2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
20 // default console to report messages
21 var _console = document.getElementById("stdout");
22 var _jvapps = new Array();
23 // jvjmols is a list associating a jmol id to { modelstofiles }
24 var _jvjmols = new Hashtable();
25 // array of model names used to lookup index in Jmol
26 var _modeltofiles = new Array();
27 // counter for jmol structures
30 function getDocumentBase() {
31 var dburi = document.baseURI;
32 // IE does not support document.baseURI
33 // logic from patch to TYPO3:
34 // http://forge.typo3.org/projects/typo3cms-core/repository/revisions/f61358afad28adb6dcaeb270ba480e998dfb0b79/diff/typo3/sysext/rtehtmlarea/htmlarea/htmlarea.js
36 var baseTags = document.getElementsByTagName('base');
37 if (baseTags.length > 0) {
38 dburi = baseTags[0].href;
43 return dburi.substring(0, dburi.lastIndexOf("/") + 1);
45 function setConsole(console) {
49 function getDestinationFrms(source, frames) {
50 var frms = new Array();
54 frid = (source!=null) && (("" + source.getSequenceSetId()) == ("" + frames[frm].currentAlignFrame
55 .getSequenceSetId()));
59 if (!frames[frm].equals(source) && !frid
60 && !frames[frm].currentAlignFrame.equals(source)) {
61 frms[frms.length] = frames[frm];
67 function mouseover(list1, list2, list3, list4) {
68 // list1 = new Object(list1);
69 var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
70 var msg = "Mouse over :\n" + "AlignFrame obj: " + list1 + " Seq : "
71 + list[1] + "\nPos: " + list[2] + "(" + list[3] + ")\n";
73 var flist = getDestinationFrms(list1, _jvapps);
75 _console.value = msg + "\n";
78 for (follower in flist) {
80 _console.value += "Sending to " + flist[follower] + "\n";
82 flist[follower].highlight(list[1], list[2], "true");
87 function sellist(list1, list2, list3, list4) {
88 // list1 = new Object(list1);
89 var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
90 var msg = "Selection:\n" + "AlignFrame obj: " + list[0] + " id : "
91 + list[1] + "\nSeqs " + list[2] + "\nColumns " + list[3] + "\n";
92 var flist = getDestinationFrms(list1, _jvapps);
94 _console.value = msg + "\n";
97 for (follower in flist) {
99 _console.value += "Sending to " + flist[follower] + "\n";
101 flist[follower].selectIn(flist[follower].getDefaultTargetFrame(),
107 function viewlist(list1, list2, list3, list4) {
108 // list1 = new Object(list1);
109 var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
110 var msg = "Viewport extent change::\n" + "AlignFrame obj: " + list[0]
111 + " id : " + list[1] + "\nRow from " + list[2] + " and to "
112 + list[3] + "\nVisible columns: " + list[4] + "\n";
113 var flist = getDestinationFrms(list1, _jvapps);
115 _console.value = msg + "\n";
118 for (follower in flist) {
120 _console.value += "Sending to " + flist[follower] + "\n";
122 flist[follower].scrollToViewIn(flist[follower].getDefaultTargetFrame(),
128 // register a jalview applet and add some handlers to it
129 // jmolView is a reference to a jmol applet that is displaying the PDB files listed (in order) in the modeltofiles Array
130 function linkJvJmol(applet, jmolView, modeltofiles) {
131 var i = _jvapps.length;
133 if (_jvapps[i].equals(applet)) {
134 throw ("Ignoring additional linkJvJmol call for "
135 + applet.getName() + ".");
138 _jvapps[_jvapps.length] = applet;
139 applet.setMouseoverListener("mouseover");
140 applet.setSelectionListener("sellist");
141 // viewListener not fully implemented in 2.7
142 // try { applet.setViewListener("viewlist"); } catch (err) {};
145 var sep = applet.getSeparator();
147 // recover full id of Jmol applet
148 jmolView=_jmolGetApplet(jmolView).id;
149 var jmbinding=_jvjmols.get(jmolView);
152 jmbinding=new Object();
153 jmbinding._modelstofiles=new Array();
154 jmbinding._fullmpath=new Array();
155 jmbinding._filetonum=new Hashtable();
156 jmbinding._jmol=jmolView;
157 jmbinding._jmhandle=oldjm;
158 _jvjmols.put(jmolView,jmbinding);
161 jmbinding._modelstofiles=jmbinding._modelstofiles.concat(jmbinding._modelstofiles,modeltofiles);
162 jmbinding._jmol=jmolView;
163 // now update structureListener list
165 var dbase = getDocumentBase();
166 for (m in jmbinding._modelstofiles)
167 { if (m>0) { mtf+=sep; }
168 mtf+=jmbinding._modelstofiles[m];
