*/
package jalview.gui;
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceI;
+import jalview.io.VamsasAppDatastore;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasListener;
+
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.File;
import java.io.IOException;
-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;
import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
-import jalview.bin.Cache;
-import jalview.io.VamsasAppDatastore;
-import jalview.io.VamsasDatastore;
-
-import uk.ac.vamsas.client.*;
-import uk.ac.vamsas.*;
-import uk.ac.vamsas.objects.*;
+import uk.ac.vamsas.client.ClientHandle;
+import uk.ac.vamsas.client.IClient;
+import uk.ac.vamsas.client.IClientDocument;
+import uk.ac.vamsas.client.InvalidSessionDocumentException;
+import uk.ac.vamsas.client.NoDefaultSessionException;
+import uk.ac.vamsas.client.UserHandle;
+import uk.ac.vamsas.client.VorbaId;
+import uk.ac.vamsas.client.picking.IMessageHandler;
+import uk.ac.vamsas.client.picking.IPickManager;
+import uk.ac.vamsas.client.picking.Message;
+import uk.ac.vamsas.client.picking.MouseOverMessage;
import uk.ac.vamsas.objects.core.Entry;
+
/**
* @author jimp
- *
+ *
*/
public class VamsasApplication
{
- IClient vclient=null;
- ClientHandle app=null;
- UserHandle user=null;
-
+ IClient vclient = null;
+
+ ClientHandle app = null;
+
+ UserHandle user = null;
+
Desktop jdesktop = null; // our jalview desktop reference
-
+
// Cache.preferences for vamsas client session arena
// preferences for check for default session at startup.
// user and organisation stuff.
- public VamsasApplication(Desktop jdesktop,
- File sessionPath)
+ public VamsasApplication(Desktop jdesktop, File sessionPath)
{
// JBPNote:
// we should create a session URI from the sessionPath and pass it to
// the clientFactory - but the vamsas api doesn't cope with that yet.
- this(jdesktop);
- throw new Error("Sorry - can't start from session file yet."); // make this a warning
+ this.jdesktop = jdesktop;
+ initClientSession(null, sessionPath);
}
- private static uk.ac.vamsas.client.IClientFactory getClientFactory() throws IOException {
+
+ private static uk.ac.vamsas.client.IClientFactory getClientFactory()
+ throws IOException
+ {
return new uk.ac.vamsas.client.simpleclient.SimpleClientFactory();
}
+
+ /**
+ * Start a new vamsas session
+ *
+ * @param jdesktop
+ */
public VamsasApplication(Desktop jdesktop)
{
- this.jdesktop = jdesktop;
- initClientSession(null);
+ this.jdesktop = jdesktop;
+ initClientSession(null, null);
+ }
+
+ /**
+ * init a connection to the session at the given url
+ *
+ * @param jdesktop
+ * @param sessionUrl
+ */
+ public VamsasApplication(Desktop jdesktop, String sessionUrl)
+ {
+ this.jdesktop = jdesktop;
+ initClientSession(sessionUrl, null);
}
+
/**
- * @throws IOException or other if clientfactory instantiation failed.
+ * @throws IOException
+ * or other if clientfactory instantiation failed.
* @return list of current sessions or null if no session exists.
*/
- public static String[] getSessionList() throws Exception {
+ public static String[] getSessionList() throws Exception
+ {
return getClientFactory().getCurrentSessions();
}
+
/**
- * initialise, possibly with e valid session url
+ * initialise, possibly with either a valid session url or a file for a new
+ * session
+ *
* @param sess
- * @return
+ * null or a valid session url
+ * @param vamsasDocument
+ * null or a valid vamsas document file
+ * @return false if no vamsas connection was made
*/
- private boolean initClientSession(String sess) {
- try {
+ private boolean initClientSession(String sess, File vamsasDocument)
+ {
+ try
+ {
// Only need to tell the library what the application is here
- app = new ClientHandle("jalview.bin.Jalview", jalview.bin.Cache.getProperty("VERSION"));
+ app = getJalviewHandle();
uk.ac.vamsas.client.IClientFactory clientfactory = getClientFactory();
- if (sess==null)
+ if (vamsasDocument != null)
{
- vclient = clientfactory.getIClient(app);
+ if (sess != null)
+ {
+ throw new Error(
+ "Implementation Error - cannot import existing vamsas document into an existing session, Yet!");
+ }
+ try
+ {
+ vclient = clientfactory.openAsNewSessionIClient(app,
+ vamsasDocument);
+ } catch (InvalidSessionDocumentException e)
+ {
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+
+ "VAMSAS Document could not be opened as a new session - please choose another",
+ "VAMSAS Document Import Failed",
+ JOptionPane.ERROR_MESSAGE);
+
+ }
}
else
{
- vclient = clientfactory.getIClient(app,sess);
+ // join existing or create a new session
+ if (sess == null)
+ {
+ vclient = clientfactory.getNewSessionIClient(app);
+ }
+ else
+ {
+ vclient = clientfactory.getIClient(app, sess);
+ }
}
-
+ // set some properties for our VAMSAS interaction
+ setVclientConfig();
user = vclient.getUserHandle();
-
- } catch (NoDefaultSessionException e)
+
+ } catch (Exception e)
{
+ jalview.bin.Cache.log
+ .error("Couldn't instantiate vamsas client !", e);
return false;
}
+ return true;
+ }
+
+ private void setVclientConfig()
+ {
+ if (vclient==null)
+ {
+ return;
+ }
+ try {
+ if (vclient instanceof uk.ac.vamsas.client.simpleclient.SimpleClient)
+ {
+ uk.ac.vamsas.client.simpleclient.SimpleClientConfig cfg = ((uk.ac.vamsas.client.simpleclient.SimpleClient) vclient).getSimpleClientConfig();
+ cfg._validatemergedroots = false;
+ cfg._validateupdatedroots= true; //we may write rubbish otherwise.
