X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasClient.java;fp=src%2Fjalview%2Fgui%2FVamsasClient.java;h=76e9599e498dc8c4c22f4898c34e76c1e6a0f5a1;hb=072fc418c393cbd2a40dfa1d3e46f90178b79572;hp=8d635a39ed144c4b26f01b632ab83bf05e57e79f;hpb=91cb798a47b512b0ac3792fd3a84f2c5bd3c7218;p=jalview.git

diff --git a/src/jalview/gui/VamsasClient.java b/src/jalview/gui/VamsasClient.java
index 8d635a3..76e9599 100755
--- a/src/jalview/gui/VamsasClient.java
+++ b/src/jalview/gui/VamsasClient.java
@@ -8,6 +8,7 @@ import java.io.FileOutputStream;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.util.Hashtable;
+import java.util.IdentityHashMap;
 import java.util.Vector;
 import java.util.jar.JarOutputStream;
 
@@ -42,9 +43,33 @@ public class VamsasClient extends ArchiveClient {
 		Cache.log.info("Jalview loading the Vamsas Session.");
 		// load in the vamsas archive for the first time
 		ClientDoc cdoc = this.getUpdateable();
+		updateJalview(cdoc);
+		
+	}
+	/**
+	 * this will close all windows currently in Jalview.
+	 *
+	 */
+	protected void closeWindows() {
+		JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+        if (frames == null)
+        {
+            return;
+        }
+
+        try
+        {	
+            for (int i = frames.length - 1; i > -1; i--) {
+            	frames[i].dispose();	
+            }
+        } catch (Exception e) {
+        	Cache.log.error("Whilst closing windows",e);
+        }
 		
 	}
 	public void get_update(VamsasArchive doc) {
+		// Close windows - load update.
 		Cache.log.info("Jalview updating from Vamsas Session.");
 	}
 	public void push_update() {
@@ -56,10 +81,22 @@ public class VamsasClient extends ArchiveClient {
 		// stop any update/watcher thread.
 		Cache.log.info("Jalview disconnecting from the Vamsas Session.");
 	}
-	java.util.Hashtable jv2vobj = null;
+	public void updateJalview(ClientDoc cdoc) {
+		
+	}
+	protected void _updateAlignFrame(ClientDoc cdoc, AlignFrame av) {
+		
+	}
+	/**
+	 * jalview object binding to VorbaIds
+	 */
+	IdentityHashMap jv2vobj = null;
+	Hashtable vobj2jv = null;
 	public void updateVamsasDocument(ClientDoc doc) {
-		if (jv2vobj==null)
-			jv2vobj = new Hashtable();
+		if (jv2vobj==null) {
+			jv2vobj = new IdentityHashMap();
+			vobj2jv = new Hashtable();
+		}
 		// wander through frames 
 		JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
@@ -83,7 +120,9 @@ public class VamsasClient extends ArchiveClient {
                 if (frames[i] instanceof AlignFrame)
                 {
                 	AlignFrame af = (AlignFrame) frames[i];
+                	
                 	// check if this frame has an associated alignment object ?
+                	
                 	// update alignment and root from frame.
 
                 }