X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=7881ec9d1af7aca6dd9172bf01d7da1b241b341a;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=16da5db1b31cd84cfdfbe5987a7784108cf2579d;hpb=9dfdf03ab75e5d95a8aba4ddf77e18730548b9f5;p=jalview.git diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index 16da5db..7881ec9 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -1,26 +1,29 @@ /* - * 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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 . + * 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.HiddenColumns; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.VamsasAppDatastore; @@ -28,24 +31,24 @@ 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.File; import java.io.IOException; -import java.util.Enumeration; 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.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; @@ -62,7 +65,7 @@ import uk.ac.vamsas.objects.core.Seg; * @author jimp * */ -public class VamsasApplication implements SelectionSource +public class VamsasApplication implements SelectionSource, VamsasSource { IClient vclient = null; @@ -72,16 +75,19 @@ public class VamsasApplication implements SelectionSource 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() @@ -115,7 +121,7 @@ public class VamsasApplication implements SelectionSource /** * @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 @@ -128,12 +134,18 @@ public class VamsasApplication implements SelectionSource * 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 { @@ -144,22 +156,30 @@ public class VamsasApplication implements SelectionSource { if (sess != null) { - throw new Error( - "Implementation Error - cannot import existing vamsas document into an existing session, Yet!"); + throw new Error(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, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, - "VAMSAS Document could not be opened as a new session - please choose another", - "VAMSAS Document Import Failed", - JOptionPane.ERROR_MESSAGE); + MessageManager.getString( + "label.vamsas_doc_couldnt_be_opened_as_new_session"), + MessageManager + .getString("label.vamsas_document_import_failed"), + JvOptionPane.ERROR_MESSAGE); } } @@ -181,8 +201,8 @@ public class VamsasApplication implements SelectionSource } catch (Exception e) { - jalview.bin.Cache.log - .error("Couldn't instantiate vamsas client !", e); + Cache.error("Couldn't instantiate vamsas client !", + e); return false; } return true; @@ -205,16 +225,14 @@ public class VamsasApplication implements SelectionSource } } catch (Error e) { - Cache.log - .warn( - "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless", - e); + Cache.warn( + "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless", + e); } catch (Exception e) { - Cache.log - .warn( - "Probable VAMSAS client incompatibility - carrying on regardless", - e); + Cache.warn( + "Probable VAMSAS client incompatibility - carrying on regardless", + e); } } @@ -225,8 +243,8 @@ public class VamsasApplication implements SelectionSource */ private ClientHandle getJalviewHandle() { - return new ClientHandle("jalview.bin.Jalview", jalview.bin.Cache - .getProperty("VERSION")); + return new ClientHandle("jalview.bin.Jalview", + Cache.getProperty("VERSION")); } /** @@ -247,16 +265,18 @@ public class VamsasApplication implements SelectionSource if (!inSession()) { throw new Error( - "Impementation error! Vamsas Operations when client not initialised and connected."); + "Implementation error! Vamsas Operations when client not initialised and connected"); } addDocumentUpdateHandler(); addStoreDocumentHandler(); startSession(); - Cache.log - .debug("Jalview loading the Vamsas Session for the first time."); + inInitialUpdate = true; + Cache.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."); + Cache.debug("... finished update for the first time."); } /** @@ -286,10 +306,9 @@ public class VamsasApplication implements SelectionSource } } catch (Exception e) { - Cache.log - .warn( - "Exception whilst refreshing jalview windows after a vamsas document update.", - e); + Cache.warn( + "Exception whilst refreshing jalview windows after a vamsas document update.", + e); } } @@ -298,43 +317,57 @@ public class VamsasApplication implements SelectionSource Thread udthread = new Thread(new Runnable() { + @Override public void run() { - Cache.log.info("Jalview updating to the Vamsas Session."); + Cache.