X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=2b7e76c94358546474a358fdb3da01ba15f858fc;hb=93642d621a7f86318a7777b0a70f6113dcd299dc;hp=777d71bbeef0d60da9df32b6a636b08530bdaed2;hpb=3642de417a2240bef7edc3810a0d0cbe24b03da3;p=jalview.git diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index 777d71b..2b7e76c 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 2.5.1) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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; @@ -72,12 +71,13 @@ 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 +86,6 @@ public class VamsasApplication implements SelectionSource initClientSession(null, sessionPath, sessionName); } - private static uk.ac.vamsas.client.IClientFactory getClientFactory() throws IOException { @@ -138,10 +137,11 @@ 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 +157,15 @@ 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) { @@ -318,7 +320,6 @@ 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 +442,7 @@ public class VamsasApplication implements SelectionSource */ public int updateVamsasDocument(IClientDocument doc) { - int storedviews=0; + int storedviews = 0; ensureJvVamsas(); errorsDuringUpdate = false; errorsDuringAppUpdate = false; @@ -554,7 +555,7 @@ 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 +575,7 @@ public class VamsasApplication implements SelectionSource } if (fromJalview) { - storedviews+=updateVamsasDocument(cdoc); + storedviews += updateVamsasDocument(cdoc); if (Cache.log.isDebugEnabled()) { Cache.log @@ -617,7 +618,7 @@ 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 +710,12 @@ 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."); } @@ -910,23 +912,22 @@ public class VamsasApplication implements SelectionSource 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); - } + // 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) @@ -1069,7 +1070,7 @@ public class VamsasApplication implements SelectionSource { 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);