X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=d58cb5ad784492b37a9173899e6eadaa373b9290;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=a62eeb50bc0815b41401e3b1ebb75048bdafdaa8;hpb=9b8d1058ff19c4277e8dad545b81816823cbec4e;p=jalview.git diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index a62eeb5..d58cb5a 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -1,26 +1,29 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 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; @@ -72,12 +75,13 @@ public class VamsasApplication implements SelectionSource Desktop jdesktop = null; // our jalview desktop reference - private boolean inInitialUpdate=true; + 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, String sessionName) + public VamsasApplication(Desktop jdesktop, File sessionPath, + String sessionName) { // JBPNote: // we should create a session URI from the sessionPath and pass it to @@ -86,7 +90,6 @@ public class VamsasApplication implements SelectionSource initClientSession(null, sessionPath, sessionName); } - private static uk.ac.vamsas.client.IClientFactory getClientFactory() throws IOException { @@ -138,10 +141,11 @@ public class VamsasApplication implements SelectionSource */ private void initClientSession(String sess, File vamsasDocument) { - initClientSession(sess,vamsasDocument,null); + initClientSession(sess, vamsasDocument, null); } - private boolean initClientSession(String sess, File vamsasDocument, String newDocSessionName) + private boolean initClientSession(String sess, File vamsasDocument, + String newDocSessionName) { try { @@ -153,27 +157,32 @@ public class VamsasApplication implements SelectionSource 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 { - if (newDocSessionName!=null) + if (newDocSessionName != null) { vclient = clientfactory.openAsNewSessionIClient(app, - vamsasDocument,newDocSessionName); - } else { + vamsasDocument, newDocSessionName); + } + else + { vclient = clientfactory.openAsNewSessionIClient(app, - vamsasDocument); + vamsasDocument); } } catch (InvalidSessionDocumentException e) { - JOptionPane + 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); } } @@ -220,14 +229,12 @@ public class VamsasApplication implements SelectionSource } 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); } } @@ -239,8 +246,8 @@ 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", + jalview.bin.Cache.getProperty("VERSION")); } /** @@ -261,7 +268,8 @@ public class VamsasApplication implements SelectionSource 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(); @@ -303,8 +311,7 @@ public class VamsasApplication implements SelectionSource } 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); } } @@ -314,11 +321,11 @@ public class VamsasApplication implements SelectionSource Thread udthread = new Thread(new Runnable() { + @Override public void run() { Cache.log.info("Jalview updating to the Vamsas Session."); - dealWithDocumentUpdate(true); Cache.log.info("Jalview finished updating to the Vamsas Session."); } @@ -347,7 +354,11 @@ public class VamsasApplication implements SelectionSource 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 { @@ -441,7 +452,7 @@ public class VamsasApplication implements SelectionSource */ public int updateVamsasDocument(IClientDocument doc) { - int storedviews=0; + int storedviews = 0; ensureJvVamsas(); errorsDuringUpdate = false; errorsDuringAppUpdate = false; @@ -554,7 +565,7 @@ public class VamsasApplication implements SelectionSource * * @param fromJalview * true to update from jalview to the vamsas document - * @return total number of stored alignments in the document after the update + * @return total number of stored alignments in the document after the update */ protected int dealWithDocumentUpdate(boolean fromJalview) { @@ -574,7 +585,7 @@ public class VamsasApplication implements SelectionSource } if (fromJalview) { - storedviews+=updateVamsasDocument(cdoc); + storedviews += updateVamsasDocument(cdoc); if (Cache.log.isDebugEnabled()) { Cache.log @@ -617,7 +628,7 @@ public class VamsasApplication implements SelectionSource // recover object map backup, since its probably corrupted with references // to Vobjects that don't exist anymore. recover_objectMappingBackup(); - storedviews=0; + storedviews = 0; } Cache.log.debug("Finished updating from document change."); disableGui(false); @@ -629,6 +640,7 @@ 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."); @@ -646,21 +658,22 @@ public class VamsasApplication implements SelectionSource uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE, new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (client.promptUser) { Cache.log .debug("Asking user if the vamsas session should be stored."); - int reply = JOptionPane + int reply = JvOptionPane .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); + JvOptionPane.YES_NO_OPTION, + JvOptionPane.QUESTION_MESSAGE); - if (reply == JOptionPane.YES_OPTION) + if (reply == JvOptionPane.YES_OPTION) { Cache.log.debug("Prompting for vamsas store filename."); Desktop.instance.vamsasSave_actionPerformed(null); @@ -709,13 +722,15 @@ public class VamsasApplication implements SelectionSource { if (_backup_vobj2jv == null) { - if (inInitialUpdate) { + if (inInitialUpdate) + { // nothing to recover so just return; } - + throw new Error( - "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made."); + MessageManager + .getString("error.implementation_error_cannot_recover_vamsas_object_mappings")); } jv2vobj.clear(); Iterator el = _backup_jv2vobj.entrySet().iterator(); @@ -756,12 +771,13 @@ public class VamsasApplication implements SelectionSource { 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) @@ -789,8 +805,8 @@ public class VamsasApplication implements SelectionSource // 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) @@ -805,7 +821,7 @@ public class VamsasApplication implements SelectionSource { // TODO: rationalise : can only clear a selection over a // referred to object - ssm.sendSelection(null, null, me); + ssm.sendSelection(null, null, null, me); return; } Class type = null; @@ -816,7 +832,7 @@ public class VamsasApplication implements SelectionSource if (jvobjs[o] == null) { // can't cope with selections for unmapped objects - // continue; + continue; } if (type == null) { @@ -902,43 +918,29 @@ public class VamsasApplication implements SelectionSource { int[] prange = uk.ac.vamsas.objects.utils.Range .getBounds(sm.getRanges()); - boolean rangeset = false; - colsel = new ColumnSelection(); + 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; - if (!rangeset) + // 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()) { - 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; - } + jselection.setStartRes(prange[p + l] - 1); } - else + if (jselection.getEndRes() <= maxWidth + && prange[p + u] == (jselection.getEndRes() + 2)) { - // 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 @@ -953,7 +955,7 @@ 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++) @@ -972,10 +974,14 @@ 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); @@ -996,8 +1002,10 @@ 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) { @@ -1011,7 +1019,7 @@ public class VamsasApplication implements SelectionSource AlignmentI visal = null; if (source instanceof AlignViewport) { - visal = ((AlignViewport) source).getAlignment(); + visal = ((AlignmentViewport) source).getAlignment(); } SelectionMessage sm = null; if ((seqsel == null || seqsel.getSize() == 0) @@ -1021,9 +1029,9 @@ public class VamsasApplication implements SelectionSource if (source instanceof AlignViewport) { // the empty selection. - sm = new SelectionMessage("jalview", new String[] - { ((AlignViewport) source).getSequenceSetId() }, null, - true); + sm = new SelectionMessage("jalview", + new String[] { ((AlignmentViewport) source) + .getSequenceSetId() }, null, true); } else { @@ -1035,10 +1043,8 @@ 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) { @@ -1065,24 +1071,24 @@ public class VamsasApplication implements SelectionSource { // gather selected columns outwith the sequence positions // too - Enumeration cols = colsel.getSelected().elements(); - while (cols.hasMoreElements()) + 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); + // int[] intervals = colsel.getVisibleContigs( + // seqsel.getStartRes(), seqsel.getEndRes() + 1); + int[] intervals = hidden.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. + // 1, not zero. s.setEnd(intervals[iv + 1] + 1); s.setInclusive(true); range.addSeg(s);