/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.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.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;
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 = jdesktop;
- initClientSession(null, sessionPath);
+ initClientSession(null, sessionPath, sessionName);
}
private static uk.ac.vamsas.client.IClientFactory getClientFactory()
/**
* @throws IOException
- * or other if clientfactory instantiation failed.
+ * or other if clientfactory instantiation failed.
* @return list of current sessions or null if no session exists.
*/
public static String[] getSessionList() throws Exception
* session
*
* @param sess
- * null or a valid session url
+ * null or a valid session url
* @param vamsasDocument
- * null or a valid vamsas document file
+ * null or a valid vamsas document file
* @return false if no vamsas connection was made
*/
- private boolean initClientSession(String sess, File vamsasDocument)
+ private void initClientSession(String sess, File vamsasDocument)
+ {
+ initClientSession(sess, vamsasDocument, null);
+ }
+
+ private boolean initClientSession(String sess, File vamsasDocument,
+ String newDocSessionName)
{
try
{
if (sess != null)
{
throw new Error(
- "Implementation Error - cannot import existing vamsas document into an existing session, Yet!");
+ MessageManager
+ .getString("error.implementation_error_cannot_import_vamsas_doc"));
}
try
{
- vclient = clientfactory.openAsNewSessionIClient(app,
- vamsasDocument);
+ if (newDocSessionName != null)
+ {
+ vclient = clientfactory.openAsNewSessionIClient(app,
+ vamsasDocument, newDocSessionName);
+ }
+ else
+ {
+ 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",
+ MessageManager
+ .getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
+ MessageManager
+ .getString("label.vamsas_document_import_failed"),
JOptionPane.ERROR_MESSAGE);
}
} catch (Error e)
{
Cache.log
- .warn(
- "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
+ .warn("Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
e);
} catch (Exception e)
{
Cache.log
- .warn(
- "Probable VAMSAS client incompatibility - carrying on regardless",
+ .warn("Probable VAMSAS client incompatibility - carrying on regardless",
e);
}
}
*/
private ClientHandle getJalviewHandle()
{
- return new ClientHandle("jalview.bin.Jalview", jalview.bin.Cache
- .getProperty("VERSION"));
+ return new ClientHandle("jalview.bin.Jalview",
+ jalview.bin.Cache.getProperty("VERSION"));
}
/**
if (!inSession())
{
throw new Error(
- "Impementation error! Vamsas Operations when client not initialised and connected.");
+ MessageManager
+ .getString("error.implementation_error_vamsas_operation_not_init"));
}
addDocumentUpdateHandler();
addStoreDocumentHandler();
startSession();
+ 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.");
}
} catch (Exception e)
{
Cache.log
- .warn(
- "Exception whilst refreshing jalview windows after a vamsas document update.",
+ .warn("Exception whilst refreshing jalview windows after a vamsas document update.",
e);
}
}
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();
}
+ /**
+ * 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)
{
+ boolean ourprompt = this.promptUser;
+ this.promptUser = promptUser;
vclient.finalizeClient();
Cache.log.info("Jalview has left the session.");
+ this.promptUser = ourprompt; // restore default value
}
else
{
ensureJvVamsas();
VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj,
baseProvEntry(), alRedoState);
- vds.updateToJalview();
+ 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;
}
}
Hashtable alRedoState = null;
- public void updateVamsasDocument(IClientDocument doc)
+ 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(), alRedoState);
// wander through frames
if (frames == null)
{
- return;
+ return 0;
}
+ Hashtable skipList = new Hashtable();
+ Hashtable viewset = new Hashtable();
try
{
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--)
+ // 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];
+ 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;
+ }
- // add any AlignedCodonFrame mappings on this alignment to any other.
- vds.storeSequenceMappings(af.getViewport(), af.getTitle());
- }
+ 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()
* do a vamsas document update or update jalview from the vamsas document
*
* @param fromJalview
- * true to update from jalview to the vamsas document
+ * 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);
}
if (fromJalview)
{
- this.updateVamsasDocument(cdoc);
+ storedviews += updateVamsasDocument(cdoc);
if (Cache.log.isDebugEnabled())
{
Cache.log
{
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()
{
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)
+ 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("Prompting for vamsas store filename.");
- Desktop.instance.vamsasSave_actionPerformed(null);
- Cache.log.debug("Finished attempt at storing document.");
+ Cache.log
+ .debug("Ignoring store document request (promptUser==false)");
}
- Cache.log
- .debug("finished dealing with REQUESTTOCLOSE event.");
}
});
Cache.log.debug("Added Jalview handler for vamsas document updates.");
Desktop.instance.setVamsasUpdate(b);
}
+ 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())
{
final IPickManager pm = vclient.getPickManager();
final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager();
+ .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();
// 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());
+ 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;
}
}
});
int i = -1;
- public void mouseOver(SequenceI seq, int index)
+ @Override
+ public void mouseOverSequence(SequenceI seq, int index,
+ VamsasSource source)
{
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);
+ // 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(),
}
}
};
+ 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);
}
}
}
+
+ public String getCurrentSession()
+ {
+ if (vclient != null)
+ {
+ return (vclient.getSessionUrn());
+ }
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff