icn3d/example/addAnnoLocal.html at master · ncbi/icn3d · GitHub

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<!DOCTYPE html><html lang="en"><head>
  <meta charset="utf-8">
  <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
<meta name="description" content="iCn3D Structure Viewer">
<meta name="keywords" content="NCBI, Structure, JavaScript, iCn3D, 3D, Viewer, WebGL, three.js, sequence, chemical">
<meta name="robots" content="index,follow,noarchive">
<meta name="ncbi_app" content="structure">
<meta name="ncbi_pdid" content="icn3d">
<meta name="ncbi_page" content="full">
<meta name="ncbi_pinger_xml_http_request_override" content="false"/>
<meta name="ncbi_pinger_click_ping_selector" content="button, a, input[type=submit], span[data-pinger], div[data-pinger], label[data-pinger]"/>
<title>iCn3D: Web-based 3D Structure Viewer</title>
<script type="text/javascript">
    window.ncbi_startTime = new Date();
</script>
</head>
<body>
  <div id="div0"></div>

  <link rel="stylesheet" href="lib/jquery-ui-1.13.2.min.css">
  <link rel="stylesheet" href="icn3d.css">
  <script src="lib/jquery-3.5.0.min.js"></script>
  <script src="lib/jquery-ui-1.13.2.min.js"></script>
  <script src="lib/three_0.151.0.min.js"></script>
  <!--script src="icn3d.min.js"></script-->

  <script type="module">
    import * as icn3d from './icn3d.module.js';
    // add new classes
    import {AnnoLocal} from './annoLocal.js';

    //$( document ).ready(function() {
      if (navigator.userAgent.indexOf("MSIE ") > 0 || !!navigator.userAgent.match(/Trident.*rv\:11\./)) { // If Internet Explorer
          $.getScript('icn3d_full_ui_2.24.7.min.js', function() {
            var version = 2;
            launchIcn3d(version);
          });
          alert("iCn3D version 3 (since May 2021) works in all browsers except IE. The old iCn3D version 2 is used instead.");
      }
      else {
          //$.getScript('icn3d.min.js', function() {
            var version = 3;
            launchIcn3d(version);
          //});
      }
      async function launchIcn3d(version) {
          var cfg_params = getConfig();
          var cfg = cfg_params.cfg;
          var params = (cfg_params.params) ? cfg_params.params : {};
          params.version = version;

          if(params.mmtfid !== undefined) {
              await setupViewer('mmtfid', params.mmtfid, cfg, params);
          }
          else if(params.pdbid !== undefined) {
              await setupViewer('pdbid', params.pdbid, cfg, params);
          }
          else if(params.opmid !== undefined) {
              await setupViewer('opmid', params.opmid, cfg, params);
          }
          else if(params.cid !== undefined) {
              await setupViewer('cid', params.cid, cfg, params);
          }
          else if(params.mmcifid !== undefined) {
              await setupViewer('mmcifid', params.mmcifid, cfg, params);
          }
          else if(params.mmdbid !== undefined) {
              await setupViewer('mmdbid', params.mmdbid, cfg, params);
          }
          else if(params.gi !== undefined) {
              await setupViewer('gi', params.gi, cfg, params);
          }
          else if(params.blast_rep_id !== undefined) {
              if( (params.from === 'blast' || params.from === 'icn3d') && params.command == '') {
                command = 'view+annotations;+set+annotation+cdd;+set+annotation+site;+set+view+detailed+view;+select+chain+'
                  + params.blast_rep_id + ';+show+selection';
              }

              await setupViewer('blast_rep_id', params.blast_rep_id, cfg, params);
          }
          else if(params.urlname !== undefined) {
              var urlname = decodeURIComponent(params.urlname);

              await setupViewer('url', params.urltype + '|' + urlname, cfg, params);
          }
          // e.g., align=103701,1,4,68563,1,167 [mmdbid1,biounit,molecule,mmdbid2,biounit,molecule]
          else if(params.align !== undefined) {
              cfg.divid = 'div0';
              cfg.align = params.align;
              cfg.showalignseq = params.showalignseq;

