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

[jalview.git] / src / jalview / schemes / Consensus.java

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 9d2c738..fe71d31 100755 (executable)
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -46,7 +46,7 @@ public class Consensus
     this.mask = setNums(s);
 
     // for (int i=0; i < mask.length; i++) {
-    // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+    // jalview.bin.Console.outPrintln(mask[i] + " " + ResidueProperties.aa[mask[i]]);
     // }
   }
 
@@ -56,7 +56,7 @@ public class Consensus
   @Deprecated
   public boolean isConserved(int[][] cons2, int col, int size)
   {
-    System.out.println("DEPRECATED!!!!");
+    jalview.bin.Console.outPrintln("DEPRECATED!!!!");
     return isConserved(cons2, col, size, true);
   }
 
@@ -75,7 +75,7 @@ public class Consensus
 
     if (tot > ((threshold * size) / 100))
     {
-      // System.out.println("True conserved "+tot+" from "+threshold+" out of
+      // jalview.bin.Console.outPrintln("True conserved "+tot+" from "+threshold+" out of
       // "+size+" : "+maskstr);
       return true;
     }