-/**
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasListener;
+import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.IOException;
import java.util.Hashtable;
import java.util.IdentityHashMap;
+import java.util.Iterator;
import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
import uk.ac.vamsas.client.ClientHandle;
import uk.ac.vamsas.client.IClient;
import uk.ac.vamsas.client.IClientDocument;
-import uk.ac.vamsas.client.NoDefaultSessionException;
+import uk.ac.vamsas.client.InvalidSessionDocumentException;
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.client.picking.SelectionMessage;
import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Input;
+import uk.ac.vamsas.objects.core.Pos;
+import uk.ac.vamsas.objects.core.Seg;
+
/**
* @author jimp
- *
+ *
*/
-public class VamsasApplication
+public class VamsasApplication implements SelectionSource, VamsasSource
{
- 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
-
+
+ private boolean inInitialUpdate = true;
+
// 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,
+ String sessionName)
{
// 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, sessionName);
}
- 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);
+ 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 void initClientSession(String sess, File vamsasDocument)
+ {
+ initClientSession(sess, vamsasDocument, null);
+ }
+
+ private boolean initClientSession(String sess, File vamsasDocument,
+ String newDocSessionName)
+ {
+ 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.getNewSessionIClient(app);
+ if (sess != null)
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_import_vamsas_doc"));
+ }
+ try
+ {
+ if (newDocSessionName != null)
+ {
+ vclient = clientfactory.openAsNewSessionIClient(app,
+ vamsasDocument, newDocSessionName);
+ }
+ else
+ {
+ vclient = clientfactory.openAsNewSessionIClient(app,
+ vamsasDocument);
+ }
+ } catch (InvalidSessionDocumentException e)
+ {
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+
+ MessageManager
+ .getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
+ MessageManager
+ .getString("label.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 (Exception e)
+
+ } catch (Exception e)
{
- jalview.bin.Cache.log.error("Couldn't instantiate vamsas client !",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)
+ {
+ Cache.log
+ .warn("Probable VAMSAS client incompatibility - carrying on regardless",
+ e);
+ }
+ }
+
+ /**
+ * 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(
+ MessageManager
+ .getString("error.implementation_error_vamsas_operation_not_init"));
}
addDocumentUpdateHandler();
+ addStoreDocumentHandler();
startSession();
- 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.
+ inInitialUpdate = true;
+ Cache.log
+ .debug("Jalview loading the Vamsas Session for the first time.");
+ dealWithDocumentUpdate(false); // we don't push an update out to the
+ inInitialUpdate = false;
+ // 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(true);
- /*
- IClientDocument cdoc=null;
- try
- {
- cdoc = vclient.getClientDocument();
- }
- catch (Exception e)
+ Thread udthread = new Thread(new Runnable()
{
- 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.");
+
+ public void run()
+ {
+ Cache.log.info("Jalview updating to the Vamsas Session.");
+
+ dealWithDocumentUpdate(true);
+ Cache.log.info("Jalview finished updating to the Vamsas Session.");
+ }
+
+ });
+ udthread.start();
}
+ /**
+ * leave a session, prompting the user to save if necessary
+ */
public void end_session()
{
+ end_session(true);
+ }
+
+ private boolean promptUser = true;
+
+ /**
+ * leave a session, optionally prompting the user to save if necessary
+ *
+ * @param promptUser
+ * when true enable prompting by this application
+ */
+
+ public void end_session(boolean promptUser)
+ {
if (!inSession())
- throw new Error("Jalview not connected to Vamsas session.");