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 + Cache.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."); - Cache.log.info("Jalview disconnecting from the Vamsas Session."); + { + throw new Error("Jalview not connected to Vamsas session"); + } + Cache.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."); + Cache.info("Jalview has left the session."); + this.promptUser = ourprompt; // restore default value } else { - Cache.log - .warn("JV Client leaving a session that's its not joined yet."); + Cache.warn( + "JV Client leaving a session that's its not joined yet."); } joinedSession = false; vclient = null; @@ -344,13 +377,13 @@ public class VamsasApplication implements SelectionSource vobj2jv = null; } catch (Exception e) { - Cache.log.error("Vamsas Session finalization threw exceptions!", e); + Cache.error("Vamsas Session finalization threw exceptions!", e); } } public void updateJalview(IClientDocument cdoc) { - Cache.log.debug("Jalview updating from sesion document .."); + Cache.debug("Jalview updating from sesion document .."); ensureJvVamsas(); VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj, baseProvEntry(), alRedoState); @@ -359,7 +392,7 @@ public class VamsasApplication implements SelectionSource vds.updateToJalview(); } catch (Exception e) { - Cache.log.error("Failed to update Jalview from vamsas document.", e); + Cache.error("Failed to update Jalview from vamsas document.", e); } try { @@ -371,10 +404,10 @@ public class VamsasApplication implements SelectionSource } } catch (Exception e) { - Cache.log.error( + Cache.error( "Exception when updating Jalview settings from Appdata.", e); } - Cache.log.debug(".. finished updating from sesion document."); + Cache.debug(".. finished updating from sesion document."); } @@ -409,9 +442,11 @@ public class VamsasApplication implements SelectionSource * bindings is made. * * @param doc + * @return number of views stored in document (updated and new views) */ - public void updateVamsasDocument(IClientDocument doc) + public int updateVamsasDocument(IClientDocument doc) { + int storedviews = 0; ensureJvVamsas(); errorsDuringUpdate = false; errorsDuringAppUpdate = false; @@ -423,7 +458,7 @@ public class VamsasApplication implements SelectionSource if (frames == null) { - return; + return 0; } Hashtable skipList = new Hashtable(); Hashtable viewset = new Hashtable(); @@ -446,11 +481,10 @@ public class VamsasApplication implements SelectionSource } catch (Exception e) { errorsDuringUpdate = true; - Cache.log.error("Exception synchronizing " - + af.getTitle() + Cache.error("Exception synchronizing " + af.getTitle() + " " - + (af.getViewport().viewName == null ? "" : " view " - + af.getViewport().viewName) + + (af.getViewport().getViewName() == null ? "" + : " view " + af.getViewport().getViewName()) + " to document.", e); stored = false; } @@ -460,6 +494,7 @@ public class VamsasApplication implements SelectionSource } 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 @@ -484,7 +519,7 @@ public class VamsasApplication implements SelectionSource } } catch (Exception e) { - Cache.log.error("Exception synchronizing Views to Document :", e); + Cache.error("Exception synchronizing Views to Document :", e); errorsDuringUpdate = true; } @@ -501,10 +536,11 @@ public class VamsasApplication implements SelectionSource } } catch (Exception e) { - Cache.log.error("Client Appdata Write exception", e); + Cache.error("Client Appdata Write exception", e); errorsDuringAppUpdate = true; } vds.clearSkipList(); + return storedviews; } private Entry baseProvEntry() @@ -521,37 +557,39 @@ public class VamsasApplication implements SelectionSource * 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."); + Cache.debug("Updating jalview from changed vamsas