Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index cbc4dca..5bb0b09 100755 (executable)
--- 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)