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.jalview_no_connected_vamsas_session"));
+ }
Cache.log.info("Jalview disconnecting from the Vamsas Session.");
try
{
- if (joinedSession) {
+ if (joinedSession)
+ {
+ boolean ourprompt = this.promptUser;
+ this.promptUser = promptUser;
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.");
+ this.promptUser = ourprompt; // restore default value
+ }
+ else
+ {
+ Cache.log
+ .warn("JV Client leaving a session that's its not joined yet.");
}
- joinedSession=false;
+ 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());
- vds.updateToJalview();
+ baseProvEntry(), alRedoState);
+ try
+ {
+ vds.updateToJalview();
+ } catch (Exception e)
+ {
+ Cache.log.error("Failed to update Jalview from vamsas document.", e);
+ }
+ try
+ {
+ if (firstUpdate)
+ {
+ vds.updateJalviewFromAppdata();
+ // Comment this out to repeatedly read in data from JalviewAppData
+ // firstUpdate=false;
+ }
+ } catch (Exception e)
+ {
+ Cache.log.error(
+ "Exception when updating Jalview settings from Appdata.", e);
+ }
Cache.log.debug(".. finished updating from sesion document.");
-
+
}
+
+ boolean firstUpdate = false;
+
private void ensureJvVamsas()
{
if (jv2vobj == null)
{
jv2vobj = new IdentityHashMap();
vobj2jv = new Hashtable();
+ alRedoState = new Hashtable();
+ firstUpdate = true;
}
}
* jalview object binding to VorbaIds
*/
IdentityHashMap jv2vobj = null;
+
Hashtable vobj2jv = null;
- public void updateVamsasDocument(IClientDocument doc)
+
+ Hashtable alRedoState = null;
+
+ boolean errorsDuringUpdate = false;
+
+ boolean errorsDuringAppUpdate = false;
+
+ /**
+ * update the document accessed through doc. A backup of the current object
+ * bindings is made.
+ *
+ * @param doc
+ * @return number of views stored in document (updated and new views)
+ */
+ public int updateVamsasDocument(IClientDocument doc)
{
+ int storedviews = 0;
ensureJvVamsas();
+ errorsDuringUpdate = false;
+ errorsDuringAppUpdate = false;
+ backup_objectMapping();
VamsasAppDatastore vds = new VamsasAppDatastore(doc, vobj2jv, jv2vobj,
- baseProvEntry());
+ baseProvEntry(), alRedoState);
// wander through frames
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
if (frames == null)
{
- return;
+ return 0;
}
+ Hashtable skipList = new Hashtable();
+ Hashtable viewset = new Hashtable();
try
{
- //REVERSE ORDER
+ // REVERSE ORDER
for (int i = frames.length - 1; i > -1; i--)
{
if (frames[i] instanceof AlignFrame)
{
AlignFrame af = (AlignFrame) frames[i];
-
- // update alignment and root from frame.
- vds.storeVAMSAS(af.getViewport(), af.getTitle());
+ if (!viewset.containsKey(af.getViewport().getSequenceSetId()))
+ {
+ // update alignment and root from frame.
+ boolean stored = false;
+ try
+ {
+ stored = vds.storeVAMSAS(af.getViewport(), af.getTitle());
+ } catch (Exception e)
+ {
+ errorsDuringUpdate = true;
+ Cache.log.error("Exception synchronizing "
+ + af.getTitle()
+ + " "
+ + (af.getViewport().viewName == null ? "" : " view "
+ + af.getViewport().viewName)
+ + " to document.", e);
+ stored = false;
+ }
+ if (!stored)
+ { // record skip in skipList
+ skipList.put(af.getViewport().getSequenceSetId(), af);
+ }
+ else
+ {
+ storedviews++;
+ // could try to eliminate sequenceSetId from skiplist ..
+ // (skipList.containsKey(af.getViewport().getSequenceSetId()))
+ // remember sequenceSetId so we can skip all the other views on
+ // same alignment
+ viewset.put(af.getViewport().getSequenceSetId(), af);
+ }
+ }
}
}
- //REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
+ // REVERSE ORDER
+ // for (int i = frames.length - 1; i > -1; i--)
+ // {
+ // if (frames[i] instanceof AlignFrame)
+ // {
+ // AlignFrame af = (AlignFrame) frames[i];
+ Iterator aframes = viewset.values().iterator();
+ while (aframes.hasNext())
{
- 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());
- }
+ AlignFrame af = (AlignFrame) aframes.next();
+ // add any AlignedCodonFrame mappings on this alignment to any other.
