//////////////////////////////////////////////////////////
// 
// jolecule - the javascript based protein/dna viewer
//
// Relies on server jolecule.appspot.com, which, in turn
// relies on the RCSB website http://www.pdb.org.
//
// embed_dict = {};
// embed_dict.pdb_id = '1mbo';
// embed_dict.canvas = '#imageView';
// embed_dict.view_id = 'view:h1tsp7';
//
///////////////////////////////////////////////////////////


var ms = 25;

  
function init() {

  // Go through the global space to look for functions
  // that loads an embedded protein into the page
  // and user-defined dictonaries that parameterize
  // each individual widget 
  var load_fns = []
  var embed_dicts = [];
  for (var name in window) {
    if (name.indexOf('load_embed_protein') > -1) {
      load_fns.push(window[name]);
    }
    if (name.indexOf('embed') > -1) {
      embed_dicts.push(window[name]);
    }
  }

  // Run the functions, will store objects pointing
  // to the embbeded objects in the variable 'proteins'
  for (var j=0; j<embed_dicts.length; j+=1) {
    var canvas_tag = embed_dicts[j].canvas_tag;
    if (exists(canvas_tag)) {
      if (canvas_tag.charAt(0) != "#") {
        canvas_tag = "#" + canvas_tag;
      }
      console.log(canvas_tag);
    }
    var pdb_id = embed_dicts[j].pdb_id;
    var view_id = embed_dicts[j].view_id;
    if (typeof(embed_dicts[j].text_height) !== 'undefined') {
      var text_height = embed_dicts[j].text_height;
    } else {
      var text_height = 100; 
    }
  
    for (var i=0; i<load_fns.length; i+=1) {
      load_fns[i](pdb_id, view_id, canvas_tag, text_height);
    }
  }
  
  var last_time = (new Date).getTime();
  var ms = 25;

  var loop = function() {
    if (typeof proteins == 'undefined') {
      return;
    }
    var curr_time = (new Date).getTime();
    var time_diff = curr_time - last_time;
    var n_step = time_diff/ms;
    if (n_step < 1) {
      n_step = 1;
    }
    for (var i=0; i<n_step; i++) {
      for (var j=0; j<proteins.length; j++) {
        proteins[j].scene.animate();
      }
    }
    for (var j=0; j<proteins.length; j++) {
      var protein = proteins[j];
      if (protein.scene.changed) {
        if (protein.scene.is_new_view_chosen) {
          protein.scene.is_new_view_chosen = false;
        }
        protein.protein_display.draw();
        protein.scene.changed = false;
      }
    }
    last_time = curr_time;
  }

  setInterval(loop, 25);
}


if (window.addEventListener) {
  window.addEventListener('load', init, false); 
}