again

README.md

-asdasd
+1. For dynamic graphs, remove html tag of "sigma-parent" and rebuild the subgraph
+
+2. JS Pre-spatialization
+
+3. New CSS
+

bootswatch/css/bootswatch.css

+body{padding-top:50px}#banner{border-bottom:0}.page-header h1{font-size:4em}.bs-docs-section{margin-top:8em}.affix{top:70px}footer{margin:5em 0}footer li{float:left;margin-right:1.5em;margin-bottom:1.5em}footer p{margin-bottom:0;clear:left}.splash{padding:6em 0 2em;color:#fff;text-align:center;background:-webkit-linear-gradient(70deg,#080f1f 30%,#2b4b5a 87%,#435e67 100%);background:-o-linear-gradient(70deg,#080f1f 30%,#2b4b5a 87%,#435e67 100%);background:-ms-linear-gradient(70deg,#080f1f 30%,#2b4b5a 87%,#435e67 100%);background:-moz-linear-gradient(70deg,#080f1f 30%,#2b4b5a 87%,#435e67 100%);background:linear-gradient(20deg,#080f1f 30%,#2b4b5a 87%,#435e67 100%);background-attachment:fixed;background-color:#1c2533}.splash .alert{margin:4em 0 2em}.splash h1{font-size:4em}.splash #social{margin-top:6em}.section-tout{padding:4em 0 3em;background-color:#eaf1f1;border-top:1px solid rgba(255,255,255,0.1);border-bottom:1px solid rgba(0,0,0,0.1)}.section-tout [class^="icon-"]{margin-right:.5em}.section-tout p{margin-bottom:3em}.section-preview{padding:4em 0 4em}.section-preview .preview{margin-bottom:4em;background-color:#eaf1f1;border:1px solid rgba(0,0,0,0.1);border-radius:6px}.section-preview .preview .image{padding:5px}.section-preview .preview .image img{border:1px solid rgba(0,0,0,0.1)}.section-preview .preview .options{padding:0 2em 2em;text-align:center}.section-preview .preview .options p{margin-bottom:2em}.section-preview .dropdown-menu{text-align:left}.section-preview .lead{margin-bottom:2em}@media(max-width:767px){.section-preview .image img{width:100%}}.bsa .one .bsa_it_ad{background-color:transparent!important;border:none!important}.bsa .one .bsa_it_ad .bsa_it_t,.bsa .one .bsa_it_ad .bsa_it_d{color:inherit!important}.bsa .one .bsa_it_p{display:none}

bootswatch/js/bootswatch.js

+$('[data-toggle="tooltip"]').tooltip();
\ No newline at end of file

bootswatch/js/bsa.js

+(function(){
+  var bsa = document.createElement('script');
+     bsa.type = 'text/javascript';
+     bsa.async = true;
+     bsa.src = 'http://s3.buysellads.com/ac/bsa.js';
+  (document.getElementsByTagName('head')[0]||document.getElementsByTagName('body')[0]).appendChild(bsa);
+})();
\ No newline at end of file