+ vds.storeSequenceMappings(af.getViewport(), af.getTitle());
}
+ } catch (Exception e)
+ {
+ Cache.log.error("Exception synchronizing Views to Document :", e);
+ errorsDuringUpdate = true;
}
- catch (Exception e)
+
+ try
+ {
+ if (viewset.size() > 0)
+ {
+ // Alignment views were synchronized, so store their state in the
+ // appData, too.
+ // The skipList ensures we don't write out any alignments not actually
+ // in the document.
+ vds.setSkipList(skipList);
+ vds.updateJalviewClientAppdata();
+ }
+ } catch (Exception e)
{
- Cache.log.error("Vamsas Document store exception", e);
+ Cache.log.error("Client Appdata Write exception", e);
+ errorsDuringAppUpdate = true;
}
+ vds.clearSkipList();
+ return storedviews;
}
private Entry baseProvEntry()
pentry.setAction("created");
return pentry;
}
+
/**
* do a vamsas document update or update jalview from the vamsas document
- * @param fromJalview true to update from jalview to the vamsas document
+ *
+ * @param fromJalview
+ * true to update from jalview to the vamsas document
+ * @return total number of stored alignments in the document after the update
*/
- protected void dealWithDocumentUpdate(boolean fromJalview)
+ protected int dealWithDocumentUpdate(boolean fromJalview)
{
+ int storedviews = 0;
// 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();
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("Time taken to get ClientDocument = "+(System.currentTimeMillis()-time));
+ Cache.log.debug("Time taken to get ClientDocument = "
+ + (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
if (fromJalview)
{
- this.updateVamsasDocument(cdoc);
+ storedviews += updateVamsasDocument(cdoc);
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("Time taken to update Vamsas Document from jalview\t= "+(System.currentTimeMillis()-time));
+ 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));
+ Cache.log.debug("Time taken to set Document Roots\t\t= "
+ + (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
- } else
+ }
+ else
{
updateJalview(cdoc);
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("Time taken to update Jalview from vamsas document Roots\t= "+(System.currentTimeMillis()-time));
+ Cache.log
+ .debug("Time taken to update Jalview from vamsas document Roots\t= "
+ + (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
vclient.updateDocument(cdoc);
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("Time taken to update Session Document\t= "+(System.currentTimeMillis()-time));
+ Cache.log.debug("Time taken to update Session Document\t= "
+ + (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
- cdoc=null;
- } catch (Exception ee) {
+ cdoc = null;
+ } catch (Exception ee)
+ {
System.err.println("Exception whilst updating :");
ee.printStackTrace(System.err);
+ // recover object map backup, since its probably corrupted with references
+ // to Vobjects that don't exist anymore.
+ recover_objectMappingBackup();
+ storedviews = 0;
}
Cache.log.debug("Finished updating from document change.");
disableGui(false);
+ return storedviews;
}
+
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.");
});
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)
+ {
+ if (client.promptUser)
+ {
+ 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.");
+ }
+ else
+ {
+ Cache.log
+ .debug("Ignoring store document request (promptUser==false)");
+ }
+ }
+ });
+ Cache.log.debug("Added Jalview handler for vamsas document updates.");
+ }
+
public void disableGui(boolean b)
{
Desktop.instance.setVamsasUpdate(b);
}
- private boolean joinedSession=false;
- private VamsasListener picker=null;
+
+ Hashtable _backup_vobj2jv;
+
+ IdentityHashMap _backup_jv2vobj;
+
+ /**
+ * make a backup of the object mappings (vobj2jv and jv2vobj)
+ */
+ public void backup_objectMapping()
+ {
+ _backup_vobj2jv = new Hashtable(vobj2jv);
+ _backup_jv2vobj = new IdentityHashMap(jv2vobj);
+ }
+
+ /**
+ * recover original object mappings from the object mapping backup if document
+ * IO failed
+ *
+ * @throws Error
+ * if backup_objectMapping was not called.