+ }
+ }
+ catch (Error e)
+ {
+ Cache.log.warn("Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",e);
+ }
catch (Exception e)
{
- jalview.bin.Cache.log.error("Couldn't instantiate vamsas client !",e);
- return false;
+ Cache.log.warn("Probable VAMSAS client incompatibility - carrying on regardless",e);
}
- return true;
}
+
+ /**
+ * make the appHandle for Jalview
+ *
+ * @return
+ */
+ private ClientHandle getJalviewHandle()
+ {
+ return new ClientHandle("jalview.bin.Jalview", jalview.bin.Cache
+ .getProperty("VERSION"));
+ }
+
/**
*
* @return true if we are registered in a vamsas session
*/
public boolean inSession()
{
- return (vclient!=null);
+ return (vclient != null);
}
+
/**
- * called to connect to session
- * inits handlers, does an initial document update.
+ * called to connect to session inits handlers, does an initial document
+ * update.
*/
public void initial_update()
{
if (!inSession())
{
- throw new Error("Impementation error! Vamsas Operations when client not initialised and connected.");
+ throw new Error(
+ "Impementation error! Vamsas Operations when client not initialised and connected.");
}
addDocumentUpdateHandler();
+ addStoreDocumentHandler();
startSession();
- Cache.log.debug("Jalview loading the Vamsas Session for the first time.");
- dealWithDocumentUpdate();
+ Cache.log
+ .debug("Jalview loading the Vamsas Session for the first time.");
+ dealWithDocumentUpdate(false); // we don't push an update out to the
+ // document yet.
Cache.log.debug("... finished update for the first time.");
}
+
/**
- * Update all windows after a vamsas datamodel change.
- * this could go on the desktop object!
+ * Update all windows after a vamsas datamodel change. this could go on the
+ * desktop object!
*
*/
- protected void updateJalviewGui()
+ protected void updateJalviewGui()
{
JInternalFrame[] frames = jdesktop.getAllFrames();
try
{
- //REVERSE ORDER
+ // REVERSE ORDER
for (int i = frames.length - 1; i > -1; i--)
{
if (frames[i] instanceof AlignFrame)
af.alignPanel.alignmentChanged();
}
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
- Cache.log.warn(
- "Exception whilst refreshing jalview windows after a vamsas document update.",
- e);
+ Cache.log
+ .warn(
+ "Exception whilst refreshing jalview windows after a vamsas document update.",
+ e);
}
}
+
public void push_update()
{
- Cache.log.info("Jalview updating to the Vamsas Session.");
- dealWithDocumentUpdate();
- /*
- IClientDocument cdoc=null;
- try
- {
- cdoc = vclient.getClientDocument();
- }
- catch (Exception e)
- {
- Cache.log.error("Failed to get client document for update.");
- // RAISE A WARNING DIALOG
- disableGui(false);
- return;
- }
- updateVamsasDocument(cdoc);
- updateJalviewGui();
- cdoc.setVamsasRoots(cdoc.getVamsasRoots()); // propagate update flags back
- vclient.updateDocument(cdoc);
- */
- Cache.log.info("Jalview finished updating to the Vamsas Session.");
+ Thread udthread = new Thread(new Runnable() {
+
+ public void run()
+ {
+ Cache.log.info("Jalview updating to the Vamsas Session.");
+
+ dealWithDocumentUpdate(true);
+ /*
+ * IClientDocument cdoc=null; try { cdoc = vclient.getClientDocument(); }
