JAL-3446 unintentially left training message in code.

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index fea99fb..36b5ea3 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -73,7 +73,6 @@ import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
-//import netscape.javascript.JSObject;
 
 /**
  * Main class for Jalview Application <br>
@@ -111,7 +110,6 @@ public class Jalview implements ApplicationSingletonI
   // }
   public static Jalview getInstance()
   {
-    System.out.println("Hello, MW!!!!!!!!!!!!");
     return (Jalview) ApplicationSingletonProvider
             .getInstance(Jalview.class);
   }
@@ -982,8 +980,7 @@ public class Jalview implements ApplicationSingletonI
    * @param aparser
    * @param format
    */
-  private void createOutputFiles(ArgsParser aparser,
-          FileFormatI format)
+  private void createOutputFiles(ArgsParser aparser, FileFormatI format)
   {
     AlignFrame af = currentAlignFrame;
     while (aparser.getSize() >= 2)
@@ -1038,28 +1035,51 @@ public class Jalview implements ApplicationSingletonI
                 "Creating image map: " + imageFile.getAbsolutePath());
         continue;
       default:
-        format = FileFormats.getInstance().forName(outputFormat);
-        if (format == null)
+        // fall through - try to parse as an alignment data export format
+        FileFormatI outFormat = null;
+        try
+        {
+          outFormat = FileFormats.getInstance().forName(outputFormat);
+        } catch (Exception formatP)
         {
-          System.out.println("Invalid file format: " + outputFormat);
-          break;
         }
-        fname = new File(aparser.nextValue()).getAbsolutePath();
-        af.saveAlignment(fname, format);
+        if (outFormat == null)
+        {
+          System.out.println("Couldn't parse " + outputFormat
+                  + " as a valid Jalview format string.");
+          continue;
+        }
+        if (!outFormat.isWritable())
+        {
+          System.out.println(
+                  "This version of Jalview does not support alignment export as "
+                          + outputFormat);
+          continue;
+        }
+        // record file as it was passed to Jalview so it is recognisable to the CLI
+        // caller
+        String file;
+        fname = new File(file = aparser.nextValue()).getAbsolutePath();
+        // JBPNote - yuck - really wish we did have a bean returned from this which gave
+        // success/fail like before !
+        af.saveAlignment(fname, outFormat);
         if (!af.isSaveAlignmentSuccessful())
         {
-          System.out.println("Error writing file " + fname + " in " + format
-                  + " format!!");
-          break;
+          System.out.println("Written alignment in " + outputFormat
+                  + " format to " + file);
+          continue;
+        }
+        else
+        {
+          System.out.println("Error writing file " + file + " in "
+                  + outputFormat + " format!!");
         }
-        continue;
       }
-      System.out.println("Unknown arg: " + outputFormat);      
-      break;
     }
+    // ??? Should report - 'ignoring' extra args here...
     while (aparser.getSize() > 0)
     {
-      System.out.println("Unknown arg: " + aparser.nextValue());
+      System.out.println("Ignoring extra argument: " + aparser.nextValue());
     }
   }