+ */
+ public void recover_objectMappingBackup()
+ {
+ if (_backup_vobj2jv == null)
+ {
+ if (inInitialUpdate)
+ {
+ // nothing to recover so just
+ return;
+ }
+
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
+ }
+ jv2vobj.clear();
+ Iterator el = _backup_jv2vobj.entrySet().iterator();
+ while (el.hasNext())
+ {
+ java.util.Map.Entry mp = (java.util.Map.Entry) el.next();
+ jv2vobj.put(mp.getKey(), mp.getValue());
+ }
+ el = _backup_vobj2jv.entrySet().iterator();
+ while (el.hasNext())
+ {
+ java.util.Map.Entry mp = (java.util.Map.Entry) el.next();
+ vobj2jv.put(mp.getKey(), mp.getValue());
+ }
+ }
+
+ private boolean joinedSession = false;
+
+ private VamsasListener picker = null;
+
+ private SelectionListener selecter;
+
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 {
+ try
+ {
final IPickManager pm = vclient.getPickManager();
- final StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager();
- pm.registerMessageHandler(new IMessageHandler() {
- String last=null;
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ final VamsasApplication me = this;
+ pm.registerMessageHandler(new IMessageHandler()
+ {
+ String last = null;
+
public void handleMessage(Message message)
{
- if (message instanceof MouseOverMessage && vobj2jv!=null)
+ if (vobj2jv == null)
+ {
+ // we are not in a session yet.
+ return;
+ }
+ if (message instanceof MouseOverMessage)
{
MouseOverMessage mm = (MouseOverMessage) message;
- String mstring = mm.getVorbaID()+" "+mm.getPosition();
- if (last!=null && mstring.equals(last))
+ 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());
- //}
+ // 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());
+ // Cache.log.debug("Handling Mouse over "+mm.getVorbaID()+"
+ // bound to "+jvobj+" at "+mm.getPosition());
+ // position is character position in aligned sequence
+ ssm.mouseOverVamsasSequence((SequenceI) jvobj,
+ mm.getPosition(), me);
+ }
+ }
+ if (message instanceof uk.ac.vamsas.client.picking.SelectionMessage)
+ {
+ // we only care about AlignmentSequence selections
+ SelectionMessage sm = (SelectionMessage) message;
+ sm.validate();
+ System.err.println("Received\n" + sm.getRawMessage());
+ Object[] jvobjs = sm.getVorbaIDs() == null ? null
+ : new Object[sm.getVorbaIDs().length];
+ if (jvobjs == null)
+ {
+ // TODO: rationalise : can only clear a selection over a
+ // referred to object
+ ssm.sendSelection(null, null, me);
+ return;
}
+ Class type = null;
+ boolean send = true;
+ for (int o = 0; o < jvobjs.length; o++)
+ {
+ jvobjs[o] = vobj2jv.get(sm.getVorbaIDs()[o]);
+ if (jvobjs[o] == null)
+ {
+ // can't cope with selections for unmapped objects
+ continue;
+ }
+ if (type == null)
+ {
+ type = jvobjs[o].getClass();
+ }
+ ;
+ if (type != jvobjs[o].getClass())
+ {
+ send = false;
+ // discard - can't cope with selections over mixed objects
+ // continue;
+ }
+ }
+ SequenceGroup jselection = null;
+ ColumnSelection colsel = null;
+ if (type == jalview.datamodel.Alignment.class)
+ {
+ if (jvobjs.length == 1)
+ {
+ // TODO if (sm.isNone())// send a message to select the
+ // specified columns over the
+ // given
+ // alignment
+
+ send = true;
+ }
+ }
+ if (type == jalview.datamodel.Sequence.class)
+ {
+
+ SequenceI seq;
+ boolean aligned = ((jalview.datamodel.Sequence) jvobjs[0])
+ .getDatasetSequence() != null;
+ int maxWidth = 0;
+ if (aligned)
+ {
+ jselection = new SequenceGroup();
+ jselection.addSequence(
+ seq = (jalview.datamodel.Sequence) jvobjs[0],
+ false);
+ maxWidth = seq.getLength();
+ }
+ for (int c = 1; aligned && jvobjs.length > 1
+ && c < jvobjs.length; c++)
+ {
+ if (((jalview.datamodel.Sequence) jvobjs[c])
+ .getDatasetSequence() == null)
+ {
+ aligned = false;
+ continue;
+ }
+ else
+ {
+ jselection.addSequence(
+ seq = (jalview.datamodel.Sequence) jvobjs[c],
+ false);
+ if (maxWidth < seq.getLength())
+ {
+ maxWidth = seq.getLength();
+ }
+
+ }
+ }
+ if (!aligned)
+ {
+ jselection = null;
+ // if cardinality is greater than one then verify all
+ // sequences are alignment sequences.