document."); disableGui(true); try { long time = System.currentTimeMillis(); IClientDocument cdoc = vclient.getClientDocument(); - if (Cache.log.isDebugEnabled()) + if (Cache.isDebugEnabled()) { - Cache.log.debug("Time taken to get ClientDocument = " + Cache.debug("Time taken to get ClientDocument = " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } if (fromJalview) { - this.updateVamsasDocument(cdoc); - if (Cache.log.isDebugEnabled()) + storedviews += updateVamsasDocument(cdoc); + if (Cache.isDebugEnabled()) { - Cache.log - .debug("Time taken to update Vamsas Document from jalview\t= " + Cache.debug( + "Time taken to update Vamsas Document from jalview\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } cdoc.setVamsasRoots(cdoc.getVamsasRoots()); - if (Cache.log.isDebugEnabled()) + if (Cache.isDebugEnabled()) { - Cache.log.debug("Time taken to set Document Roots\t\t= " + Cache.debug("Time taken to set Document Roots\t\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } @@ -559,19 +597,19 @@ public class VamsasApplication implements SelectionSource else { updateJalview(cdoc); - if (Cache.log.isDebugEnabled()) + if (Cache.isDebugEnabled()) { - Cache.log - .debug("Time taken to update Jalview from vamsas document Roots\t= " + Cache.debug( + "Time taken to update Jalview from vamsas document Roots\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } } vclient.updateDocument(cdoc); - if (Cache.log.isDebugEnabled()) + if (Cache.isDebugEnabled()) { - Cache.log.debug("Time taken to update Session Document\t= " + Cache.debug("Time taken to update Session Document\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } @@ -582,10 +620,12 @@ public class VamsasApplication implements SelectionSource ee.printStackTrace(System.err); // recover object map backup, since its probably corrupted with references // to Vobjects that don't exist anymore. - this.recover_objectMappingBackup(); + recover_objectMappingBackup(); + storedviews = 0; } - Cache.log.debug("Finished updating from document change."); + Cache.debug("Finished updating from document change."); disableGui(false); + return storedviews; } private void addDocumentUpdateHandler() @@ -593,14 +633,15 @@ public class VamsasApplication implements SelectionSource final VamsasApplication client = this; vclient.addDocumentUpdateHandler(new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { - Cache.log.debug("Dealing with document update event."); + Cache.debug("Dealing with document update event."); client.dealWithDocumentUpdate(false); - Cache.log.debug("finished dealing with event."); + Cache.debug("finished dealing with event."); } }); - Cache.log.debug("Added Jalview handler for vamsas document updates."); + Cache.debug("Added Jalview handler for vamsas document updates."); } private void addStoreDocumentHandler() @@ -610,34 +651,43 @@ public class VamsasApplication implements SelectionSource uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE, new PropertyChangeListener() { + @Override 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.debug( + "Asking user if the vamsas session should be stored."); + int reply = JvOptionPane.showInternalConfirmDialog( + Desktop.desktop, + "The current VAMSAS session has unsaved data - do you want to save it ?", + "VAMSAS Session Shutdown", + JvOptionPane.YES_NO_OPTION, + JvOptionPane.QUESTION_MESSAGE); + + if (reply == JvOptionPane.YES_OPTION) + { + Cache.debug("Prompting for vamsas store filename."); + Desktop.instance.vamsasSave_actionPerformed(null); + Cache.debug("Finished attempt at storing document."); + } + Cache.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.