8 }, new int[]
-    { 1, 2 }, 3, 1);
+    map = new MapList(new int[] { 1, 2, 4, 5, 7, 8 }, new int[] { 1, 2 },
+            3, 1);
     acf.addMap(seq2.getDatasetSequence(), aseq2.getDatasetSequence(), map);
 
     assertEquals("[2, 4]",
@@ -111,7 +103,7 @@ public class AlignedCodonFrameTest
     assertNull(acf.getMappedRegion(seq1, aseq2, 1));
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testGetMappedCodon()
   {
     final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
@@ -129,11 +121,10 @@ public class AlignedCodonFrameTest
     /*
      * Set up the mappings for the exons (upper-case bases)
      */
-    MapList map = new MapList(new int[]
-    { 2, 4, 6, 6, 8, 9 }, new int[]
-    { 1, 2 }, 3, 1);
+    MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
+        1, 2 }, 3, 1);
     acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
-    
+
     assertEquals("[G, T, A]", Arrays.toString(acf.getMappedCodon(
             aseq1.getDatasetSequence(), 1)));
     assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(