X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=5ee7e36821a730cb8f29b3bbd6a3d61655a9d1bf;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=2879c2faa71d73fb47d42ed94589101a44b3e059;hpb=85c063b49c067bbb850941da79a796cbd5ef032f;p=jalview.git diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index 2879c2f..5ee7e36 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -1,20 +1,20 @@ /* - * 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 2.8.1) + * Copyright (C) 2014 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 + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; @@ -28,6 +28,7 @@ import jalview.structure.SelectionListener; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasListener; +import jalview.structure.VamsasSource; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; @@ -45,7 +46,6 @@ 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 +62,7 @@ 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 +72,19 @@ 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() @@ -133,7 +136,13 @@ public class VamsasApplication implements SelectionSource * 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 { @@ -149,8 +158,16 @@ public class VamsasApplication implements SelectionSource } 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 @@ -206,14 +223,12 @@ 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); } } @@ -225,8 +240,8 @@ 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")); } /** @@ -252,9 +267,11 @@ public class VamsasApplication implements SelectionSource 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."); } @@ -287,8 +304,7 @@ 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); } } @@ -420,9 +436,11 @@ 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; @@ -434,7 +452,7 @@ public class VamsasApplication implements SelectionSource if (frames == null) { - return; + return 0; } Hashtable skipList = new Hashtable(); Hashtable viewset = new Hashtable(); @@ -471,6 +489,7 @@ 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 @@ -516,6 +535,7 @@ public class VamsasApplication implements SelectionSource errorsDuringAppUpdate = true; } vds.clearSkipList(); + return storedviews; } private Entry baseProvEntry() @@ -533,9 +553,11 @@ 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 */ - 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); @@ -551,7 +573,7 @@ public class VamsasApplication implements SelectionSource } if (fromJalview) { - this.updateVamsasDocument(cdoc); + storedviews += updateVamsasDocument(cdoc); if (Cache.log.isDebugEnabled()) { Cache.log @@ -593,10 +615,12 @@ 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."); disableGui(false); + return storedviews; } private void addDocumentUpdateHandler() @@ -684,6 +708,12 @@ public class VamsasApplication implements SelectionSource { 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."); } @@ -726,8 +756,8 @@ 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; @@ -759,8 +789,8 @@ 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) @@ -786,7 +816,7 @@ public class VamsasApplication implements SelectionSource if (jvobjs[o] == null) { // can't cope with selections for unmapped objects - // continue; + continue; } if (type == null) { @@ -872,43 +902,29 @@ 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 @@ -942,7 +958,8 @@ public class VamsasApplication implements SelectionSource int i = -1; - public void mouseOver(SequenceI seq, int index) + public void mouseOver(SequenceI seq, int index, + VamsasSource source) { if (jv2vobj == null) return; @@ -1005,10 +1022,8 @@ 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) { @@ -1046,13 +1061,13 @@ public class VamsasApplication implements SelectionSource } else { - int[] intervals = colsel.getVisibleContigs(seqsel - .getStartRes(), seqsel.getEndRes() + 1); + 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. + // 1, not zero. s.setEnd(intervals[iv + 1] + 1); s.setInclusive(true); range.addSeg(s);