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."); + Cache.debug("Added Jalview handler for vamsas document updates."); } public void disableGui(boolean b) { - Desktop.instance.setVamsasUpdate(b); + // JAL-3311 TODO: remove this class! + // Desktop.instance.setVamsasUpdate(b); } Hashtable _backup_vobj2jv; @@ -658,14 +708,20 @@ public class VamsasApplication implements SelectionSource * IO failed * * @throws Error - * if backup_objectMapping was not called. + * 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( - "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made."); + "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made"); } jv2vobj.clear(); Iterator el = _backup_jv2vobj.entrySet().iterator(); @@ -699,19 +755,20 @@ public class VamsasApplication implements SelectionSource } catch (Exception e) { // Complain to GUI - Cache.log.error("Failed to join vamsas session.", e); + Cache.error("Failed to join vamsas session.", e); vclient = null; } try { final IPickManager pm = vclient.getPickManager(); final StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(); - final SelectionSource me = this; + .getStructureSelectionManager(Desktop.instance); + final VamsasApplication me = this; pm.registerMessageHandler(new IMessageHandler() { String last = null; + @Override public void handleMessage(Message message) { if (vobj2jv == null) @@ -727,20 +784,20 @@ public class VamsasApplication implements SelectionSource { return; } - // if (Cache.log.isDebugEnabled()) + // if (Cache.isDebugEnabled()) // { - // Cache.log.debug("Received MouseOverMessage "+mm.getVorbaID()+" + // Cache.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()+" + // Cache.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) @@ -748,12 +805,14 @@ public class VamsasApplication implements SelectionSource // 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) + 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); + // TODO: rationalise : can only clear a selection over a + // referred to object + ssm.sendSelection(null, null, null, me); return; } Class type = null; @@ -764,7 +823,7 @@ public class VamsasApplication implements SelectionSource if (jvobjs[o] == null) { // can't cope with selections for unmapped objects - //continue; + continue; } if (type == null) { @@ -773,9 +832,9 @@ public class VamsasApplication implements SelectionSource ; if (type != jvobjs[o].getClass()) { - send=false; + send = false; // discard - can't cope with selections over mixed objects - //continue; + // continue; } } SequenceGroup jselection = null; @@ -784,7 +843,8 @@ public class VamsasApplication implements SelectionSource { if (jvobjs.length == 1) { - // TODO if (sm.isNone())// send a message to select the specified columns over the + // TODO if (sm.isNone())// send a message to select the + // specified columns over the // given // alignment @@ -797,15 +857,17 @@ public class VamsasApplication implements SelectionSource SequenceI seq; boolean aligned = ((jalview.datamodel.Sequence) jvobjs[0]) .getDatasetSequence() != null; - int maxWidth=0; + int maxWidth = 0; if (aligned) { jselection = new SequenceGroup(); - jselection.addSequence(seq = - (jalview.datamodel.Sequence) jvobjs[0], false); + jselection.addSequence( + seq = (jalview.datamodel.Sequence) jvobjs[0], + false); maxWidth = seq.getLength(); } - for (int c = 1; aligned && jvobjs.length > 1 && c < jvobjs.length; c++) + for (int c = 1; aligned && jvobjs.length > 1 + && c < jvobjs.length; c++) { if (((jalview.datamodel.Sequence) jvobjs[c]) .getDatasetSequence() == null) @@ -816,12 +878,13 @@ public class VamsasApplication implements SelectionSource else { jselection.addSequence( - seq = (jalview.datamodel.Sequence) jvobjs[c], false); - if (maxWidth 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)) { - if (jselection!=null) - { - // set the bounds of the selected area using the first interval. - jselection.setStartRes(prange[p]-1); - jselection.setEndRes(prange[p+1]-1); - rangeset=true; - } - } else { - // 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); - } + 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) + for (int sr = prange[p], er = prange[p + 1], de = er + + d; sr != de; sr += d) { - colsel.addElement(sr-1); + colsel.addElement(sr - 1); } } } @@ -887,7 +946,7 @@ public class VamsasApplication implements SelectionSource } if (send) { - ssm.sendSelection(jselection, colsel, me); + ssm.sendSelection(jselection, colsel, null, me); } // discard message. for (int c = 0; c < jvobjs.length; c++) @@ -906,17 +965,22 @@ public class VamsasApplication implements