X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FTestAlignSeq.java;fp=test%2Fjalview%2Fanalysis%2FTestAlignSeq.java;h=05575f454a95a308480a6368c8707800488b36c7;hp=44bea811761f89441dd095ff44945226bf985eb5;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hpb=cb31e23d9138e481479623374aed7767bf8934d2

diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java
index 44bea81..05575f4 100644
--- a/test/jalview/analysis/TestAlignSeq.java
+++ b/test/jalview/analysis/TestAlignSeq.java
@@ -87,22 +87,23 @@ public class TestAlignSeq
     assertEquals(as.getAStr1(), as.getAStr2());
 
     Mapping s1tos2 = as.getMappingFromS1(false);
-    checkMapping(s1tos2,s1,s2);
+    checkMapping(s1tos2, s1, s2);
   }
 
-  public void checkMapping(Mapping s1tos2,SequenceI _s1,SequenceI _s2)
+  public void checkMapping(Mapping s1tos2, SequenceI _s1, SequenceI _s2)
   {
     System.out.println(s1tos2.getMap().toString());
     for (int i = _s2.getStart(); i < _s2.getEnd(); i++)
     {
-      int p=s1tos2.getPosition(i);
-      char s2c=_s2.getCharAt(i-_s2.getStart());
-      char s1c=_s1.getCharAt(p-_s1.getStart());
-      System.out.println("Position in s2: " + i +s2c 
-      + " maps to position in s1: " +p+s1c);
-      assertEquals(s1c,s2c);
+      int p = s1tos2.getPosition(i);
+      char s2c = _s2.getCharAt(i - _s2.getStart());
+      char s1c = _s1.getCharAt(p - _s1.getStart());
+      System.out.println("Position in s2: " + i + s2c
+              + " maps to position in s1: " + p + s1c);
+      assertEquals(s1c, s2c);
     }
   }
+
   @Test(groups = { "Functional" })
   /**
    * simple test that mapping from alignment corresponds identical positions.
@@ -121,9 +122,9 @@ public class TestAlignSeq
     assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
 
     Mapping s1tos2 = as.getMappingFromS1(false);
-    assertEquals("ASdFA",as.getAStr2());
+    assertEquals("ASdFA", as.getAStr2());
     // verify mapping is consistent between original all-caps sequences
-    checkMapping(s1tos2,s1,s2);
+    checkMapping(s1tos2, s1, s2);
   }
 
   @Test(groups = { "Functional" })