Merge branch 'patch/JAL-3561_JAL-3660_fileformatexport_CLI' into releases/Release_2_1...

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 35b21df..341bcba 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,6 +20,28 @@
  */
 package jalview.bin;
 
+import jalview.ext.so.SequenceOntology;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.PromptUserConfig;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.FileLoader;
+import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.jws2.Jws2Discoverer;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -626,18 +648,34 @@ public class Jalview
             af.createEPS(outputFile);
             continue;
           }
-
-          if (af.saveAlignment(file, format))
-          {
-            System.out.println("Written alignment in " + format
-                    + " format to " + file);
+          FileFormatI outFormat=null;
+          try {
+            outFormat = FileFormats.getInstance().forName(outputFormat);
+          } catch (Exception formatP) {
+            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
+            {
+              if (af.saveAlignment(file, outFormat))
+              {
+                System.out.println("Written alignment in " + format
+                        + " format to " + file);
+              }
+              else
+              {
+                System.out.println("Error writing file " + file + " in "
+                        + format + " format!!");
+              }
+            }
           }
-
         }
 
         while (aparser.getSize() > 0)
@@ -817,27 +855,22 @@ public class Jalview
 
   private static boolean setCrossPlatformLookAndFeel()
   {
-    boolean set = false;
-    try
-    {
-      UIManager.setLookAndFeel(
-              UIManager.getCrossPlatformLookAndFeelClassName());
-      set = true;
-    } catch (Exception ex)
-    {
-      Cache.log.error("Unexpected Look and Feel Exception");
-      Cache.log.error(ex.getMessage());
-      Cache.log.debug(Cache.getStackTraceString(ex));
-    }
-    return set;
+    return setGenericLookAndFeel(false);
   }
 
   private static boolean setSystemLookAndFeel()
   {
+    return setGenericLookAndFeel(true);
+  }
+
+  private static boolean setGenericLookAndFeel(boolean system)
+  {
     boolean set = false;
     try
     {
-      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+      UIManager.setLookAndFeel(
+              system ? UIManager.getSystemLookAndFeelClassName()
+                      : UIManager.getCrossPlatformLookAndFeelClassName());
       set = true;
     } catch (Exception ex)
     {