X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=05024ecc0b6f3eef6d7b0ca81008ed01eb302bdf;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=a62eeb50bc0815b41401e3b1ebb75048bdafdaa8;hpb=9b8d1058ff19c4277e8dad545b81816823cbec4e;p=jalview.git diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index a62eeb5..05024ec 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -1,20 +1,19 @@ /* - * 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 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * - * 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. * - * 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 + * 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 . */ package jalview.gui; @@ -28,6 +27,7 @@ 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; @@ -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; @@ -72,12 +72,13 @@ 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 +87,6 @@ public class VamsasApplication implements SelectionSource initClientSession(null, sessionPath, sessionName); } - private static uk.ac.vamsas.client.IClientFactory getClientFactory() throws IOException { @@ -138,10 +138,11 @@ 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 { @@ -157,13 +158,15 @@ public class VamsasApplication implements SelectionSource } 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) { @@ -220,14 +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); } } @@ -239,8 +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")); } /** @@ -303,8 +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); } } @@ -318,7 +318,6 @@ public class VamsasApplication implements SelectionSource { Cache.log.info("Jalview updating to the Vamsas Session."); - dealWithDocumentUpdate(true); Cache.log.info("Jalview finished updating to the Vamsas Session."); } @@ -441,7 +440,7 @@ public class VamsasApplication implements SelectionSource */ public int updateVamsasDocument(IClientDocument doc) { - int storedviews=0; + int storedviews = 0; ensureJvVamsas(); errorsDuringUpdate = false; errorsDuringAppUpdate = false; @@ -554,7 +553,7 @@ 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 +573,7 @@ public class VamsasApplication implements SelectionSource } if (fromJalview) { - storedviews+=updateVamsasDocument(cdoc); + storedviews += updateVamsasDocument(cdoc); if (Cache.log.isDebugEnabled()) { Cache.log @@ -617,7 +616,7 @@ 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); @@ -709,11 +708,12 @@ 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."); } @@ -756,8 +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; @@ -789,8 +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) @@ -816,7 +816,7 @@ public class VamsasApplication implements SelectionSource if (jvobjs[o] == null) { // can't cope with selections for unmapped objects - // continue; + continue; } if (type == null) { @@ -902,43 +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 @@ -972,7 +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; @@ -1035,10 +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) { @@ -1076,13 +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);