+ * catch (Exception e) { Cache.log.error("Failed to get client document for
+ * update."); // RAISE A WARNING DIALOG disableGui(false); return; }
+ * updateVamsasDocument(cdoc); updateJalviewGui();
+ * cdoc.setVamsasRoots(cdoc.getVamsasRoots()); // propagate update flags
+ * back vclient.updateDocument(cdoc);
+ */
+ Cache.log.info("Jalview finished updating to the Vamsas Session.");
+ // TODO Auto-generated method stub
+ }
+
+ });
+ udthread.start();
}
public void end_session()
Cache.log.info("Jalview disconnecting from the Vamsas Session.");
try
{
- if (joinedSession) {
+ if (joinedSession)
+ {
vclient.finalizeClient();
Cache.log.info("Jalview has left the session.");
- } else {
- Cache.log.warn("JV Client leaving a session that's its not joined yet.");
}
- joinedSession=false;
+ else
+ {
+ Cache.log
+ .warn("JV Client leaving a session that's its not joined yet.");
+ }
+ joinedSession = false;
vclient = null;
- app=null; user = null;
+ app = null;
+ user = null;
jv2vobj = null;
vobj2jv = null;
- }
- catch (Exception e)
+ } catch (Exception e)
{
- Cache.log.error("Vamsas Session finalization threw exceptions!",e);
+ Cache.log.error("Vamsas Session finalization threw exceptions!", e);
}
}
Cache.log.debug("Jalview updating from sesion document ..");
ensureJvVamsas();
VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj,
- baseProvEntry());
+ baseProvEntry(), alRedoState);
vds.updateToJalview();
Cache.log.debug(".. finished updating from sesion document.");
-
+
}
+
private void ensureJvVamsas()
{
if (jv2vobj == null)
{
jv2vobj = new IdentityHashMap();
vobj2jv = new Hashtable();
+ alRedoState = new Hashtable();
}
}
* jalview object binding to VorbaIds
*/
IdentityHashMap jv2vobj = null;
+
Hashtable vobj2jv = null;
+ Hashtable alRedoState = null;
public void updateVamsasDocument(IClientDocument doc)
{
ensureJvVamsas();
VamsasAppDatastore vds = new VamsasAppDatastore(doc, vobj2jv, jv2vobj,
- baseProvEntry());
+ baseProvEntry(), alRedoState);
// wander through frames
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
try
{
- //REVERSE ORDER
+ // REVERSE ORDER
for (int i = frames.length - 1; i > -1; i--)
{
if (frames[i] instanceof AlignFrame)
vds.storeVAMSAS(af.getViewport(), af.getTitle());
}
}
- }
- catch (Exception e)
+ // REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) frames[i];
+
+ // add any AlignedCodonFrame mappings on this alignment to any other.
+ vds.storeSequenceMappings(af.getViewport(), af.getTitle());
+ }
+ }
+ } catch (Exception e)
{
Cache.log.error("Vamsas Document store exception", e);
}
uk.ac.vamsas.objects.core.Entry pentry = new uk.ac.vamsas.objects.core.Entry();
pentry.setUser(user.getFullName());
pentry.setApp(app.getClientUrn());
- pentry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
+ pentry.setDate(new java.util.Date());
pentry.setAction("created");
return pentry;
}
- protected void dealWithDocumentUpdate()
+
+ /**
+ * do a vamsas document update or update jalview from the vamsas document
+ *
+ * @param fromJalview
+ * true to update from jalview to the vamsas document
+ */
+ protected void dealWithDocumentUpdate(boolean fromJalview)
{
// called by update handler for document update.
