--- /dev/null
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+
+
+
+
+
+
+
+
+// default console to report messages
+var _console = document.getElementById("stdout");
+var _jvapps = new Array();
+// jvjmols is a list associating a jmol id to { modelstofiles }
+var _jvjmols = new Hashtable();
+// array of model names used to lookup index in Jmol
+var _modeltofiles = new Array();
+// counter for jmol structures
+var mnum = 1;
+
+function getDocumentBase() {
+ var dburi = document.baseURI;
+ // IE does not support document.baseURI
+ // logic from patch to TYPO3:
+ // http://forge.typo3.org/projects/typo3cms-core/repository/revisions/f61358afad28adb6dcaeb270ba480e998dfb0b79/diff/typo3/sysext/rtehtmlarea/htmlarea/htmlarea.js
+ if (!dburi) {
+ var baseTags = document.getElementsByTagName('base');
+ if (baseTags.length > 0) {
+ dburi = baseTags[0].href;
+ } else {
+ dburi = document.URL;
+ }
+ }
+ return dburi.substring(0, dburi.lastIndexOf("/") + 1);
+}
+function setConsole(console) {
+ _console = console;
+}
+
+function getDestinationFrms(source, frames) {
+ var frms = new Array();
+ var frid = "";
+ for (frm in frames) {
+ try {
+ frid = (source!=null) && (("" + source.getSequenceSetId()) == ("" + frames[frm].currentAlignFrame
+ .getSequenceSetId()));
+ } catch (q) {
+ };
+
+ if (!frames[frm].equals(source) && !frid
+ && !frames[frm].currentAlignFrame.equals(source)) {
+ frms[frms.length] = frames[frm];
+ }
+ }
+ return frms;
+}
+
+function mouseover(list1, list2, list3, list4) {
+ // list1 = new Object(list1);
+ var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
+ var msg = "Mouse over :\n" + "AlignFrame obj: " + list1 + " Seq : "
+ + list[1] + "\nPos: " + list[2] + "(" + list[3] + ")\n";
+
+ var flist = getDestinationFrms(list1, _jvapps);
+ if (_console) {
+ _console.value = msg + "\n";
+ }
+
+ for (follower in flist) {
+ if (_console) {
+ _console.value += "Sending to " + flist[follower] + "\n";
+ }
+ flist[follower].highlight(list[1], list[2], "true");
+ }
+ return true;
+}
+
+function sellist(list1, list2, list3, list4) {
+ // list1 = new Object(list1);
+ var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
+ var msg = "Selection:\n" + "AlignFrame obj: " + list[0] + " id : "
+ + list[1] + "\nSeqs " + list[2] + "\nColumns " + list[3] + "\n";
+ var flist = getDestinationFrms(list1, _jvapps);
+ if (_console) {
+ _console.value = msg + "\n";
+ }
+
+ for (follower in flist) {
+ if (_console) {
+ _console.value += "Sending to " + flist[follower] + "\n";
+ }
+ flist[follower].selectIn(flist[follower].getDefaultTargetFrame(),
+ list[2], list[3])
+ }
+ return true;
+}
+
+function viewlist(list1, list2, list3, list4) {
+ // list1 = new Object(list1);
+ var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
+ var msg = "Viewport extent change::\n" + "AlignFrame obj: " + list[0]
+ + " id : " + list[1] + "\nRow from " + list[2] + " and to "
+ + list[3] + "\nVisible columns: " + list[4] + "\n";
+ var flist = getDestinationFrms(list1, _jvapps);
+ if (_console) {
+ _console.value = msg + "\n";
+ }
+
+ for (follower in flist) {
+ if (_console) {
+ _console.value += "Sending to " + flist[follower] + "\n";
+ }
+ flist[follower].scrollToViewIn(flist[follower].getDefaultTargetFrame(),
+ list[2], "-1");
+ }
+ return true;
+}
+
+// register a jalview applet and add some handlers to it
+// jmolView is a reference to a jmol applet that is displaying the PDB files listed (in order) in the modeltofiles Array
