X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fpacked%2FParsePackedSet.java;h=ef231e5a4c0584e9b5bddd7b251a58c599ad30c8;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=37dd66b60cb3f0bf83069ab38d84ba7ac35cbdff;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git

diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index 37dd66b..ef231e5 100644
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -246,8 +246,9 @@ public class ParsePackedSet
           fp = new FileParse(file, AppletFormatAdapter.checkProtocol(file));
         } catch (Exception e)
         {
-          System.err.println("Couldn't handle datasource of type " + jtype
-                  + " using URI " + file);
+          jalview.bin.Console
+                  .errPrintln("Couldn't handle datasource of type " + jtype
+                          + " using URI " + file);
           e.printStackTrace();
           return;
         }
@@ -255,7 +256,7 @@ public class ParsePackedSet
       }
       else
       {
-        System.out.println("Couldn't parse source type token '"
+        jalview.bin.Console.outPrintln("Couldn't parse source type token '"
                 + type.toUpperCase(Locale.ROOT) + "'");
       }
     }
@@ -269,7 +270,7 @@ public class ParsePackedSet
       System.out.print("\n");
 
     }
-    System.out.println("Now trying to parse set:");
+    jalview.bin.Console.outPrintln("Now trying to parse set:");
     JalviewDataset context;
     Object[] newdm;
     ParsePackedSet pps;
@@ -279,7 +280,7 @@ public class ParsePackedSet
               .getAlignment(context = new JalviewDataset(), dp);
     } catch (Exception e)
     {
-      System.out.println("Test failed for these arguments.\n");
+      jalview.bin.Console.outPrintln("Test failed for these arguments.\n");
       e.printStackTrace(System.out);
       return;
     }
@@ -287,7 +288,8 @@ public class ParsePackedSet
     {
       for (Object o : newdm)
       {
-        System.out.println("Will need to create an " + o.getClass());
+        jalview.bin.Console
+                .outPrintln("Will need to create an " + o.getClass());
       }
 
       // now test uniquify/deuniquify stuff
@@ -300,7 +302,7 @@ public class ParsePackedSet
     {
       if (context.getLastAlignmentSet().isModified())
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Initial alignment set was modified and any associated views should be updated.");
       }
     }