X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAAFrequencyTest.java;h=d71497080453865cf5af3182f7a4ac06eaa19025;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=93c95ce5bb7b1c32cc79d74e598ae2254ba86483;hpb=e7338a61f3ce96dadf44ac80b2b32cc5ba4b94c8;p=jalview.git

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index 93c95ce..d714970 100644
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -57,8 +57,7 @@ public class AAFrequencyTest
     SequenceI seq4 = new Sequence("Seq4", "CA--t");
     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
     int width = seq1.getLength();
-    ProfilesI result = AAFrequency.calculate(seqs, width, 0, width,
-            false);
+    ProfilesI result = AAFrequency.calculate(seqs, width, 0, width, false);
 
     // col 0 is 100% C
     ProfileI col = result.get(0);
@@ -106,8 +105,7 @@ public class AAFrequencyTest
     SequenceI seq4 = new Sequence("Seq4", "CA-t");
     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
     int width = seq1.getLength();
-    ProfilesI result = AAFrequency.calculate(seqs, width, 0, width,
-            true);
+    ProfilesI result = AAFrequency.calculate(seqs, width, 0, width, true);
 
     ProfileI profile = result.get(0);
     assertEquals(4, profile.getCounts().getCount('C'));
@@ -176,8 +174,8 @@ public class AAFrequencyTest
 
     AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
             "PID", new Annotation[width]);
-    AAFrequency
-            .completeConsensus(consensus, profiles, 0, 5, false, true, 4);
+    AAFrequency.completeConsensus(consensus, profiles, 0, 5, false, true,
+            4);
 
     Annotation ann = consensus.annotations[0];
     assertEquals("C 100%", ann.description);
@@ -214,12 +212,12 @@ public class AAFrequencyTest
     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
     int width = seq1.getLength();
     ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true);
-  
+
     AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
             "PID", new Annotation[width]);
-    AAFrequency
-            .completeConsensus(consensus, profiles, 0, 5, true, false, 4);
-  
+    AAFrequency.completeConsensus(consensus, profiles, 0, 5, true, false,
+            4);
+
     Annotation ann = consensus.annotations[0];
     assertEquals("C 100%", ann.description);
     assertEquals("C", ann.displayCharacter);
@@ -298,7 +296,7 @@ public class AAFrequencyTest
     counts.put('L', 38);
     counts.put('H', 2);
     profile.setCounts(counts);
-  
+
     /*
      * [0, noOfValues, totalPercent, char1, count1, ...]
      * G: 70/200 = 35%
@@ -309,10 +307,9 @@ public class AAFrequencyTest
      */
     int[] extracted = AAFrequency.extractProfile(profile, false);
     int[] expected = new int[] { AlignmentAnnotation.SEQUENCE_PROFILE, 4,
-        85, 'G', 35, 'R', 30, 'L', 19, 'H',
-        1 };
+        85, 'G', 35, 'R', 30, 'L', 19, 'H', 1 };
     org.testng.Assert.assertEquals(extracted, expected);
-  
+
     /*
      * add some counts of 1; these round down to 0% and should be discarded
      */
@@ -323,7 +320,7 @@ public class AAFrequencyTest
     expected = new int[] { AlignmentAnnotation.SEQUENCE_PROFILE, 4, 84, 'G',
         34, 'R', 30, 'L', 19, 'H', 1 };
     org.testng.Assert.assertEquals(extracted, expected);
-  
+
   }
 
   @Test(groups = { "Functional" })
@@ -356,7 +353,7 @@ public class AAFrequencyTest
     codonCounts[0] = 120;
     codonCounts[1] = 110;
     profile.put(AAFrequency.PROFILE, codonCounts);
-  
+
     /*
      * [0, noOfValues, totalPercent, char1, count1, ...]
      * codon1: 30/110 = 27.2 = 27% 
@@ -379,7 +376,7 @@ public class AAFrequencyTest
      * max count 70 for modal residue 'G'
      */
     Hashtable profile = new Hashtable();
-  
+
     /*
      *  cdna profile is {seqCount, ungappedCount, codonCount1, ...codonCount64}
      * where 1..64 positions correspond to encoded codons
@@ -401,7 +398,7 @@ public class AAFrequencyTest
     codonCounts[0] = 120;
     codonCounts[1] = 110;
     profile.put(AAFrequency.PROFILE, codonCounts);
-  
+
     /*
      * [0, noOfValues, totalPercent, char1, count1, ...]
      * codon1: 30/120 = 25%