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 a1b0325..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);
   }
 
   /**
@@ -482,8 +482,8 @@ public class AAFrequency
    * @param hashtable
    * @return
    */
-  public static int[] extractCdnaProfile(Hashtable hashtable,
-          boolean ignoreGaps)
+  public static int[] extractCdnaProfile(
+          Hashtable<String, Object> hashtable, boolean ignoreGaps)
   {
     // this holds #seqs, #ungapped, and then codon count, indexed by encoded
     // codon triplet
@@ -546,7 +546,7 @@ public class AAFrequency
    *          the consensus data stores to be populated (one per column)
    */
   public static void calculateCdna(AlignmentI alignment,
-          Hashtable[] hconsensus)
+          Hashtable<String, Object>[] hconsensus)
   {
     final char gapCharacter = alignment.getGapCharacter();
     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
@@ -559,7 +559,7 @@ public class AAFrequency
     for (int col = 0; col < cols; col++)
     {
       // todo would prefer a Java bean for consensus data
-      Hashtable<String, int[]> columnHash = new Hashtable<>();
+      Hashtable<String, Object> columnHash = new Hashtable<>();
       // #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
       int[] codonCounts = new int[66];
       codonCounts[0] = alignment.getSequences().size();
@@ -579,6 +579,7 @@ public class AAFrequency
           {
             codonCounts[codonEncoded + 2]++;
             ungappedCount++;
+            break;
           }
         }
       }
@@ -604,7 +605,8 @@ public class AAFrequency
    */
   public static void completeCdnaConsensus(
           AlignmentAnnotation consensusAnnotation,
-          Hashtable[] consensusData, boolean showProfileLogo, int nseqs)
+          Hashtable<String, Object>[] consensusData,
+          boolean showProfileLogo, int nseqs)
   {
     if (consensusAnnotation == null
             || consensusAnnotation.annotations == null
@@ -619,7 +621,7 @@ public class AAFrequency
     consensusAnnotation.scaleColLabel = true;
     for (int col = 0; col < consensusData.length; col++)
     {
-      Hashtable hci = consensusData[col];
+      Hashtable<String, Object> hci = consensusData[col];
       if (hci == null)
       {
         // gapped protein column?