+ if (jvobjs.length == 1)
+ {
+ // find all instances of this dataset sequence in the
+ // displayed alignments containing the associated range and
+ // select them.
+ }
+ }
+ else
+ {
+ jselection.setStartRes(0);
+ jselection.setEndRes(maxWidth);
+ // locate the alignment containing the given sequences and
+ // select the associated ranges on them.
+ if (sm.getRanges() != null)
+ {
+ int[] prange = uk.ac.vamsas.objects.utils.Range
+ .getBounds(sm.getRanges());
+ jselection.setStartRes(prange[0] - 1);
+ jselection.setEndRes(prange[1] - 1);
+ prange = uk.ac.vamsas.objects.utils.Range
+ .getIntervals(sm.getRanges());
+ colsel = new ColumnSelection();
+ for (int p = 0; p < prange.length; p += 2)
+ {
+ int d = (prange[p] <= prange[p + 1]) ? 1 : -1;
+ // try to join up adjacent columns to make a larger
+ // selection
+ // lower and upper bounds
+ int l = (d < 0) ? 1 : 0;
+ int u = (d > 0) ? 1 : 0;
+
+ if (jselection.getStartRes() > 0
+ && prange[p + l] == jselection.getStartRes())
+ {
+ jselection.setStartRes(prange[p + l] - 1);
+ }
+ if (jselection.getEndRes() <= maxWidth
+ && prange[p + u] == (jselection.getEndRes() + 2))
+ {
+ jselection.setEndRes(prange[p + u] - 1);
+ }
+ // mark all the columns in the range.
+ for (int sr = prange[p], er = prange[p + 1], de = er
+ + d; sr != de; sr += d)
+ {
+ colsel.addElement(sr - 1);
+ }
+ }
+ }
+ send = true;
+ }
+ }
+ if (send)
+ {
+ ssm.sendSelection(jselection, colsel, me);
+ }
+ // discard message.
+ for (int c = 0; c < jvobjs.length; c++)
+ {
+ jvobjs[c] = null;
+ }
+ ;
+ jvobjs = null;
+ return;
}
}
});
- picker = new VamsasListener() {
- SequenceI last=null;
- int i=-1;
- public void mouseOver(SequenceI seq, int index)
+ picker = new VamsasListener()
+ {
+ SequenceI last = null;
+
+ int i = -1;
+
+ @Override
+ public void mouseOverSequence(SequenceI seq, int index,
+ VamsasSource source)
{
- if (jv2vobj==null)
+ if (jv2vobj == null)
+ {
return;
- if (seq!=last || i!=index)
+ }
+ if (seq != last || i != index)
{
VorbaId v = (VorbaId) jv2vobj.get(seq);
- if (v!=null)
+ if (v != null)
{
- Cache.log.debug("Mouse over "+v.getId()+" bound to "+seq+" at "+index);
+ // this should really be a trace message.