css/custom.css

+.navbar { 
+	margin-bottom:1px;
+}
+
+#sigma-example {
+    width: 100%;
+    height: 300px;
+    position:relative;
+    float:right;
+}
+
+/*.btn-sm[normal] {*/
+/*  background-image: -webkit-linear-gradient(#5f8ab9, #3e648d 50%, #385a7f);*/
+/*  background-image: linear-gradient(#5f8ab9, #3e648d 50%, #385a7f);*/
+/*  background-repeat: no-repeat;*/
+/*  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5f8ab9', endColorstr='#ff385a7f', GradientType=0);*/
+/*  filter: none;*/
+/*  border: 1px solid #2e4b69;*/
+/*}*/
+
+#left{
+  display: inline-block;
+}
+
+
+/*.modal-vertical-centered {*/
+#loader{
+    text-align:center;
+    transform: translate(0, 50%) !important;
+    -ms-transform: translate(0, 50%) !important;  /*IE 9*/ 
+    -webkit-transform: translate(0, 50%) !important;  /*Safari and Chrome */
+}
+
+
+#selectionsBox{
+    text-align:center;
+    background-color:white;
+    color:#250587;
+    margin: 7px;
+    border: 1px solid #666;
+    -moz-border-radius: 3px;
+    -webkit-border-radius: 3px;
+    -border-radius: 3px;
+    -moz-box-shadow: 0px 2px 6px #000;
+    -webkit-box-shadow: 0px 2px 6px #000;
+    box-shadow: 0px 2px 6px #000;
+}
+
+#opossitesBox{
+    margin: 7px;
+    padding: 10px 0px 10px 10px;
+    border-style:solid;
+    background-color:white;
+    color:black;
+    margin: 7px;
+    border: 1px solid #666;
+    -moz-border-radius: 3px;
+    -webkit-border-radius: 3px;
+    -border-radius: 3px;
+    -moz-box-shadow: 0px 2px 6px #000;
+    -webkit-box-shadow: 0px 2px 6px #000;
+    box-shadow: 0px 2px 6px #000;
+}
+
+#topPapers{
+    margin: 7px;
+    padding: 10px 0px 10px 10px;
+    border-style:solid;
+    background-color:white;
+    color:black;
+    margin: 7px;
+    border: 1px solid #666;
+    -moz-border-radius: 3px;
+    -webkit-border-radius: 3px;
+    -border-radius: 3px;
+    -moz-box-shadow: 0px 2px 6px #000;
+    -webkit-box-shadow: 0px 2px 6px #000;
+    box-shadow: 0px 2px 6px #000;
+}
+
+
+.grey {
+    color: #cccccc; font-style: italic;
+}
+
+
+/* ZOOM IN OUT */
+
+#ctlzoom {
+    position: absolute; left: 5px; bottom: 5px; list-style: none; padding: 0; margin: 0;
+}
+
+#ctlzoom li {
+    padding: 0; margin: 10px 0; width: 36px; text-align: center;
+}
+
+#zoomSliderzone {
+    height: 120px;
+}
+
+#zoomMinusButton, #zoomPlusButton {
+    display: block; width: 24px; height: 24px; background:url("../tinawebJS/img/plusmoins.png");  margin: 0 auto;
+}
+
+#zoomMinusButton {
+    background-position: 0 -24px;
+}
+
+#zoomMinusButton:hover {
+    background-position: -24px -24px;
+}
+
+#zoomPlusButton {
+    background-position: 0 0;
+}
+
+#zoomPlusButton:hover {
+    background-position: -24px 0;
+}
+
+
+#lensButton {
+    display: block; width: 36px; height: 36px; background:url("../tinawebJS/img/loupe-edges2.png"); margin: 0 auto;
+}
+
+#lensButton {
+    background-position: -72px 0;
+}
+
+#lensButton:hover {
+    background-position: -36px 0;
+}
+
+#lensButton.off {
+    background-position: 0 0;
+}
+
+#lensButton.off:hover {
+    background-position: -108px 0;
+}
+
+#edgesButton {
+    display: block; width: 36px; height: 36px; background:url("../tinawebJS/img/loupe-edges.png"); margin: 0 auto;
+}
+
+#edgesButton {
+    background-position: -72px -36px;
+}
+
+#edgesButton:hover {
+    background-position: -36px -36px;
+}
+
+#edgesButton.off {
+    background-position: 0 -36px;
+}
+
+#edgesButton.off:hover {
+    background-position: -108px -36px;
+}
+
+#saveAs {
+    display: block; width: 30px; height: 30px; background:url("../tinawebJS/img/Save.png"); margin: 0 auto;
+}
+
+#zoomSlider {
+    background:#fff;
+    border:1px solid #aaa;
+    height: 120px; margin: 0 auto;
+}
+
+
+#showChat{
+    position: absolute; top: 16px; left: -14px; width: 20px; height: 100px; background: rgb(250, 250, 252); padding: 2px 2px 2px 0; border-top-right-radius: 5px; border-bottom-right-radius: 5px; box-shadow: 1px 1px 2px #808090;
+}
+
+#aShowChat {
+    float: left; width: 100%; height: 100%; background-image: url("../tinawebJS/img/chat.png");
+}
+
+
+
+/* GESTION DE LA BARRE DE GAUCHE */
+
+#unfold {
+    position: absolute; top: 16px; right: -14px; width: 12px; height: 12px; background: rgb(250, 250, 252); padding: 2px 2px 2px 0; border-top-right-radius: 5px; border-bottom-right-radius: 5px; box-shadow: 1px 1px 2px #808090;
+}
+
+#aUnfold {
+    float: left; width: 12px; height: 12px; background-image: url("../tinawebJS/img/fleches-horiz.png");
+}
+
+.leftarrow {
+    background-position: -12px 0;
+}
+
+.rightarrow {
+    background-position: 0 0;
+}
+
+.leftarrow:hover {
+    background-position: -12px -12px;
+}
+
+.rightarrow:hover {
+    background-position: 0 -12px;
+}
+
+/* AUTOCOMPLETE */
+
+#autocomplete {
+    position: absolute; display: none; padding: 0; margin: 0;
+    border-style: none solid; border-color: #ccc; border-width: 1px;
+}
+
+#autocomplete div {
+    border-bottom: 1px solid #ccc; padding: 0; margin: 0; float: left; clear: both; background: #fff;
+}
+
+#autocomplete h4 {
+    float: left; width: 80px; margin: 5px; font-size: 12px;
+}
+
+#autocomplete ul {
+    float: left; width: 240px; list-style: none; padding: 0; margin: 0;
+}
+
+#autocomplete li {
+    margin: 0; width: 240px; height: 28px; font-size: 12px; clear: both;
+}
+
+#autocomplete li a {
+    display: block; width: 240px; height: 28px; background: #fff; color: #06a8de;
+}
+
+#autocomplete li.hover a {
+    color: #fff; background: #06a8de;
+}
+
+#autocomplete span {
+    float: left; margin: 0; padding: 6px 2px 0;
+}
+
+#autocomplete img {
+    float: left; border: 0; width: 24px; height: 24px; margin: 2px 6px;
+}