+function linkJvJmol(applet, jmolView, modeltofiles) {
+ var i = _jvapps.length;
+ while (i--) {
+ if (_jvapps[i].equals(applet)) {
+ throw ("Ignoring additional linkJvJmol call for "
+ + applet.getName() + ".");
+ }
+ }
+ _jvapps[_jvapps.length] = applet;
+ applet.setMouseoverListener("mouseover");
+ applet.setSelectionListener("sellist");
+ // viewListener not fully implemented in 2.7
+ // try { applet.setViewListener("viewlist"); } catch (err) {};
+ if (jmolView)
+ {
+ var sep = applet.getSeparator();
+ var oldjm=jmolView;
+ // recover full id of Jmol applet
+ jmolView=jmolFindTarget(jmolView)._id; // Jmol 14.2.14
+ var jmbinding=_jvjmols.get(jmolView);
+ if (!jmbinding)
+ {
+ jmbinding=new Object();
+ jmbinding._modelstofiles=new Array();
+ jmbinding._fullmpath=new Array();
+ jmbinding._filetonum=new Hashtable();
+ jmbinding._jmol=jmolView;
+ jmbinding._jmhandle=oldjm;
+ _jvjmols.put(jmolView,jmbinding);
+ }
+
+ jmbinding._modelstofiles=jmbinding._modelstofiles.concat(jmbinding._modelstofiles,modeltofiles);
+ jmbinding._jmol=jmolView;
+ // now update structureListener list
+ mtf="";
+ var dbase = getDocumentBase();
+ for (m in jmbinding._modelstofiles)
+ { if (m>0) { mtf+=sep; }
+ mtf+=jmbinding._modelstofiles[m];
+ if (jmbinding._modelstofiles[m].indexOf("//")==-1)
+ { jmbinding._fullmpath[m] = dbase+((jmbinding._modelstofiles[m].indexOf("/")==0) ? jmbinding._modelstofiles[m].substring(1) : jmbinding._modelstofiles[m]); }
+ jmbinding._filetonum.put(jmbinding._modelstofiles[m], m+1);
+ jmbinding._filetonum.put(jmbinding._fullmpath[m], m+1);
+
+ }
+ applet.setStructureListener("_structure", mtf);
+ }
+}
+
+/*function _addJmolModel(jmolid, modelname) {
+ modelname=""+modelname;
+ var jminf = _jvjmols[jmolid];
+ if (!jminf) {
+ jminf = new Object();
+ jminf._modelstofiles = new Array(); //new Hashtable();
+ jminf._jmol = jmolid;
+ jminf._modellist=new Array();
+ _jvjmols[jmolid] = jminf;
+ }
+ var obj = new Object();
+ jminf._modeltofiles[modelname] = obj; // .put(modelname, obj);
+ obj.id = modelname;
+ obj.mnum = jminf._modeltofiles.length;
+ jminf._modellist+=modelname;
+}*/
+
+
+
+// jmol Jalview Methods
+
+function _structure(list1, list2, list3, list4) {
+ var follower;
+ // if (_console) { if (!_console.value) { _console.value="";} }
+ if (list1 == "mouseover") {
+ var list = new Array(("" + list1), ("" + list2), ("" + list3),
+ ("" + list4));
+ // 1 is pdb file, 2 is residue number, 3 is chain
+ // list1 = new Object(list1);
+ var base = list[1].indexOf(getDocumentBase()); // .indexOf(_path);
+ if (base==0) { base = getDocumentBase(); }
+ var sid = list[1]; // .substring(base);
+ base = list[1].substring(0, base);
+ if (_console) {
+ _console.value += "Model is " + list[1] + ", Structure id is : "
+ + sid + "\n";
+ }
+ ;
+ var siddat;
+ for ( var jmolappi in _jvjmols.values()) {
+ var jmolapp=_jvjmols.values()[jmolappi];
+ var msg = "";
+ if (siddat = jmolapp._filetonum.get(sid)) {
+ // we don't putin chain number because there isn't one ?
+ // skip select 0 bit
+ var ch = ""+list[3];
+ if ((""+list[2]).trim().length==1)
+ {
+ ch+=":"+list[2];
+ }
+ msg = "select (" + ch + " /" + siddat + ") ;";
+ }
+ if (msg) {
+ if (_console) {
+ _console.value += "Sending '" + msg + "' to jmol." + "\n";
+ }
+ }
+ jmolScriptWait(msg, "" + jmolapp._jmhandle);
+ // only do highlight for one jmol ?
