clargs documentation, new vamsas session import and join args. apply gpl development...

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index bfae7e0..a2ef369 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -83,12 +83,15 @@ public class Jalview
                       + "-eps FILE\tCreate EPS file FILE from alignment.\n"
                       + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
                       + "-noquestionnaire\tTurn off questionnaire check.\n"
+                      + "-nousagestats\tTurn off google analytics tracking for this session.\n"
                       + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
-                      + "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)"
+//                      + "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)"
                       + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments.\n"
                       +"\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
                       +"\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
                       + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
+//                      + "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
+//                      + "-vses vamsas-session\tJoin session with given URN\n"
                       + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
                       + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
       System.exit(0);
@@ -204,7 +207,57 @@ public class Jalview
       System.out.println("No files to open!");
       System.exit(1);
     }
-
+    String vamsasImport=aparser.getValue("vdoc"),vamsasSession=aparser.getValue("vsess");
+    if (vamsasImport!=null || vamsasSession!=null)
+    {
+      if (desktop==null || headless)
+      {
+        System.out.println("Headless vamsas sessions not yet supported. Sorry.");
+        System.exit(1);
+      }
+      // if we have a file, start a new session and import it.
+      boolean inSession = false;
+      if (vamsasImport!=null)
+      {
+        try {
+          inSession = desktop.vamsasImport(new File(vamsasImport));
+            
+          } catch (Exception e)
+          {
+            System.err.println("Exeption when importing "+vamsasImport+" as a vamsas document.");
+            e.printStackTrace();
+          }
+          if (!inSession) {
+            System.err.println("Failed to import "+vamsasImport+" as a vamsas document.");
+          } else {
+            System.out.println("Imported Successfully into new session "+desktop.getVamsasApplication().getCurrentSession());
+        }
+      } 
+      if (vamsasSession!=null) {
+        if (vamsasImport!=null) {
+       // close the newly imported session and import the Jalview specific remnants into the new session later on.
+          desktop.vamsasStop_actionPerformed(null);
+        }
+        // now join the new session
+        try {
+          if (desktop.joinVamsasSession(vamsasSession)) {
+            System.out.println("Successfully joined vamsas session "+vamsasSession);
+          } else {
+            System.err.println("WARNING: Failed to join vamsas session "+vamsasSession);
+          }
+        } catch (Exception e)
+        {
+          System.err.println("ERROR: Failed to join vamsas session "+vamsasSession);
+          e.printStackTrace();
+        }
+        if (vamsasImport!=null) {
+          // the Jalview specific remnants can now be imported into the new session at the user's leisure.
+          Cache.log.info("Skipping Push for import of data into existing vamsas session."); // TODO: enable this when debugged
+          // desktop.getVamsasApplication().push_update();
+        }
+      }
+    }
+    // Finally, deal with the remaining input data.
     if (file != null)
     {
       System.out.println("Opening file: " + file);
@@ -384,7 +437,7 @@ public class Jalview
     // We'll only open the default file if the desktop is visible.
     // And the user
     // ////////////////////
-    if (!headless && file == null
+    if (!headless && file == null && vamsasImport==null
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     {
       file = jalview.bin.Cache.getDefault("STARTUP_FILE",