css/sidebar.css

+#cuerpo {
+
+}
+
+#leftcolumn {
+  margin-left: -210px;
+  margin-right: 0px;
+  left: 210px;
+  width: 210px;
+  background: url(../img/climpek.png) repeat;
+  position: fixed;
+  height: 100%;
+  border: 1px #888888 solid;
+-moz-box-shadow: 0px 0px 3px 0px #888888;
+-webkit-box-shadow: 0px 0px 3px 0px #888888;
+box-shadow: 0px 0px 3px 0px #888888;
+  overflow-y: auto;
+  z-index: 1000;
+  transition: all 0.4s ease 0s;
+}
+
+#page-content-wrapper {
+  width: 100%;
+}
+
+

force.html

+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+<meta http-equiv="content-type" content="text/html; charset=UTF-8">
+
+</head>
+  <body>
+<div id="sigma-hola"></div>
+    <script src="libs/jquery/jquery-1.9.1.js"></script>
+    <script src="libs/jquery/jquery-ui.js" type="text/javascript"></script>
+    <script src="libs/jquery/jquery.ba-dotimeout.min.js" type="text/javascript"></script>
+    <script src="tinawebJS/js/sigma.min.js" type="text/javascript"></script>
+    lalalaalal<br>
+    <div id="log"></div>
+
+    <script src="FA2.js"></script>
+    <script src="genesis.js"></script>
+</body>
+</html>

genesis.js

+
+function pr(msg){
+	console.log(msg);
+}
+
+var counter=0;
+
+$( window ).resize(function() {
+  counter++;
+  $("#log").html("redimension numero: "+counter);
+});
+

