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

[jalview.git] / src / jalview / io / packed / ParsePackedSet.java

diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index 37dd66b..3ce774e 100644 (file)
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -246,7 +246,7 @@ public class ParsePackedSet
           fp = new FileParse(file, AppletFormatAdapter.checkProtocol(file));
         } catch (Exception e)
         {
-          System.err.println("Couldn't handle datasource of type " + jtype
+          jalview.bin.Console.errPrintln("Couldn't handle datasource of type " + jtype
                   + " using URI " + file);
           e.printStackTrace();
           return;
@@ -255,7 +255,7 @@ 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 +269,7 @@ 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 +279,7 @@ 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 +287,7 @@ 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 +300,7 @@ 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.");
       }
     }