+ // return 1;
+ }
+ }
+ if (list1 == "colourstruct") {
+ if (_console) {
+ _console.value += 'colourStruct("' + list1 + '","' + list2
+ + '") [' + list4 + ']' + "\n";
+ }
+ setTimeout('colourStruct("'+list4+'","' + list1 + '","' + list2 + '")', 1);
+ return 1;
+ }
+ return 1;
+}
+// last colour message
+var _lastMsg = "";
+// indicator - if _colourStruct==0 then no colouring is going on
+var _colourStruct = 0;
+
+function colourStruct(involves, msg, handle) {
+ if (_colourStruct == 0) {
+ _colourStruct = 1;
+ for (ap in _jvapps) {
+ var _msg = "";
+ do {
+ if (_msg.match(/\S/)) {
+ _lastMsg += _msg;
+ }
+ _msg = "" + _jvapps[ap].getJsMessage(msg, handle);
+ } while (_msg.match(/\S/));
+ }
+ // locate the jmol that should get the message
+ for (var jmol in _jvjmols.values())
+ {
+ var jml=_jvjmols.values()[jmol];
+ if (jml._filetonum.get(involves))
+ {
+ colourStructs(jml._jmhandle);
+ }
+ }
+ _colourStruct = 0;
+ } else {
+ // setTimeout('colourStruct("'+msg+'","'+handle+'")',3);
+ }
+}
+
+function colourStructs(jmolapp) {
+ dbg(0, "Colouring the structures\n");
+ jmolScriptWait("set selectionhalos false;" + _lastMsg
+ + "; select 0; set selectionhalos true;", jmolapp);
+ _lastMsg = "";
+}
+var _jmolhovermsg="";
+function _jmolhover(jmid, atomlabel, atomidx) {
+ var msg=""+jmid+" "+atomlabel+" "+atomidx;
+ if (_jmolhovermsg==msg)
+ {
+ return;
+ }
+ _jmolhovermsg=msg;
+ modeltofiles = _jvjmols.get(jmid)._modelstofiles;
+ // atomlabel=(""+atomlabel).match(/\[(.+)\](\d+):(.)\.(\S+)\s*\/(\d+)\..+/);
+ // relaxed third parameter - may be null or a model number for multi model
+ // views
+ atomlabel = ("" + atomlabel)
+ .match(/\[(.+)\](\d+):(.)\.([^\/]+)(\/\d+\.|).+/);
+ atomidx = "" + atomidx;
+ if (atomlabel[5]) {
+ atomlabel[5] = atomlabel[5].match(/\/(.+)\./)[1];
+ atomlabel[5] = parseInt(atomlabel[5])-1;
+ } else {
+ // default - first model
+ atomlabel[5] = 0;
+ }
+ // use atomlabel[5] to look up model filename so we can highlight associated positions in any jalviews
+ for (ap in _jvapps) {
+ pdb = getDocumentBase() + modeltofiles[atomlabel[5]];
+ _jvapps[ap].mouseOverStructure(atomlabel[2], atomlabel[3], pdb);
+ msg = _jmolhovermsg;
+ }
+}
+function _jmolpick(jmid, atomlabel, atomidx) {
+ atomlabel = "" + atomlabel;
+ atomidx = "" + atomidx;
+ // label is atom id, atom number, and xyz coordinates in the form:
+ // C6 #6 -0.30683374 -1.6836332 -0.716934
+ // atom index, starting with 0.
+
+}
+function _jmolMessagecallback(jmid, statmess) {
+ // if (statmess.indexOf("Script Terminated")==0)
+ {
+ var thisTime = new Date();
+ if (_console) {
+ _console.value += "Last script execution took : "
+ + (thisTime.valueOf() - _lastTime.valueOf()) / 1000.0
+ + " seconds.";
+ }
+ _lastTime = thisTime;
+
+ }
+}
+
+
+ function lJvApp() {
+ setTimeout(function() {
+ //alert("in lJvApp");
+ var jvapp = document.getElementById("jvapp");
+ var jvfollower = document.getElementById("jvfollower");
+ //console.log(">>>>>>>> lJvApp" + jvapp);
+ linkJvJmol(jvapp);
+ }, 200);
+ setConsole(document.getElementById("stdout"));
+ };
+
+ function lJvFollow() {
+ setTimeout(function() {
+ //alert("in lJvFollow");
+ var jvapp = document.getElementById("jvapp");
+ var jvfollower = document.getElementById("jvfollower");
+ console.log(">>>>>>> lJvFollow" + jvfollower);
+ linkJvJmol(jvfollower);
+ }, 200);
+ };
+
+ function lJvA() {
+ setTimeout(function() {
+ //alert("lJvA");
+ jvfollower = document.getElementById("jvA");
+ setConsole(document.getElementById("stdout"));
+ //sep = jvfollower.getSeparator();
+ //jvapp.setSeparator(""+jvapp.getSeparator());
+ linkJvJmol(jvfollower, "jmolView", modeltofiles);
+ }, 100);
+ };
+
git://source.jalview.org / jalview.git / blobdiff