libs/bootstrap/js/bootstrap-modal.js

+/* =========================================================
+ * bootstrap-modal.js v2.0.2
+ * http://twitter.github.com/bootstrap/javascript.html#modals
+ * =========================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ========================================================= */
+
+
+!function( $ ){
+
+  "use strict"
+
+ /* MODAL CLASS DEFINITION
+  * ====================== */
+
+  var Modal = function ( content, options ) {
+    this.options = options
+    this.$element = $(content)
+      .delegate('[data-dismiss="modal"]', 'click.dismiss.modal', $.proxy(this.hide, this))
+  }
+
+  Modal.prototype = {
+
+      constructor: Modal
+
+    , toggle: function () {
+        return this[!this.isShown ? 'show' : 'hide']()
+      }
+
+    , show: function () {
+        var that = this
+
+        if (this.isShown) return
+
+        $('body').addClass('modal-open')
+
+        this.isShown = true
+        this.$element.trigger('show')
+
+        escape.call(this)
+        backdrop.call(this, function () {
+          var transition = $.support.transition && that.$element.hasClass('fade')
+
+          !that.$element.parent().length && that.$element.appendTo(document.body) //don't move modals dom position
+
+          that.$element
+            .show()
+
+          if (transition) {
+            that.$element[0].offsetWidth // force reflow
+          }
+
+          that.$element.addClass('in')
+
+          transition ?
+            that.$element.one($.support.transition.end, function () { that.$element.trigger('shown') }) :
+            that.$element.trigger('shown')
+
+        })
+      }
+
+    , hide: function ( e ) {
+        e && e.preventDefault()
+
+        if (!this.isShown) return
+
+        var that = this
+        this.isShown = false
+
+        $('body').removeClass('modal-open')
+
+        escape.call(this)
+
+        this.$element
+          .trigger('hide')
+          .removeClass('in')
+
+        $.support.transition && this.$element.hasClass('fade') ?
+          hideWithTransition.call(this) :
+          hideModal.call(this)
+      }
+
+  }
+
+
+ /* MODAL PRIVATE METHODS
+  * ===================== */
+
+  function hideWithTransition() {
+    var that = this
+      , timeout = setTimeout(function () {
+          that.$element.off($.support.transition.end)
+          hideModal.call(that)
+        }, 500)
+
+    this.$element.one($.support.transition.end, function () {
+      clearTimeout(timeout)
+      hideModal.call(that)
+    })
+  }
+
+  function hideModal( that ) {
+    this.$element
+      .hide()
+      .trigger('hidden')
+
+    backdrop.call(this)
+  }
+
+  function backdrop( callback ) {
+    var that = this
+      , animate = this.$element.hasClass('fade') ? 'fade' : ''
+
+    if (this.isShown && this.options.backdrop) {
+      var doAnimate = $.support.transition && animate
+
+      this.$backdrop = $('<div class="modal-backdrop ' + animate + '" />')
+        .appendTo(document.body)
+
+      if (this.options.backdrop != 'static') {
+        this.$backdrop.click($.proxy(this.hide, this))
+      }
+
+      if (doAnimate) this.$backdrop[0].offsetWidth // force reflow
+
+      this.$backdrop.addClass('in')
+
+      doAnimate ?
+        this.$backdrop.one($.support.transition.end, callback) :
+        callback()
+
+    } else if (!this.isShown && this.$backdrop) {
+      this.$backdrop.removeClass('in')
+
+      $.support.transition && this.$element.hasClass('fade')?
+        this.$backdrop.one($.support.transition.end, $.proxy(removeBackdrop, this)) :
+        removeBackdrop.call(this)
+
+    } else if (callback) {
+      callback()
+    }
+  }
+
+  function removeBackdrop() {
+    this.$backdrop.remove()
+    this.$backdrop = null
+  }
+
+  function escape() {
+    var that = this
+    if (this.isShown && this.options.keyboard) {
+      $(document).on('keyup.dismiss.modal', function ( e ) {
+        e.which == 27 && that.hide()
+      })
+    } else if (!this.isShown) {
+      $(document).off('keyup.dismiss.modal')
+    }
+  }
+
+
+ /* MODAL PLUGIN DEFINITION
+  * ======================= */
+
+  $.fn.modal = function ( option ) {
+    return this.each(function () {
+      var $this = $(this)
+        , data = $this.data('modal')
+        , options = $.extend({}, $.fn.modal.defaults, $this.data(), typeof option == 'object' && option)
+      if (!data) $this.data('modal', (data = new Modal(this, options)))
+      if (typeof option == 'string') data[option]()
+      else if (options.show) data.show()
+    })
+  }
+
+  $.fn.modal.defaults = {
+      backdrop: true
+    , keyboard: true
+    , show: true
+  }
+
+  $.fn.modal.Constructor = Modal
+
+
+ /* MODAL DATA-API
+  * ============== */
+
+  $(function () {
+    $('body').on('click.modal.data-api', '[data-toggle="modal"]', function ( e ) {
+      var $this = $(this), href
+        , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7
+        , option = $target.data('modal') ? 'toggle' : $.extend({}, $target.data(), $this.data())
+
+      e.preventDefault()
+      $target.modal(option)
+    })
+  })
+
+}( window.jQuery );
\ No newline at end of file

