Merge branch 'merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609...

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index b1ea60b..642efdb 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -60,6 +60,7 @@ 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;
@@ -287,17 +288,6 @@ public class Jalview
     ArgsParser aparser = new ArgsParser(args);
     boolean headless = false;
 
-    if (aparser.contains("help") || aparser.contains("h"))
-    {
-      showUsage();
-      System.exit(0);
-    }
-    if (aparser.contains("nodisplay") || aparser.contains("nogui")
-            || aparser.contains("headless"))
-    {
-      System.setProperty("java.awt.headless", "true");
-      headless = true;
-    }
     String usrPropsFile = aparser.getValue("props");
     Cache.loadProperties(usrPropsFile); // must do this before
     if (usrPropsFile != null)
@@ -397,6 +387,7 @@ public class Jalview
 
     if (!headless)
     {
+      Desktop.nosplash = aparser.contains("nosplash");
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
 
@@ -427,7 +418,10 @@ public class Jalview
        * @j2sIgnore
        */
       {
-        desktop.startServiceDiscovery();
+        if (!aparser.contains("nowebservicediscovery"))
+        {
+          desktop.startServiceDiscovery();
+        }
         if (!aparser.contains("nousagestats"))
         {
           startUsageStats(desktop);
@@ -733,17 +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!!");
+              }
+            }
           }
 
         }
@@ -779,12 +793,7 @@ public class Jalview
         Cache.removeProperty("STARTUP_FILE");
       }
 
-      protocol = DataSourceType.FILE;
-
-      if (file.indexOf("http:") > -1)
-      {
-        protocol = DataSourceType.URL;
-      }
+      protocol = AppletFormatAdapter.checkProtocol(file);
 
       if (file.endsWith(".jar"))
       {