JAL-3311 remove menus and documentation relating to VAMSAS - dead code will be backed...

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index b5fa7fa..86499c8 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -52,6 +52,11 @@ import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
+import java.security.AllPermission;
+import java.security.CodeSource;
+import java.security.PermissionCollection;
+import java.security.Permissions;
+import java.security.Policy;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
@@ -59,7 +64,6 @@ import java.util.Vector;
 import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
 
-import com.sun.xml.ws.policy.Policy;
 import com.threerings.getdown.util.LaunchUtil;
 
 import groovy.lang.Binding;
@@ -94,8 +98,6 @@ public class Jalview
   static
   {
     // grab all the rights we can the JVM
-    Policy.createEmptyPolicy();
-    /*
     Policy.setPolicy(new Policy()
     {
       @Override
@@ -111,7 +113,6 @@ public class Jalview
       {
       }
     });
-    */
   }
 
   /**
@@ -201,6 +202,8 @@ public class Jalview
     System.out.println(System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
             + System.getProperty("os.version"));
+    // report Jalview version
+    Cache.loadBuildProperties(true);
 
     String appdirString = System.getProperty("getdownappdir");
     if (appdirString != null && appdirString.length() > 0)
@@ -359,10 +362,12 @@ public class Jalview
         JalviewTaskbar.setTaskbar(this);
       } catch (Exception e)
       {
-        e.printStackTrace();
+        System.out.println("Cannot set Taskbar");
+        // e.printStackTrace();
       } catch (Throwable t)
       {
-        t.printStackTrace();
+        System.out.println("Cannot set Taskbar");
+        // t.printStackTrace();
       }
 
       desktop.setVisible(true);
@@ -433,91 +438,6 @@ public class Jalview
       System.out.println("No files to open!");
       System.exit(1);
     }
-    String vamsasImport = aparser.getValue("vdoc");
-    String 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
-        {
-          DataSourceType viprotocol = AppletFormatAdapter
-                  .checkProtocol(vamsasImport);
-          if (viprotocol == DataSourceType.FILE)
-          {
-            inSession = desktop.vamsasImport(new File(vamsasImport));
-          }
-          else if (viprotocol == DataSourceType.URL)
-          {
-            inSession = desktop.vamsasImport(new URL(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();
-        }
-      }
-    }
     long progress = -1;
     // Finally, deal with the remaining input data.
     if (file != null)
@@ -754,7 +674,7 @@ public class Jalview
     // And the user
     // ////////////////////
 
-    if (!headless && file == null && vamsasImport == null
+    if (!headless && file == null
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     {
       file = jalview.bin.Cache.getDefault("STARTUP_FILE",
@@ -860,10 +780,6 @@ public class Jalview
                     // passed in correctly)"
                     + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\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");
   }