From e99c06994dd1e8e0d1740b7eaa89cd2c63861e89 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 16 Jun 2020 17:12:54 +0100
Subject: [PATCH] JAL-3660 JAL-3561 output alignment as requested file format
 as validated by FileFormats - report if format cannot be
 resolved or FileFormatI does not support export. Merged jbp
 patch for 2.11.1.0 to rhanson's Jalview-JS/develop
 reworking of args parsing

---
 src/jalview/bin/Jalview.java |   52 +++++++++++++++++++++++++++---------------
 1 file changed, 33 insertions(+), 19 deletions(-)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index fea99fb..b8aa928 100755
--- 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>
@@ -1038,28 +1037,43 @@ public class Jalview implements ApplicationSingletonI
                 "Creating image map: " + imageFile.getAbsolutePath());
         continue;
       default:
-        format = FileFormats.getInstance().forName(outputFormat);
-        if (format == null)
-        {
-          System.out.println("Invalid file format: " + outputFormat);
-          break;
-        }
-        fname = new File(aparser.nextValue()).getAbsolutePath();
-        af.saveAlignment(fname, format);
-        if (!af.isSaveAlignmentSuccessful())
-        {
-          System.out.println("Error writing file " + fname + " in " + format
-                  + " format!!");
-          break;
-        }
-        continue;
+	  // fall through - try to parse as an alignment data export format
+          FileFormatI outFormat=null;
+          try {
+            outFormat = FileFormats.getInstance().forName(outputFormat);
+          } catch (Exception formatP) {
+          }
+          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("Written alignment in " + outputFormat
+                      + " format to " + file);
+	      continue;
+          } else {
+                System.out.println("Error writing file " + file + " in "
+                        + outputFormat + " format!!");
+          }
       }
-      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());
     }
   }
 
-- 
1.7.10.2