SelectionSource 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.debug("Mouse over " + v.getId() + " bound to " + // + seq + " at " + index); last = seq; i = index; MouseOverMessage message = new MouseOverMessage(v.getId(), @@ -929,32 +993,41 @@ public class VamsasApplication implements SelectionSource selecter = new SelectionListener() { + @Override public void selection(SequenceGroup seqsel, - ColumnSelection colsel, SelectionSource source) + ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source) { - if (vobj2jv==null) + if (vobj2jv == null) { - Cache.log.warn("Selection listener still active for dead session."); + Cache.warn( + "Selection listener still active for dead session."); // not in a session. return; } if (source != me) { - AlignmentI visal=null; + AlignmentI visal = null; if (source instanceof AlignViewport) { - visal = ((AlignViewport) source).getAlignment(); + visal = ((AlignmentViewport) source).getAlignment(); } SelectionMessage sm = null; if ((seqsel == null || seqsel.getSize() == 0) - && (colsel == null || colsel.getSelected() == null || colsel - .getSelected().size() == 0)) + && (colsel == null || colsel.getSelected() == null + || colsel.getSelected().size() == 0)) { if (source instanceof AlignViewport) { // the empty selection. - sm = new SelectionMessage("jalview", new String[] { ((AlignViewport)source).getSequenceSetId()}, null, true); - } else { + sm = new SelectionMessage("jalview", + new String[] + { ((AlignmentViewport) source) + .getSequenceSetId() }, + null, true); + } + else + { // the empty selection. sm = new SelectionMessage("jalview", null, null, true); } @@ -963,10 +1036,8 @@ public class VamsasApplication implements SelectionSource { String[] vobj = new String[seqsel.getSize()]; int o = 0; - Enumeration sels = seqsel.getSequences(null).elements(); - while (sels.hasMoreElements()) + for (SequenceI sel : seqsel.getSequences(null)) { - SequenceI sel = (SequenceI) sels.nextElement(); VorbaId v = (VorbaId) jv2vobj.get(sel); if (v != null) { @@ -981,39 +1052,57 @@ public class VamsasApplication implements SelectionSource t = null; } Input range = null; - if (seqsel!=null && colsel != 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()) + if (colsel.getSelected() != null + && colsel.getSelected().size() > 0 + && visal != null + && seqsel.getSize() == visal.getHeight()) { - // gather selected columns outwith the sequence positions too - Enumeration cols = colsel.getSelected().elements(); - while (cols.hasMoreElements()) + // gather selected columns outwith the sequence positions + // too + for (Integer ival : colsel.getSelected()) { - int ival = ((Integer) cols.nextElement()).intValue(); Pos p = new Pos(); - p.setI(ival+1); + p.setI(ival.intValue() + 1); range.addPos(p); } - } else { - int[] intervals = colsel.getVisibleContigs(seqsel.getStartRes(), seqsel.getEndRes()+1); - for (int iv=0;iv intervals = hidden + .getVisContigsIterator(seqsel.getStartRes(), + seqsel.getEndRes() + 1, false); + while (intervals.hasNext()) { + int[] region = intervals.next(); Seg s = new Seg(); - s.setStart(intervals[iv]+1); // vamsas indices begin at 1, not zero. - s.setEnd(intervals[iv+1]+1); + s.setStart(region[0] + 1); // vamsas indices begin at 1, + // not zero. + s.setEnd(region[1] + 1); s.setInclusive(true); range.addSeg(s); } } } - sm = new SelectionMessage("jalview", vobj, range); + if (vobj.length > 0) + { + sm = new SelectionMessage("jalview", vobj, range); + } + else + { + sm = null; + } + } + if (sm != null) + { + sm.validate(); // debug + Cache.debug("Selection Message\n" + sm.getRawMessage()); + pm.sendMessage(sm); } - sm.validate(); // debug - Cache.log.debug("Selection Message\n"+sm.getRawMessage()); - pm.sendMessage(sm); } } @@ -1022,8 +1111,17 @@ public class VamsasApplication implements SelectionSource ssm.addSelectionListener(selecter); } catch (Exception e) { - Cache.log.error("Failed to init Vamsas Picking", e); + Cache.error("Failed to init Vamsas Picking", e); } } } + + public String getCurrentSession() + { + if (vclient != null) + { + return (vclient.getSessionUrn()); + } + return null; + } }