From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 27 Nov 2020 17:24:08 +0000 (+0000)
Subject: JAL-3660 Fix for specified output format when using command line arg to convert a... 
X-Git-Tag: Develop-2_11_2_0-d20201215~15^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=91f5bc8371da7a2c3330477d0b4c716e5fd27dec;p=jalview.git

JAL-3660 Fix for specified output format when using command line arg to convert a file
---

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index b5ec365..642efdb 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -727,17 +727,37 @@ public class Jalview
             af.createEPS(outputFile);
             continue;
           }
-
-          af.saveAlignment(file, format);
-          if (af.isSaveAlignmentSuccessful())
+          FileFormatI outFormat = null;
+          try
+          {
+            outFormat = FileFormats.getInstance().forName(outputFormat);
+          } catch (Exception formatP)
           {
-            System.out.println("Written alignment in " + format
-                    + " format to " + file);
+            System.out.println("Couldn't parse " + outFormat
+                    + " as a valid Jalview format string.");
           }
-          else
+          if (outFormat != null)
           {
-            System.out.println("Error writing file " + file + " in "
-                    + format + " format!!");
+            if (!outFormat.isWritable())
+            {
+              System.out.println(
+                      "This version of Jalview does not support alignment export as "
+                              + outputFormat);
+            }
+            else
+            {
+              af.saveAlignment(file, outFormat);
+              if (af.isSaveAlignmentSuccessful())
+              {
+                System.out.println("Written alignment in "
+                        + outFormat.getName() + " format to " + file);
+              }
+              else
+              {
+                System.out.println("Error writing file " + file + " in "
+                        + outFormat.getName() + " format!!");
+              }
+            }
           }
 
         }