+++ /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