libs/bootstrap/js/bootstrap-transition.js

+/* ===================================================
+ * bootstrap-transition.js v2.0.2
+ * http://twitter.github.com/bootstrap/javascript.html#transitions
+ * ===================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ========================================================== */
+
+!function( $ ) {
+
+  $(function () {
+
+    "use strict"
+
+    /* CSS TRANSITION SUPPORT (https://gist.github.com/373874)
+     * ======================================================= */
+
+    $.support.transition = (function () {
+      var thisBody = document.body || document.documentElement
+        , thisStyle = thisBody.style
+        , support = thisStyle.transition !== undefined || thisStyle.WebkitTransition !== undefined || thisStyle.MozTransition !== undefined || thisStyle.MsTransition !== undefined || thisStyle.OTransition !== undefined
+
+      return support && {
+        end: (function () {
+          var transitionEnd = "TransitionEnd"
+//          if ( $.browser.webkit ) {
+//          	transitionEnd = "webkitTransitionEnd"
+//          } else if ( $.browser.mozilla ) {
+//          	transitionEnd = "transitionend"
+//          } else if ( $.browser.opera ) {
+//          	transitionEnd = "oTransitionEnd"
+//          }
+          return transitionEnd
+        }())
+      }
+    })()
+
+  })
+
+}( window.jQuery );
\ No newline at end of file

libs/jquery/AUTHORS.txt

+jQuery UI Authors (http://jqueryui.com/about)
+
+This software consists of voluntary contributions made by many
+individuals. For exact contribution history, see the revision history
+and logs, available at http://github.com/jquery/jquery-ui
+
+Brandon Aaron
+Paul Bakaus (paulbakaus.com)
+David Bolter
+Rich Caloggero
+Chi Cheng (cloudream@gmail.com)
+Colin Clark (http://colin.atrc.utoronto.ca/)
+Michelle D'Souza
+Aaron Eisenberger (aaronchi@gmail.com)
+Ariel Flesler
+Bohdan Ganicky
+Scott González
+Marc Grabanski (m@marcgrabanski.com)
+Klaus Hartl (stilbuero.de)
+Scott Jehl
+Cody Lindley
+Eduardo Lundgren (eduardolundgren@gmail.com)
+Todd Parker
+John Resig
+Patty Toland
+Ca-Phun Ung (yelotofu.com)
+Keith Wood (kbwood@virginbroadband.com.au)
+Maggie Costello Wachs
+Richard D. Worth (rdworth.org)
+Jörn Zaefferer (bassistance.de)

libs/jquery/jquery.ba-dotimeout.min.js

+/*
+ * jQuery doTimeout: Like setTimeout, but better! - v1.0 - 3/3/2010
+ * http://benalman.com/projects/jquery-dotimeout-plugin/
+ * 
+ * Copyright (c) 2010 "Cowboy" Ben Alman
+ * Dual licensed under the MIT and GPL licenses.
+ * http://benalman.com/about/license/
+ */
+(function($){var a={},c="doTimeout",d=Array.prototype.slice;$[c]=function(){return b.apply(window,[0].concat(d.call(arguments)))};$.fn[c]=function(){var f=d.call(arguments),e=b.apply(this,[c+f[0]].concat(f));return typeof f[0]==="number"||typeof f[1]==="number"?this:e};function b(l){var m=this,h,k={},g=l?$.fn:$,n=arguments,i=4,f=n[1],j=n[2],p=n[3];if(typeof f!=="string"){i--;f=l=0;j=n[1];p=n[2]}if(l){h=m.eq(0);h.data(l,k=h.data(l)||{})}else{if(f){k=a[f]||(a[f]={})}}k.id&&clearTimeout(k.id);delete k.id;function e(){if(l){h.removeData(l)}else{if(f){delete a[f]}}}function o(){k.id=setTimeout(function(){k.fn()},j)}if(p){k.fn=function(q){if(typeof p==="string"){p=g[p]}p.apply(m,d.call(n,i))===true&&!q?o():e()};o()}else{if(k.fn){j===undefined?e():k.fn(j===false);return true}else{e()}}}})(jQuery);
\ No newline at end of file

