preliminary notes on javliew sync with vamsas document

diff --git a/src/jalview/gui/VamsasClient.java b/src/jalview/gui/VamsasClient.java
index 46881ef..8d635a3 100755 (executable)
--- a/src/jalview/gui/VamsasClient.java
+++ b/src/jalview/gui/VamsasClient.java
@@ -7,6 +7,7 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
+import java.util.Hashtable;
 import java.util.Vector;
 import java.util.jar.JarOutputStream;
 
@@ -33,15 +34,15 @@ public class VamsasClient extends ArchiveClient {
        // user and organisation stuff.
        public VamsasClient(Desktop jdesktop,
                        File sessionPath) {
-               super("Jalview User", "Dundee", "jalview","2.7",
+               super(System.getProperty("user.name"),System.getProperty("host.name"), "jalview","2.7",
                                sessionPath);
                us=jdesktop;
        }
        public void initial_update() {
                Cache.log.info("Jalview loading the Vamsas Session.");
                // load in the vamsas archive for the first time
+               ClientDoc cdoc = this.getUpdateable();
                
-               // VamsasArchive doc = new VamsasArchive();
        }
        public void get_update(VamsasArchive doc) {
                Cache.log.info("Jalview updating from Vamsas Session.");
@@ -55,7 +56,10 @@ public class VamsasClient extends ArchiveClient {
                // stop any update/watcher thread.
                Cache.log.info("Jalview disconnecting from the Vamsas Session.");
        }
-       public void updateVamsasDocument(VamsasDocument doc) {
+       java.util.Hashtable jv2vobj = null;
+       public void updateVamsasDocument(ClientDoc doc) {
+               if (jv2vobj==null)
+                       jv2vobj = new Hashtable();
                // wander through frames 
                JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
@@ -66,6 +70,11 @@ public class VamsasClient extends ArchiveClient {
 
         try
         {      
+               // Mapping
+               // Alignframe.alignment (non-null dataset)==alignment
+               // alignframe .alignment (dataset==null) = VAMAS[]
+               // Tree.alignment = vamsas[].tree (vamsas[] given by dataset, alignment given by local ref]
+               
                Vector shortNames = new Vector();
                
                //REVERSE ORDER
@@ -76,36 +85,6 @@ public class VamsasClient extends ArchiveClient {
                        AlignFrame af = (AlignFrame) frames[i];
                        // check if this frame has an associated alignment object ?
                        // update alignment and root from frame.
-                       
-                       
-                    String shortName = af.getTitle();
-
-                    if (shortName.indexOf(File.separatorChar) > -1)
-                    {
-                        shortName = shortName.substring(shortName.lastIndexOf(
-                                    File.separatorChar) + 1);
-                    }
-
-                    int count = 1;
-
-                    while (shortNames.contains(shortName))
-                    {
-                        if (shortName.endsWith("_" + (count - 1)))
-                        {
-                            shortName = shortName.substring(0,
-                                    shortName.lastIndexOf("_"));
-                        }
-
-                        shortName = shortName.concat("_" + count);
-                        count++;
-                    }
-
-                    shortNames.addElement(shortName);
-
-                    if (!shortName.endsWith(".xml"))
-                    {
-                        shortName = shortName + ".xml";
-                    }
 
                 }
             }