169 if (jmbinding._modelstofiles[m].indexOf("//")==-1)
170 { jmbinding._fullmpath[m] = dbase+((jmbinding._modelstofiles[m].indexOf("/")==0) ? jmbinding._modelstofiles[m].substring(1) : jmbinding._modelstofiles[m]); }
171 jmbinding._filetonum.put(jmbinding._modelstofiles[m], m+1);
172 jmbinding._filetonum.put(jmbinding._fullmpath[m], m+1);
175 applet.setStructureListener("_structure", mtf);
179 /*function _addJmolModel(jmolid, modelname) {
180 modelname=""+modelname;
181 var jminf = _jvjmols[jmolid];
183 jminf = new Object();
184 jminf._modelstofiles = new Array(); //new Hashtable();
185 jminf._jmol = jmolid;
186 jminf._modellist=new Array();
187 _jvjmols[jmolid] = jminf;
189 var obj = new Object();
190 jminf._modeltofiles[modelname] = obj; // .put(modelname, obj);
192 obj.mnum = jminf._modeltofiles.length;
193 jminf._modellist+=modelname;
198 // jmol Jalview Methods
200 function _structure(list1, list2, list3, list4) {
202 // if (_console) { if (!_console.value) { _console.value="";} }
203 if (list1 == "mouseover") {
204 var list = new Array(("" + list1), ("" + list2), ("" + list3),
206 // 1 is pdb file, 2 is residue number, 3 is chain
207 // list1 = new Object(list1);
208 var base = list[1].indexOf(getDocumentBase()); // .indexOf(_path);
209 if (base==0) { base = getDocumentBase(); }
210 var sid = list[1]; // .substring(base);
211 base = list[1].substring(0, base);
213 _console.value += "Model is " + list[1] + ", Structure id is : "
218 for ( var jmolappi in _jvjmols.values()) {
219 var jmolapp=_jvjmols.values()[jmolappi];
221 if (siddat = jmolapp._filetonum.get(sid)) {
222 // we don't putin chain number because there isn't one ?
225 if ((""+list[2]).trim().length==1)
229 msg = "select (" + ch + " /" + siddat + ") ;";
233 _console.value += "Sending '" + msg + "' to jmol." + "\n";
236 jmolScriptWait(msg, "" + jmolapp._jmhandle);
237 // only do highlight for one jmol ?
241 if (list1 == "colourstruct") {
243 _console.value += 'colourStruct("' + list1 + '","' + list2
244 + '") [' + list4 + ']' + "\n";
246 setTimeout('colourStruct("'+list4+'","' + list1 + '","' + list2 + '")', 1);
251 // last colour message
253 // indicator - if _colourStruct==0 then no colouring is going on
254 var _colourStruct = 0;
256 function colourStruct(involves, msg, handle) {
257 if (_colourStruct == 0) {
259 for (ap in _jvapps) {
262 if (_msg.match(/\S/)) {
265 _msg = "" + _jvapps[ap].getJsMessage(msg, handle);
266 } while (_msg.match(/\S/));
268 // locate the jmol that should get the message
269 for (var jmol in _jvjmols.values())
271 var jml=_jvjmols.values()[jmol];
272 if (jml._filetonum.get(involves))
274 colourStructs(jml._jmhandle);
279 // setTimeout('colourStruct("'+msg+'","'+handle+'")',3);
283 function colourStructs(jmolapp) {
284 dbg(0, "Colouring the structures\n");
285 jmolScriptWait("set selectionhalos false;" + _lastMsg
286 + "; select 0; set selectionhalos true;", jmolapp);
289 var _jmolhovermsg="";
290 function _jmolhover(jmid, atomlabel, atomidx) {
291 var msg=""+jmid+" "+atomlabel+" "+atomidx;
292 if (_jmolhovermsg==msg)
297 modeltofiles = _jvjmols.get(jmid)._modelstofiles;
298 // atomlabel=(""+atomlabel).match(/\[(.+)\](\d+):(.)\.(\S+)\s*\/(\d+)\..+/);
299 // relaxed third parameter - may be null or a model number for multi model
301 atomlabel = ("" + atomlabel)
302 .match(/\[(.+)\](\d+):(.)\.([^\/]+)(\/\d+\.|).+/);
303 atomidx = "" + atomidx;
305 atomlabel[5] = atomlabel[5].match(/\/(.+)\./)[1];
306 atomlabel[5] = parseInt(atomlabel[5])-1;
308 // default - first model
311 // use atomlabel[5] to look up model filename so we can highlight associated positions in any jalviews
312 for (ap in _jvapps) {
313 _jvapps[ap].mouseOverStructure(atomlabel[2], atomlabel[3],
316 modeltofiles[atomlabel[5]]);
320 function _jmolpick(jmid, atomlabel, atomidx) {
321 atomlabel = "" + atomlabel;
322 atomidx = "" + atomidx;
323 // label is atom id, atom number, and xyz coordinates in the form:
324 // C6 #6 -0.30683374 -1.6836332 -0.716934
325 // atom index, starting with 0.
328 function _jmolMessagecallback(jmid, statmess) {
329 // if (statmess.indexOf("Script Terminated")==0)
331 var thisTime = new Date();
333 _console.value += "Last script execution took : "
334 + (thisTime.valueOf() - _lastTime.valueOf()) / 1000.0
337 _lastTime = thisTime;