libs/jquery/jquery.dynacloud-5.js

+/*
+
+DynaCloud v5
+
+A dynamic JavaScript tag/keyword cloud with jQuery.
+
+<http://johannburkard.de/blog/programming/javascript/dynacloud-a-dynamic-javascript-tag-keyword-cloud-with-jquery.html>
+
+MIT license.
+
+Johann Burkard
+<http://johannburkard.de>
+<mailto:jb@eaio.com>
+
+*/
+
+jQuery.fn.highlight = function(pat) {
+ function innerHighlight(node, pat) {
+  var skip = 0;
+  if (node.nodeType == 3) {
+   var pos = node.data.toUpperCase().indexOf(pat);
+   if (pos >= 0) {
+    var spannode = document.createElement('span');
+    spannode.className = 'highlight';
+    var middlebit = node.splitText(pos);
+    var endbit = middlebit.splitText(pat.length);
+    var middleclone = middlebit.cloneNode(true);
+    spannode.appendChild(middleclone);
+    middlebit.parentNode.replaceChild(spannode, middlebit);
+    skip = 1;
+   }
+  }
+  else if (node.nodeType == 1 && node.childNodes && !/(script|style)/i.test(node.tagName)) {
+   for (var i = 0; i < node.childNodes.length; ++i) {
+    i += innerHighlight(node.childNodes[i], pat);
+   }
+  }
+  return skip;
+ }
+ return this.each(function() {
+  innerHighlight(this, pat.toUpperCase());
+ });
+};
+
+jQuery.fn.removeHighlight = function() {
+ return this.find("span.highlight").each(function() {
+  this.parentNode.firstChild.nodeName;
+  with (this.parentNode) {
+   replaceChild(this.firstChild, this);
+   normalize();
+  }
+ }).end();
+};
+
+jQuery.dynaCloud = {
+
+ max: 20,
+ sort: true,
+ auto: true,
+ single: true,
+ wordStats: true,
+ scale: 4,
+
+// Adapted from <http://www.perseus.tufts.edu/Texts/engstop.html>
+
+ stopwords: [ "a", "about", "above", "accordingly", "after",
+  "again", "against", "ah", "all", "also", "although", "always", "am", "among", "amongst", "an",
+  "and", "any", "anymore", "anyone", "are", "as", "at", "away", "be", "been",
+  "begin", "beginning", "beginnings", "begins", "begone", "begun", "being",
+  "below", "between", "but", "by", "ca", "can", "cannot", "come", "could",
+  "did", "do", "doing", "during", "each", "either", "else", "end", "et",
+  "etc", "even", "ever", "far", "ff", "following", "for", "from", "further", "furthermore",
+  "get", "go", "goes", "going", "got", "had", "has", "have", "he", "her",
+  "hers", "herself", "him", "himself", "his", "how", "i", "if", "in", "into",
+  "is", "it", "its", "itself", "last", "lastly", "less", "many", "may", "me",
+  "might", "more", "must", "my", "myself", "near", "nearly", "never", "new",
+  "next", "no", "not", "now", "o", "of", "off", "often", "oh", "on", "only",
+  "or", "other", "otherwise", "our", "ourselves", "out", "over", "perhaps",
+  "put", "puts", "quite", "s", "said", "saw", "say", "see", "seen", "shall",
+  "she", "should", "since", "so", "some", "such", "t", "than", "that", "the",
+  "their", "them", "themselves", "then", "there", "therefore", "these", "they",
+  "this", "those", "though", "throughout", "thus", "to", "too",
+  "toward", "unless", "until", "up", "upon", "us", "ve", "very", "was", "we",
+  "were", "what", "whatever", "when", "where", "which", "while", "who",
+  "whom", "whomever", "whose", "why", "with", "within", "without", "would",
+  "yes", "your", "yours", "yourself", "yourselves" ]
+
+};
+
+jQuery(function() {