Cache.log.debug("Updating jalview from changed vamsas document.");
disableGui(true);
- try {
+ try
+ {
+ long time = System.currentTimeMillis();
IClientDocument cdoc = vclient.getClientDocument();
- updateJalview(cdoc);
- // cdoc.setVamsasRoots(cdoc.getVamsasRoots());
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Time taken to get ClientDocument = "
+ + (System.currentTimeMillis() - time));
+ time = System.currentTimeMillis();
+ }
+ if (fromJalview)
+ {
+ this.updateVamsasDocument(cdoc);
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log
+ .debug("Time taken to update Vamsas Document from jalview\t= "
+ + (System.currentTimeMillis() - time));
+ time = System.currentTimeMillis();
+ }
+ cdoc.setVamsasRoots(cdoc.getVamsasRoots());
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Time taken to set Document Roots\t\t= "
+ + (System.currentTimeMillis() - time));
+ time = System.currentTimeMillis();
+ }
+ }
+ else
+ {
+ updateJalview(cdoc);
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log
+ .debug("Time taken to update Jalview from vamsas document Roots\t= "
+ + (System.currentTimeMillis() - time));
+ time = System.currentTimeMillis();
+ }
+
+ }
vclient.updateDocument(cdoc);
- cdoc=null;
- } catch (Exception ee) {
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Time taken to update Session Document\t= "
+ + (System.currentTimeMillis() - time));
+ time = System.currentTimeMillis();
+ }
+ cdoc = null;
+ } catch (Exception ee)
+ {
System.err.println("Exception whilst updating :");
ee.printStackTrace(System.err);
}
Cache.log.debug("Finished updating from document change.");
disableGui(false);
}
+
private void addDocumentUpdateHandler()
{
final VamsasApplication client = this;
- vclient.addDocumentUpdateHandler(new PropertyChangeListener() {
+ vclient.addDocumentUpdateHandler(new PropertyChangeListener()
+ {
public void propertyChange(PropertyChangeEvent evt)
{
Cache.log.debug("Dealing with document update event.");
- client.dealWithDocumentUpdate();
+ client.dealWithDocumentUpdate(false);
Cache.log.debug("finished dealing with event.");
}
});
Cache.log.debug("Added Jalview handler for vamsas document updates.");
}
+
+ private void addStoreDocumentHandler()
+ {
+ final VamsasApplication client = this;
+ vclient.addVorbaEventHandler(uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE, new PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ Cache.log.debug("Asking user if the vamsas session should be stored.");
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "The current VAMSAS session has unsaved data - do you want to save it ?",
+ "VAMSAS Session Shutdown",
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+ if(reply==JOptionPane.YES_OPTION)
+ {
+ Cache.log.debug("Prompting for vamsas store filename.");
+ Desktop.instance.vamsasSave_actionPerformed(null);
+ Cache.log.debug("Finished attempt at storing document.");
+ }
+ Cache.log.debug("finished dealing with REQUESTTOCLOSE event.");
+ }
+ });
+ Cache.log.debug("Added Jalview handler for vamsas document updates.");
+ }
public void disableGui(boolean b)
{
Desktop.instance.setVamsasUpdate(b);
}
- private boolean joinedSession=false;
+
+ private boolean joinedSession = false;
+
+ private VamsasListener picker = null;
+
private void startSession()
{
if (inSession())
{
- try {
+ try
+ {
vclient.joinSession();
- joinedSession=true;
- }
- catch (Exception e)
+ joinedSession = true;
+ } catch (Exception e)
{
// Complain to GUI
- Cache.log.error("Failed to join vamsas session.",e);
- vclient=null;
+ Cache.log.error("Failed to join vamsas session.", e);
+ vclient = null;
+ }
+ try
+ {
+ final IPickManager pm = vclient.getPickManager();
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager();
+ pm.registerMessageHandler(new IMessageHandler()
+ {
+ String last = null;
+
+ public void handleMessage(Message message)
+ {
+ if (message instanceof MouseOverMessage && vobj2jv != null)
+ {
+ MouseOverMessage mm = (MouseOverMessage) message;
+ String mstring = mm.getVorbaID() + " " + mm.getPosition();
+ if (last != null && mstring.equals(last))
+ {
+ return;
+ }
+ // if (Cache.log.isDebugEnabled())
+ // {
+ // Cache.log.debug("Received MouseOverMessage "+mm.getVorbaID()+"
+ // "+mm.getPosition());
+ // }
+ Object jvobj = vobj2jv.get(mm.getVorbaID());
+ if (jvobj != null && jvobj instanceof SequenceI)
+ {
+ last = mstring;
+ // Cache.log.debug("Handling Mouse over "+mm.getVorbaID()+"
+ // bound to "+jvobj+" at "+mm.getPosition());
+ // position is in sequence or in aligned sequence ???????
+ ssm.mouseOverVamsasSequence((SequenceI) jvobj, mm
+ .getPosition());
+ }
+ }
+ }
+ });
+ picker = new VamsasListener()
+ {
+ SequenceI last = null;
+
+ int i = -1;
+
+ public void mouseOver(SequenceI seq, int index)
+ {
+ if (jv2vobj == null)
+ return;
+ if (seq != last || i != index)
+ {
+ VorbaId v = (VorbaId) jv2vobj.get(seq);
+ if (v != null)
+ {
+ Cache.log.debug("Mouse over " + v.getId() + " bound to "
+ + seq + " at " + index);
+ last = seq;
+ i = index;
+ MouseOverMessage message = new MouseOverMessage(v.getId(),
+ index);
+ pm.sendMessage(message);
+ }
+ }
+ }
+ };
+ ssm.addStructureViewerListener(picker); // better method here
+ } catch (Exception e)
+ {
+ Cache.log.error("Failed to init Vamsas Picking", e);
}
}
}
git://source.jalview.org / jalview.git / blobdiff