X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSeqCigarTest.java;h=f71f574c0055929c09a059076241f5c678b5b123;hb=52288466dd1e71946a06fd1e6ea15fa8e652c693;hp=3b50ce129dea6bdcb1e9aab9b883f9d5db5f8514;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/test/jalview/datamodel/SeqCigarTest.java b/test/jalview/datamodel/SeqCigarTest.java
index 3b50ce1..f71f574 100644
--- a/test/jalview/datamodel/SeqCigarTest.java
+++ b/test/jalview/datamodel/SeqCigarTest.java
@@ -15,7 +15,7 @@ public class SeqCigarTest
    * 
    * TODO: split into separate tests
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testSomething() throws Exception
   {
     String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt";
@@ -51,7 +51,7 @@ public class SeqCigarTest
      */
     assertEquals("Failed getWidth", sub_gapped_s.length(),
             sub_gapped.getWidth());
-  
+
     sub_gapped.getFullWidth();
     assertFalse("hasDeletedRegions is incorrect",
             sub_gapped.hasDeletedRegions());
@@ -86,9 +86,8 @@ public class SeqCigarTest
       }
     }
 
-    SeqCigar[] set = new SeqCigar[]
-    { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
-        new SeqCigar(s_gapped) };
+    SeqCigar[] set = new SeqCigar[] { new SeqCigar(s),
+        new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
     Alignment al = new Alignment(set);
     for (int i = 0; i < al.getHeight(); i++)
     {
@@ -99,9 +98,8 @@ public class SeqCigarTest
     }
 
     System.out.println("Gapped.");
-    set = new SeqCigar[]
-    { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
-        new SeqCigar(s_gapped) };
+    set = new SeqCigar[] { new SeqCigar(s),
+        new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
     set[0].deleteRange(20, 25);
     al = new Alignment(set);
     for (int i = 0; i < al.getHeight(); i++)
@@ -126,18 +124,14 @@ public class SeqCigarTest
    * @return String
    */
 
-
   protected void testCigar_string(Sequence seq, String ex_cs_gapped)
   {
     SeqCigar c_sgapped = new SeqCigar(seq);
     String cs_gapped = c_sgapped.getCigarstring();
-    assertEquals("Failed getCigarstring", ex_cs_gapped,
-            cs_gapped);
+    assertEquals("Failed getCigarstring", ex_cs_gapped, cs_gapped);
   }
 
-
-  protected void testSeqRecovery(SeqCigar gen_sgapped,
-          SequenceI s_gapped)
+  protected void testSeqRecovery(SeqCigar gen_sgapped, SequenceI s_gapped)
   {
     // this is non-rigorous - start and end recovery is not tested.
     SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');