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

[jalview.git] / src / jalview / gui / WsJobParameters.java

diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index e1613da..196eb32 100644 (file)
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -493,7 +493,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     else
     {
       // TODO: show warning
-      System.err.println("Invalid name. Not saved.");
+      jalview.bin.Console.errPrintln("Invalid name. Not saved.");
     }
   }
 
@@ -642,7 +642,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
           }
           else
           {
-            System.err.println("Ignoring unknown service argument type "
+            jalview.bin.Console.errPrintln("Ignoring unknown service argument type "
                     + myarg.getClass().getName());
           }
         }
@@ -685,7 +685,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
         {
           if (arg instanceof OptionI)
           {
-            // System.out.println("Setting option "
+            // jalview.bin.Console.outPrintln("Setting option "
             // + System.identityHashCode(arg) + ":" + arg.getName()
             // + " with " + arg.getDefaultValue());
             opanp.selectOption((OptionI) arg, arg.getValue());
@@ -874,7 +874,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
         if (cw + 120 > panewidth)
         {
           jobOptions.add(pbox, "wrap");
-          // System.out.println("Wrap on "+pbox.option.getName());
+          // jalview.bin.Console.outPrintln("Wrap on "+pbox.option.getName());
           cw = hgap + pbox.getSize().width;
           fh = true;
         }
@@ -946,7 +946,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     }
     // TODO: waste some time trying to eliminate any unnecessary .validate calls
     // here
-    // System.out.println("Size will be : "+w+","+os);
+    // jalview.bin.Console.outPrintln("Size will be : "+w+","+os);
     // optsAndparams.setPreferredSize(null);
     // paramPane.getViewport().setView(optsAndparams);
     paramPane.getViewport().setAutoscrolls(true);
@@ -976,7 +976,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
       disc.run();
     } catch (Exception e)
     {
-      System.err.println("Aborting. Problem discovering services.");
+      jalview.bin.Console.errPrintln("Aborting. Problem discovering services.");
       e.printStackTrace();
       return;
     }
@@ -1023,7 +1023,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
               pr = en.next();
             }
             {
-              System.out.println("Testing opts dupes for "
+              jalview.bin.Console.outPrintln("Testing opts dupes for "
                       + lastserv.getUri() + " : " + lastserv.getActionText()
                       + ":" + pr.getName());
               List<Option> rg = lastserv.getRunnerConfig().getOptions();
@@ -1034,17 +1034,17 @@ public class WsJobParameters extends JPanel implements ItemListener,
                   Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
                 } catch (Exception e)
                 {
-                  System.err.println("Failed to copy " + o.getName());
+                  jalview.bin.Console.errPrintln("Failed to copy " + o.getName());
                   e.printStackTrace();
                 } catch (Error e)
                 {
-                  System.err.println("Failed to copy " + o.getName());
+                  jalview.bin.Console.errPrintln("Failed to copy " + o.getName());
                   e.printStackTrace();
                 }
               }
             }
             {
-              System.out.println("Testing param dupes:");
+              jalview.bin.Console.outPrintln("Testing param dupes:");
               List<Parameter> rg = lastserv.getRunnerConfig()
                       .getParameters();
               for (Parameter o : rg)
@@ -1055,17 +1055,17 @@ public class WsJobParameters extends JPanel implements ItemListener,
                           .copyParameter(o);
                 } catch (Exception e)
                 {
-                  System.err.println("Failed to copy " + o.getName());
+                  jalview.bin.Console.errPrintln("Failed to copy " + o.getName());
                   e.printStackTrace();
                 } catch (Error e)
                 {
-                  System.err.println("Failed to copy " + o.getName());
+                  jalview.bin.Console.errPrintln("Failed to copy " + o.getName());
                   e.printStackTrace();
                 }
               }
             }
             {
-              System.out.println("Testing param write:");
+              jalview.bin.Console.outPrintln("Testing param write:");
               List<String> writeparam = null, readparam = null;
               try
               {
@@ -1073,7 +1073,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
                         .writeParameterSet(
                                 pr.getArguments(lastserv.getRunnerConfig()),
                                 " ");
-                System.out.println("Testing param read :");
+                jalview.bin.Console.outPrintln("Testing param read :");
                 List<Option> pset = jalview.ws.jws2.ParameterUtils
                         .processParameters(writeparam,
                                 lastserv.getRunnerConfig(), " ");
@@ -1087,7 +1087,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
                   String on = o.next(), sn = s.next(), st = t.next();
                   if (!sn.equals(st))
                   {
-                    System.out.println(
+                    jalview.bin.Console.outPrintln(
                             "Original was " + on + " Phase 1 wrote " + sn
                                     + "\tPhase 2 wrote " + st);
                     failed = true;
@@ -1095,11 +1095,11 @@ public class WsJobParameters extends JPanel implements ItemListener,
                 }
                 if (failed)
                 {
-                  System.out.println(
+                  jalview.bin.Console.outPrintln(
                           "Original parameters:\n" + pr.getOptions());
-                  System.out.println(
+                  jalview.bin.Console.outPrintln(
                           "Wrote parameters in first set:\n" + writeparam);
-                  System.out.println(
+                  jalview.bin.Console.outPrintln(
                           "Wrote parameters in second set:\n" + readparam);
 
                 }
@@ -1223,7 +1223,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
    * + storeSetName + ": ", jobParams); }
    * 
    * private void writeParam(String nm, List<ArgumentI> params) { for (ArgumentI
-   * p : params) { System.out.println(nm + ":" + System.identityHashCode(p) +
+   * p : params) { jalview.bin.Console.outPrintln(nm + ":" + System.identityHashCode(p) +
    * " Name: " + p.getName() + " Value: " + p.getDefaultValue()); } }
    * 
    * private Object[] _getUserPreset(String setName) { Object[] pset =
@@ -1376,7 +1376,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
         return;
       }
       settingDialog = true;
-      System.out.println("Prompting to save " + lsetname);
+      jalview.bin.Console.outPrintln("Prompting to save " + lsetname);
       if (JvOptionPane.showConfirmDialog(this, "Parameter set '" + lsetname
               + "' is modifed, and your changes will be lost.\nReally change preset ?",
               "Warning: Unsaved Changes",
@@ -1388,7 +1388,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
         settingDialog = false;
         // and leave.
         return;
-        // System.out.println("Saving for " + lsetname);
+        // jalview.bin.Console.outPrintln("Saving for " + lsetname);
         // _storeCurrentPreset(lsetname);
 
       }
@@ -1467,7 +1467,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
           return;
         }
         curSetName = newname;
-        System.err.println("New name for user setting " + curSetName
+        jalview.bin.Console.errPrintln("New name for user setting " + curSetName
                 + " (was " + setName.getSelectedItem() + ")");
         if (curSetName.equals(setName.getSelectedItem()))
         {