+ // Cache.log.debug("Mouse over " + v.getId() + " bound to "
+ // + seq + " at " + index);
last = seq;
- i=index;
- MouseOverMessage message = new MouseOverMessage(v.getId(), index);
+ i = index;
+ MouseOverMessage message = new MouseOverMessage(v.getId(),
+ index);
pm.sendMessage(message);
}
}
}
};
+ selecter = new SelectionListener()
+ {
+
+ public void selection(SequenceGroup seqsel,
+ ColumnSelection colsel, SelectionSource source)
+ {
+ if (vobj2jv == null)
+ {
+ Cache.log
+ .warn("Selection listener still active for dead session.");
+ // not in a session.
+ return;
+ }
+ if (source != me)
+ {
+ AlignmentI visal = null;
+ if (source instanceof AlignViewport)
+ {
+ visal = ((AlignmentViewport) source).getAlignment();
+ }
+ SelectionMessage sm = null;
+ if ((seqsel == null || seqsel.getSize() == 0)
+ && (colsel == null || colsel.getSelected() == null || colsel
+ .getSelected().size() == 0))
+ {
+ if (source instanceof AlignViewport)
+ {
+ // the empty selection.
+ sm = new SelectionMessage("jalview",
+ new String[] { ((AlignmentViewport) source)
+ .getSequenceSetId() }, null, true);
+ }
+ else
+ {
+ // the empty selection.
+ sm = new SelectionMessage("jalview", null, null, true);
+ }
+ }
+ else
+ {
+ String[] vobj = new String[seqsel.getSize()];
+ int o = 0;
+ for (SequenceI sel : seqsel.getSequences(null))
+ {
+ VorbaId v = (VorbaId) jv2vobj.get(sel);
+ if (v != null)
+ {
+ vobj[o++] = v.toString();
+ }
+ }
+ if (o < vobj.length)
+ {
+ String t[] = vobj;
+ vobj = new String[o];
+ System.arraycopy(t, 0, vobj, 0, o);
+ t = null;
+ }
+ Input range = null;
+ if (seqsel != null && colsel != null)
+ {
+ // deparse the colsel into positions on the vamsas alignment
+ // sequences
+ range = new Input();
+ if (colsel.getSelected() != null
+ && colsel.getSelected().size() > 0
+ && visal != null
+ && seqsel.getSize() == visal.getHeight())
+ {
+ // gather selected columns outwith the sequence positions
+ // too
+ for (Object obj : colsel.getSelected())
+ {
+ int ival = ((Integer) obj).intValue();
+ Pos p = new Pos();
+ p.setI(ival + 1);
+ range.addPos(p);
+ }
+ }
+ else
+ {
+ int[] intervals = colsel.getVisibleContigs(
+ seqsel.getStartRes(), seqsel.getEndRes() + 1);
+ for (int iv = 0; iv < intervals.length; iv += 2)
+ {
+ Seg s = new Seg();
+ s.setStart(intervals[iv] + 1); // vamsas indices begin at
+ // 1, not zero.
+ s.setEnd(intervals[iv + 1] + 1);
+ s.setInclusive(true);
+ range.addSeg(s);
+ }
+ }
+ }
+ if (vobj.length > 0)
+ {
+ sm = new SelectionMessage("jalview", vobj, range);
+ }
+ else
+ {
+ sm = null;
+ }
+ }
+ if (sm != null)
+ {
+ sm.validate(); // debug
+ Cache.log.debug("Selection Message\n" + sm.getRawMessage());
+ pm.sendMessage(sm);
+ }
+ }
+ }
+
+ };
ssm.addStructureViewerListener(picker); // better method here
+ ssm.addSelectionListener(selecter);
} catch (Exception e)
{
- Cache.log.error("Failed to init Vamsas Picking",e);
+ Cache.log.error("Failed to init Vamsas Picking", e);
}
}
}
+
+ public String getCurrentSession()
+ {
+ if (vclient != null)
+ {
+ return (vclient.getSessionUrn());
+ }
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff