1 /*******************************************************************************
2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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 *******************************************************************************/
18 // default console to report messages
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19 var _console = document.getElementById("stdout");
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20 var _jvapps = new Array();
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21 // jvjmols is a list associating a jmol id to { modelstofiles }
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22 var _jvjmols = new Hashtable();
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23 // array of model names used to lookup index in Jmol
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24 var _modeltofiles = new Array();
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25 // counter for jmol structures
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28 function setConsole(console) {
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32 function getDestinationFrms(source, frames) {
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33 var frms = new Array();
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35 for (frm in frames) {
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37 frid = (source!=null) && (("" + source.getSequenceSetId()) == ("" + frames[frm].currentAlignFrame
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38 .getSequenceSetId()));
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42 if (!frames[frm].equals(source) && !frid
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43 && !frames[frm].currentAlignFrame.equals(source)) {
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44 frms[frms.length] = frames[frm];
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50 function mouseover(list1, list2, list3, list4) {
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51 // list1 = new Object(list1);
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52 var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
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53 var msg = "Mouse over :\n" + "AlignFrame obj: " + list1 + " Seq : "
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54 + list[1] + "\nPos: " + list[2] + "(" + list[3] + ")\n";
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56 var flist = getDestinationFrms(list1, _jvapps);
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58 _console.value = msg + "\n";
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61 for (follower in flist) {
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63 _console.value += "Sending to " + flist[follower] + "\n";
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65 flist[follower].highlight(list[1], list[2], "true");
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70 function sellist(list1, list2, list3, list4) {
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71 // list1 = new Object(list1);
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72 var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
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73 var msg = "Selection:\n" + "AlignFrame obj: " + list[0] + " id : "
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74 + list[1] + "\nSeqs " + list[2] + "\nColumns " + list[3] + "\n";
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75 var flist = getDestinationFrms(list1, _jvapps);
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77 _console.value = msg + "\n";
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80 for (follower in flist) {
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82 _console.value += "Sending to " + flist[follower] + "\n";
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84 flist[follower].selectIn(flist[follower].getDefaultTargetFrame(),
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90 function viewlist(list1, list2, list3, list4) {
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91 // list1 = new Object(list1);
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92 var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
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93 var msg = "Viewport extent change::\n" + "AlignFrame obj: " + list[0]
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94 + " id : " + list[1] + "\nRow from " + list[2] + " and to "
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95 + list[3] + "\nVisible columns: " + list[4] + "\n";
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96 var flist = getDestinationFrms(list1, _jvapps);
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98 _console.value = msg + "\n";
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101 for (follower in flist) {
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103 _console.value += "Sending to " + flist[follower] + "\n";
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105 flist[follower].scrollToViewIn(flist[follower].getDefaultTargetFrame(),
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111 // register a jalview applet and add some handlers to it
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112 // jmolView is a reference to a jmol applet that is displaying the PDB files listed (in order) in the modeltofiles Array
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113 function linkJvJmol(applet, jmolView, modeltofiles) {
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114 var i = _jvapps.length;
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116 if (_jvapps[i].equals(applet)) {
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117 throw ("Ignoring additional linkJvJmol call for "
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118 + applet.getName() + ".");
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121 _jvapps[_jvapps.length] = applet;
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122 applet.setMouseoverListener("mouseover");
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123 applet.setSelectionListener("sellist");
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124 // viewListener not fully implemented in 2.7
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125 // try { applet.setViewListener("viewlist"); } catch (err) {};
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128 var sep = applet.getSeparator();
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129 var oldjm=jmolView;
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130 // recover full id of Jmol applet
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131 jmolView=_jmolGetApplet(jmolView).id;
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132 var jmbinding=_jvjmols.get(jmolView);
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135 jmbinding=new Object();
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136 jmbinding._modelstofiles=new Array();
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137 jmbinding._fullmpath=new Array();
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138 jmbinding._filetonum=new Hashtable();
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139 jmbinding._jmol=jmolView;
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140 jmbinding._jmhandle=oldjm;
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141 _jvjmols.put(jmolView,jmbinding);
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144 jmbinding._modelstofiles=jmbinding._modelstofiles.concat(jmbinding._modelstofiles,modeltofiles);
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145 jmbinding._jmol=jmolView;
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146 // now update structureListener list
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148 var dbase = document.baseURI.substring(0,document.baseURI.lastIndexOf("/")+1);
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149 for (m in jmbinding._modelstofiles)
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150 { if (m>0) { mtf+=sep; }
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151 mtf+=jmbinding._modelstofiles[m];
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152 if (jmbinding._modelstofiles[m].indexOf("//")==-1)
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153 { jmbinding._fullmpath[m] = dbase+((jmbinding._modelstofiles[m].indexOf("/")==0) ? jmbinding._modelstofiles[m].substring(1) : jmbinding._modelstofiles[m]); }
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154 jmbinding._filetonum.put(jmbinding._modelstofiles[m], m+1);
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155 jmbinding._filetonum.put(jmbinding._fullmpath[m], m+1);
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158 applet.setStructureListener("_structure", mtf);
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162 /*function _addJmolModel(jmolid, modelname) {
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163 modelname=""+modelname;
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164 var jminf = _jvjmols[jmolid];
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166 jminf = new Object();
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167 jminf._modelstofiles = new Array(); //new Hashtable();
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168 jminf._jmol = jmolid;
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169 jminf._modellist=new Array();
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170 _jvjmols[jmolid] = jminf;
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172 var obj = new Object();
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173 jminf._modeltofiles[modelname] = obj; // .put(modelname, obj);
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174 obj.id = modelname;
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175 obj.mnum = jminf._modeltofiles.length;
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176 jminf._modellist+=modelname;
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181 // jmol Jalview Methods
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183 function _structure(list1, list2, list3, list4) {
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185 // if (_console) { if (!_console.value) { _console.value="";} }
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186 if (list1 == "mouseover") {
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187 var list = new Array(("" + list1), ("" + list2), ("" + list3),
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189 // 1 is pdb file, 2 is residue number, 3 is chain
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190 // list1 = new Object(list1);
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191 var base = list[1].indexOf(document.baseURI
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192 .substring(0, document.baseURI.lastIndexOf('/'))
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193 ); // .indexOf(_path);
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194 if (base==0) { base = document.baseURI.lastIndexOf('/'); }
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195 var sid = list[1]; // .substring(base);
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196 base = list[1].substring(0, base);
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198 _console.value += "Model is " + list[1] + ", Structure id is : "
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203 for ( var jmolappi in _jvjmols.values()) {
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204 var jmolapp=_jvjmols.values()[jmolappi];
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206 if (siddat = jmolapp._filetonum.get(sid)) {
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207 // we don't putin chain number because there isn't one ?
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208 // skip select 0 bit
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209 var ch = ""+list[3];
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210 if ((""+list[2]).trim().length==1)
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214 msg = "select (" + ch + " /" + siddat + ") ;";
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218 _console.value += "Sending '" + msg + "' to jmol." + "\n";
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221 jmolScriptWait(msg, "" + jmolapp._jmhandle);
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222 // only do highlight for one jmol ?
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226 if (list1 == "colourstruct") {
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228 _console.value += 'colourStruct("' + list1 + '","' + list2
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229 + '") [' + list4 + ']' + "\n";
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231 setTimeout('colourStruct("'+list4+'","' + list1 + '","' + list2 + '")', 1);
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236 // last colour message
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238 // indicator - if _colourStruct==0 then no colouring is going on
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239 var _colourStruct = 0;
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241 function colourStruct(involves, msg, handle) {
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242 if (_colourStruct == 0) {
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244 for (ap in _jvapps) {
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247 if (_msg.match(/\S/)) {
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250 _msg = "" + _jvapps[ap].getJsMessage(msg, handle);
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251 } while (_msg.match(/\S/));
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253 // locate the jmol that should get the message
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254 for (var jmol in _jvjmols.values())
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256 var jml=_jvjmols.values()[jmol];
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257 if (jml._filetonum.get(involves))
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259 colourStructs(jml._jmhandle);
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264 // setTimeout('colourStruct("'+msg+'","'+handle+'")',3);
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268 function colourStructs(jmolapp) {
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269 dbg(0, "Colouring the structures\n");
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270 jmolScriptWait("set selectionhalos false;" + _lastMsg
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271 + "; select 0; set selectionhalos true;", jmolapp);
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274 var _jmolhovermsg="";
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275 function _jmolhover(jmid, atomlabel, atomidx) {
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276 var msg=""+jmid+" "+atomlabel+" "+atomidx;
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277 if (_jmolhovermsg==msg)
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282 modeltofiles = _jvjmols.get(jmid)._modelstofiles;
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283 // atomlabel=(""+atomlabel).match(/\[(.+)\](\d+):(.)\.(\S+)\s*\/(\d+)\..+/);
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284 // relaxed third parameter - may be null or a model number for multi model
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286 atomlabel = ("" + atomlabel)
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287 .match(/\[(.+)\](\d+):(.)\.([^\/]+)(\/\d+\.|).+/);
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288 atomidx = "" + atomidx;
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289 if (atomlabel[5]) {
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290 atomlabel[5] = atomlabel[5].match(/\/(.+)\./)[1];
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291 atomlabel[5] = parseInt(atomlabel[5])-1;
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293 // default - first model
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296 // use atomlabel[5] to look up model filename so we can highlight associated positions in any jalviews
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297 for (ap in _jvapps) {
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298 _jvapps[ap].mouseOverStructure(atomlabel[2], atomlabel[3],
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300 .substring(0, document.baseURI.lastIndexOf('/'))
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302 modeltofiles[atomlabel[5]]);
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303 msg = _jmolhovermsg;
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306 function _jmolpick(jmid, atomlabel, atomidx) {
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307 atomlabel = "" + atomlabel;
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308 atomidx = "" + atomidx;
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309 // label is atom id, atom number, and xyz coordinates in the form:
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310 // C6 #6 -0.30683374 -1.6836332 -0.716934
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311 // atom index, starting with 0.
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314 function _jmolMessagecallback(jmid, statmess) {
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315 // if (statmess.indexOf("Script Terminated")==0)
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317 var thisTime = new Date();
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319 _console.value += "Last script execution took : "
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320 + (thisTime.valueOf() - _lastTime.valueOf()) / 1000.0
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323 _lastTime = thisTime;
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