X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FGffHelperBase.java;fp=src%2Fjalview%2Fio%2Fgff%2FGffHelperBase.java;h=dccfd27eed8ba2672003c696c6d4c46055e0c512;hp=22386d46ba972dd743e930e8c11554a52635635b;hb=f680b9a507cc1643c9eead990e15026c1eca4e6e;hpb=265e81c0b3599a09c312f17188e3a892e9d96c4e

diff --git a/src/jalview/io/gff/GffHelperBase.java b/src/jalview/io/gff/GffHelperBase.java
index 22386d4..dccfd27 100644
--- a/src/jalview/io/gff/GffHelperBase.java
+++ b/src/jalview/io/gff/GffHelperBase.java
@@ -114,7 +114,7 @@ public abstract class GffHelperBase implements GffHelperI
      */
     if (!trimMapping(from, to, fromRatio, toRatio))
     {
-      System.err.println("Ignoring mapping from " + Arrays.toString(from)
+      jalview.bin.Console.errPrintln("Ignoring mapping from " + Arrays.toString(from)
               + " to " + Arrays.toString(to) + " as counts don't match!");
       return null;
     }
@@ -166,7 +166,7 @@ public abstract class GffHelperBase implements GffHelperI
       {
         from[1] += fromOverlap / toRatio;
       }
-      System.err.println(Arrays.toString(from));
+      jalview.bin.Console.errPrintln(Arrays.toString(from));
       return true;
     }
     else if (fromOverlap < 0 && fromOverlap % fromRatio == 0)
@@ -185,7 +185,7 @@ public abstract class GffHelperBase implements GffHelperI
       {
         to[1] += fromOverlap / fromRatio;
       }
-      System.err.println(Arrays.toString(to));
+      jalview.bin.Console.errPrintln(Arrays.toString(to));
       return true;
     }
 
@@ -444,7 +444,7 @@ public abstract class GffHelperBase implements GffHelperI
       return sf;
     } catch (NumberFormatException nfe)
     {
-      System.err.println("Invalid number in gff: " + nfe.getMessage());
+      jalview.bin.Console.errPrintln("Invalid number in gff: " + nfe.getMessage());
       return null;
     }
   }
@@ -504,7 +504,7 @@ public abstract class GffHelperBase implements GffHelperI
 
     if (!valid)
     {
-      System.err.println(INVALID_GFF_ATTRIBUTE_FORMAT + s);
+      jalview.bin.Console.errPrintln(INVALID_GFF_ATTRIBUTE_FORMAT + s);
       return map;
     }
 
@@ -526,7 +526,7 @@ public abstract class GffHelperBase implements GffHelperI
       theKey = theKey.trim();
       if (theKey.isEmpty())
       {
-        System.err.println(INVALID_GFF_ATTRIBUTE_FORMAT + s);
+        jalview.bin.Console.errPrintln(INVALID_GFF_ATTRIBUTE_FORMAT + s);
         map.clear();
         return map;
       }