              var icn3dui = (params.version == 2) ? new iCn3DUI(cfg) : new icn3d.iCn3DUI(cfg);

              await icn3dui.show3DStructure();
          }
          else if(params.chainalign !== undefined) {
              cfg.divid = 'div0';
              cfg.chainalign = params.chainalign;
              cfg.resnum = params.resnum;
              cfg.showalignseq = params.showalignseq;

              var icn3dui = (params.version == 2) ? new iCn3DUI(cfg) : new icn3d.iCn3DUI(cfg);

              await icn3dui.show3DStructure();
          }
          else if(params.mmdbafid !== undefined) {
              cfg.divid = 'div0';

              var icn3dui = (params.version == 2) ? new iCn3DUI(cfg) : new icn3d.iCn3DUI(cfg);

              await icn3dui.show3DStructure();
          }
          else {
              await setupViewer('', '', cfg, params);
          }
      }

      async function setupViewer(idName, idValue, cfg, params) {
        var maxStructure = 5; // show max 5 structures

        var idArray = idValue.replace(/\s/g, '').split(',');

        if(idArray.length > 1) {
          resize = false;

          if(cfg.width && cfg.width.indexOf('%') != -1) {
            cfg.width = 400;
            cfg.height = 400;
          }
        }

        if(cfg.options === undefined || cfg.options === 'undefined') cfg.options = {};

        //Options are available at: https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#DisplayOptions
        //cfg.options['chemicalbinding'] = 'show';

        for(var i = 0, il = idArray.length; i < il && i < maxStructure; ++i) {
          cfg.divid = 'div' + i;

          if(params) {
              cfg.blast_rep_id = params.blast_rep_id;
              cfg.query_id = params.query_id;
              cfg.rid = params.rid;
          }

          if(idName !== '') cfg[idName] = idArray[i];

          var icn3dui = (params.version == 2) ? new iCn3DUI(cfg) : new icn3d.iCn3DUI(cfg);

          await icn3dui.show3DStructure();

          // hide all default annotations
          ic.annotationCls.hideAnnoTabAll();

          // update annotation header
          let title = 'My local annotation';
          let annoHtml = "<span style='white-space:nowrap'>" + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_" + ic.annotationCls.shortLabel + "' checked>" + title + "</span>";
          $("#" + me.pre + "annoHeader").html(annoHtml);

          // show your local annotation
          ic.annoLocalCls.updateLocalAnno();
          ic.annoLocalCls.setAnnoTabLocal();

          // enable to show orhide
          ic.annoLocalCls.clickLocalAnno();

          if(idName === '') $("#div" + i + "_wait").hide();
        }
      }

      function getConfig() {
        // separating the GET parameters from the current URL
        // repalce "color #" with "color " in the url
        var url = document.URL.replace(/\#/g, '');

        var bNopara = false;
        var ampPos = url.indexOf("?");
        if(ampPos === -1) {
        //  alert("Please include '?pdbid=1GPK,2POR,...' in your url");
            bNopara = true;
        }

        var getParams = url.split("?");
        // transforming the GET parameters into a dictionary
        var search = getParams[getParams.length - 1];
        var params = {};
        var inpara = "";

        var command;
        if(!bNopara) {
            var decodeSearch = decodeURIComponent(search);

            // command could contains '&', for example when loading statefile 'load mmdb 1kq2 | parameters &atype=1'
            var commandPos = decodeSearch.indexOf('&command=');
            if(commandPos != -1) {
                command = decodeSearch.substr(commandPos + 9); // ";" separated commands
                decodeSearch = decodeSearch.substr(0, commandPos);

                var paraPos = decodeSearch.indexOf(' | parameters ');

                if(paraPos != -1) { //When loading statefile (e.g., 'load mmdb 1kq2 | parameters &atype=1'), the commands ends with '}}'.
                    var tmpPos = command.indexOf('}}&');
                    if(tmpPos != -1) { // more parameters after the command
                      decodeSearch += command.substr(tmpPos + 2);
                      command = command.substr(0, tmpPos + 2);
                    }
                }
                else {
                    var tmpPos = command.indexOf('&');
                    if(tmpPos != -1) {
                      decodeSearch += command.substr(tmpPos);
                      command = command.substr(0, tmpPos);
                    }
                }
            }
            else {
                command = '';
            }

            var hashes = decodeSearch.split('&');
            for (var i = 0; i < hashes.length; i++) {
                var hash = hashes[i].split('=');
                params[hash[0].trim()] = (hash[1] !== undefined) ? hash[1].trim() : undefined;
            }

