X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=5bb0b0946b9e2a25a441194bd7befed66b3574e4;hb=9d465da4f21e403c20b835264929906b538c0c9b;hp=6cc9dd344addced46f9e8f5a06f7184ce47a86a7;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 6cc9dd3..5bb0b09 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -243,13 +243,13 @@ public class Conservation
       }
       else
       {
-        System.out.println("SEQUENCE HAS BEEN DELETED!!!");
+        jalview.bin.Console.outPrintln("SEQUENCE HAS BEEN DELETED!!!");
       }
     }
     else
     {
       // JBPNote INFO level debug
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
     }
   }
@@ -711,7 +711,7 @@ public class Conservation
       // tmp = ((max - tmp) * (size - cons2[j][23])) / size;
       tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
 
-      // System.out.println(tmp+ " " + j);
+      // jalview.bin.Console.outPrintln(tmp+ " " + j);
       quality.setElementAt(Double.valueOf(tmp), j);
 
       if (tmp > newmax)
@@ -814,8 +814,8 @@ public class Conservation
         float vprop = value - qmin;
         vprop /= qmax;
         String description = FORMAT_3DP.form(value);
-        quality2.annotations[i] = new Annotation(" ", description,
-                ' ', value, new Color(minR + (maxR * vprop),
+        quality2.annotations[i] = new Annotation(" ", description, ' ',
+                value, new Color(minR + (maxR * vprop),
                         minG + (maxG * vprop), minB + (maxB * vprop)));
       }
     }