From: jprocter Date: Mon, 8 Jun 2009 11:17:06 +0000 (+0000) Subject: refactored for non-interactive import and initiation of sessions. apply gpl developme... X-Git-Tag: Release_2_5~284 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=85c063b49c067bbb850941da79a796cbd5ef032f refactored for non-interactive import and initiation of sessions. apply gpl development license --- diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index 16da5db..2879c2f 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -1,6 +1,6 @@ /* - * 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 (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, 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 @@ -115,7 +115,7 @@ 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 @@ -128,9 +128,9 @@ 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) @@ -303,24 +303,32 @@ public class VamsasApplication implements SelectionSource Cache.log.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 } }); 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."); @@ -328,8 +336,11 @@ public class VamsasApplication implements SelectionSource { if (joinedSession) { + boolean ourprompt = this.promptUser; + this.promptUser = promptUser; vclient.finalizeClient(); Cache.log.info("Jalview has left the session."); + this.promptUser = ourprompt; // restore default value } else { @@ -521,7 +532,7 @@ 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 */ protected void dealWithDocumentUpdate(boolean fromJalview) { @@ -612,24 +623,33 @@ public class VamsasApplication implements SelectionSource { 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.log.debug("Prompting for vamsas store filename."); - Desktop.instance.vamsasSave_actionPerformed(null); - Cache.log.debug("Finished attempt at storing document."); + 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) + { + Cache.log.debug("Prompting for vamsas store filename."); + Desktop.instance.vamsasSave_actionPerformed(null); + Cache.log + .debug("Finished attempt at storing document."); + } + Cache.log + .debug("finished dealing with REQUESTTOCLOSE event."); + } + else + { + Cache.log + .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."); @@ -658,7 +678,7 @@ 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() { @@ -748,12 +768,14 @@ 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, me); return; } Class type = null; @@ -764,7 +786,7 @@ public class VamsasApplication implements SelectionSource if (jvobjs[o] == null) { // can't cope with selections for unmapped objects - //continue; + // continue; } if (type == null) { @@ -773,9 +795,9 @@ 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 +806,8 @@ 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 +820,17 @@ 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 +841,13 @@ public class VamsasApplication implements SelectionSource else { jselection.addSequence( - seq = (jalview.datamodel.Sequence) jvobjs[c], false); - if (maxWidth0) ? 1 : 0; - - if (jselection.getStartRes()>0 && prange[p+l]==jselection.getStartRes()) + 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); + jselection.setStartRes(prange[p + l] - 1); } - if (jselection.getEndRes()<=maxWidth && prange[p+u]==(jselection.getEndRes()+2)) + 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); } } } @@ -915,8 +951,9 @@ public class VamsasApplication implements SelectionSource 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.log.debug("Mouse over " + v.getId() + " bound to " + // + seq + " at " + index); last = seq; i = index; MouseOverMessage message = new MouseOverMessage(v.getId(), @@ -932,15 +969,16 @@ public class VamsasApplication implements SelectionSource public void selection(SequenceGroup seqsel, ColumnSelection colsel, SelectionSource source) { - if (vobj2jv==null) + if (vobj2jv == null) { - Cache.log.warn("Selection listener still active for dead session."); + Cache.log + .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(); @@ -953,8 +991,12 @@ public class VamsasApplication implements SelectionSource 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[] + { ((AlignViewport) source).getSequenceSetId() }, null, + true); + } + else + { // the empty selection. sm = new SelectionMessage("jalview", null, null, true); } @@ -981,39 +1023,57 @@ 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 + // gather selected columns outwith the sequence positions + // too Enumeration cols = colsel.getSelected().elements(); while (cols.hasMoreElements()) { int ival = ((Integer) cols.nextElement()).intValue(); Pos p = new Pos(); - p.setI(ival+1); + p.setI(ival + 1); range.addPos(p); } - } else { - int[] intervals = colsel.getVisibleContigs(seqsel.getStartRes(), seqsel.getEndRes()+1); - for (int iv=0;iv 0) + { + sm = new SelectionMessage("jalview", vobj, range); + } + else + { + sm = null; + } + } + if (sm != null) + { + sm.validate(); // debug + Cache.log.debug("Selection Message\n" + sm.getRawMessage()); + pm.sendMessage(sm); } - sm.validate(); // debug - Cache.log.debug("Selection Message\n"+sm.getRawMessage()); - pm.sendMessage(sm); } } @@ -1026,4 +1086,13 @@ public class VamsasApplication implements SelectionSource } } } + + public String getCurrentSession() + { + if (vclient != null) + { + return (vclient.getSessionUrn()); + } + return null; + } }