            // for mmdb structures, pass the parameters after the first "&" sign
            inpara = "&" + url.substr(ampPos + 1);
        }

        var gi = params.gi;
        var blast_rep_id = params.blast_rep_id;
        var query_id = params.query_id;
        var rid = params.RID;

        var mmdbid = params.mmdbid;
        var mmtfid = params.mmtfid;
        var pdbid = params.pdbid;
        var opmid = params.opmid;
        var cid = params.cid;
        var mmcifid = params.mmcifid;
        var urlname = params.url;
        if(urlname && urlname.indexOf('%3A%2F%2F') === -1) { // decoded URL
            // should encode it
            urlname = encodeURIComponent(urlname);
        }
        var urltype = (params.type === undefined) ? 'pdb' : params.type;

        var align = params.align;
        var chainalign = params.chainalign;
        var resnum = params.resnum;

        var width = params.width;
        var height = params.height;

        var from = params.from;

        var date = getValue(params.date);
        var version = getValue(params.v);

        if(version !== undefined && window.localStorage && localStorage.getItem('fixedversion')) {
            //var version = getVersion(date);
            var fixedUrl = url.replace('full.html', 'full_' + version + '.html');
            window.open(fixedUrl, '_self');

            localStorage.removeItem('fixedversion');
        }

        // use PDB residue number in MMDB input
        var usepdbnum = getValue(params.usepdbnum);
        //if(usepdbnum === undefined) usepdbnum = (date !== undefined && date >= '20201222') ? true : false;

        var resize = getValue(params.resize);

        var showmenu = getValue(params.showmenu);

        var showtitle = getValue(params.showtitle);

        var showcommand = getValue(params.showcommand);

        //var simplemenu = getValue(params.simplemenu);

        var mobilemenu = getValue(params.mobilemenu);

        var imageonly = getValue(params.imageonly);

        var closepopup = getValue(params.closepopup);

        var showanno = getValue(params.showanno);

        var showseq = getValue(params.showseq);

        // backward compatible with showseq
        showanno = showanno || showseq;

        // for alignment
        var showalignseq = getValue(params.showalignseq);

        var show2d = getValue(params.show2d);

        var showsets = getValue(params.showsets);

        var replay = getValue(params.replay);

        var notebook = getValue(params.notebook);

        var rotate = params.rotate;

        var shownote = 1; //params.shownote;

        var options = (params.options !== undefined) ? JSON.parse(params.options) : undefined;

        var cfg = {
          inpara: inpara,
          width: width,
          height: height,
          resize: resize,
          rotate: rotate,
          showmenu: showmenu,
          showtitle: showtitle,
          showcommand: showcommand,
          showanno: showanno,
          show2d: show2d,
          showsets: showsets,
          //simplemenu: simplemenu,
          mobilemenu: mobilemenu,
          imageonly: imageonly,
          closepopup: closepopup,
          replay: replay,
          notebook: notebook,
          shownote: shownote,
          options: options,
          usepdbnum: usepdbnum,
          date: date,
          command: command
        };

        return {cfg: cfg, params: params};
      }

      function getValue(input) {
        if(input == 'true' || input == '1') {
          input = true;
        }
        else if(input == 'false' || input == '0') {
          input = false;
        }

        return input;
      }
    //}); // document ready
  </script>

  <!-- log & Google Analytics -->
  <script type="text/javascript" src="https://www.ncbi.nlm.nih.gov/core/pinger/pinger.js"></script>
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