JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

[jalview.git] / src / jalview / analysis / AAFrequency.java

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 52dedcf..6967885 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -147,7 +147,7 @@ public class AAFrequency
       {
         if (sequences[row] == null)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "WARNING: Consensus skipping null sequence - possible race condition.");
           continue;
         }
@@ -188,7 +188,7 @@ public class AAFrequency
     }
     return new Profiles(result);
     // long elapsed = System.currentTimeMillis() - now;
-    // System.out.println(elapsed);
+    // jalview.bin.Console.outPrintln(elapsed);
   }
 
   /**
@@ -285,7 +285,7 @@ public class AAFrequency
               ' ', value);
     }
     // long elapsed = System.currentTimeMillis() - now;
-    // System.out.println(-elapsed);
+    // jalview.bin.Console.outPrintln(-elapsed);
   }
 
   /**
@@ -483,8 +483,7 @@ public class AAFrequency
    * @return
    */
   public static int[] extractCdnaProfile(
-          Hashtable<String, Object> hashtable,
-          boolean ignoreGaps)
+          Hashtable<String, Object> hashtable, boolean ignoreGaps)
   {
     // this holds #seqs, #ungapped, and then codon count, indexed by encoded
     // codon triplet
@@ -606,8 +605,8 @@ public class AAFrequency
    */
   public static void completeCdnaConsensus(
           AlignmentAnnotation consensusAnnotation,
-          Hashtable<String, Object>[] consensusData, boolean showProfileLogo,
-          int nseqs)
+          Hashtable<String, Object>[] consensusData,
+          boolean showProfileLogo, int nseqs)
   {
     if (consensusAnnotation == null
             || consensusAnnotation.annotations == null