+ jQuery.dynaCloud.stopwords = new RegExp("\\s((" + jQuery.dynaCloud.stopwords.join("|") + ")\\s)+", "gi");
+ if (jQuery.dynaCloud.auto) {
+  jQuery('.dynacloud').dynaCloud();
+ }
+});
+
+jQuery.fn.dynaCloud = function(outElement) {
+ var cloud = {};
+ return this.each(function() {
+
+  var cl = [];
+  var max = 0;
+
+  if (jQuery.wordStats && jQuery.dynaCloud.wordStats) {
+   jQuery.wordStats.computeTopWords(jQuery.dynaCloud.max, this);
+   for (var i = 0, j = jQuery.wordStats.topWords.length; i < j && i <= jQuery.dynaCloud.max; ++i) {
+    var t = jQuery.wordStats.topWords[i].substring(1);
+    if (typeof cloud[t] == 'undefined') {
+     cloud[t] = { count: jQuery.wordStats.topWeights[i], el: t };
+    }
+    else {
+     cloud[t].count += jQuery.wordStats.topWeights[i];
+    }
+    max = Math.max(cloud[t].count, max);
+   }
+   jQuery.wordStats.clear();
+  }
+  else {
+   var elems = jQuery(this).text().replace(/[^A-Z\xC4\xD6\xDCa-z\xE4\xF6\xFC\xDF0-9_]/g, ' ').replace(jQuery.dynaCloud.stopwords, ' ').split(' ');
+   var word = /^[a-z\xE4\xF6\xFC]*[A-Z\xC4\xD6\xDC]([A-Z\xC4\xD6\xDC\xDF]+|[a-z\xE4\xF6\xFC\xDF]{3,})/;
+
+   jQuery.each(elems, function(i, n) {
+    if (word.test(n)) {
+     var t = n.toLowerCase();
+     if (typeof cloud[t] == 'undefined') {
+      cloud[t] = { count: 1, el: n };
+     }
+     else {
+      cloud[t].count += 1;
+     }
+     max = Math.max(cloud[t].count, max);
+    }
+   });
+  }
+
+  jQuery.each(cloud, function(i, n) {
+   cl[cl.length] = n;
+  });
+
+  if (jQuery.dynaCloud.sort) {
+   cl.sort(function(a, b) {
+    if (a.count == b.count) {
+     return a.el < b.el ? -1 : (a.el == b.el ? 0 : 1);
+    }
+    else {
+     return a.count < b.count ? 1 : -1;
+    }
+   });
+  }
+
+  var out;
+  if ((out = jQuery(outElement ? outElement : '#dynacloud')).length == 0) {
+   jQuery(document.body).append('<p id="dynacloud"><\/p>');
+   out = jQuery('#dynacloud');
+  }
+
+  out.empty();
+
+  var l = jQuery.dynaCloud.max == -1 ? cl.length : Math.min(jQuery.dynaCloud.max, cl.length);
+
+  for (var i = 0; i < l; ++i) {
+   out.append('<a href="#' + cl[i].el + '" style="font-size: ' + Math.ceil((cl[i].count / max) * jQuery.dynaCloud.scale) + 'em"><span>' + cl[i].el + '</span></a> &nbsp; ');
+  }
+  
+  var target = this;
+
+  jQuery('a', out).each(function() {
+   jQuery(this).click(function() {
+
+    if (jQuery.dynaCloud.single) {
+     jQuery(document.body).removeHighlight();
+    }
+
+    var text = jQuery(this).text().toUpperCase();
+    jQuery(target).each(function() {
+     jQuery(this).highlight(text);
+    });
+    return false;
+   });
+  });
+
+ });
+};

libs/jquery/jquery.highlight-3.js

+/*
+
+highlight v3
+
+Highlights arbitrary terms.
+
+<http://johannburkard.de/blog/programming/javascript/highlight-javascript-text-higlighting-jquery-plugin.html>
+
+MIT license.
+
+Johann Burkard
+<http://johannburkard.de>
+<mailto:jb@eaio.com>
+
+*/
+
+jQuery.fn.highlight = function(pat) {
+ function innerHighlight(node, pat) {
+  var skip = 0;
+  if (node.nodeType == 3) {
+   var pos = node.data.toUpperCase().indexOf(pat);
+   if (pos >= 0) {
+    var spannode = document.createElement('span');
+    spannode.className = 'highlight';
+    var middlebit = node.splitText(pos);
+    var endbit = middlebit.splitText(pat.length);
+    var middleclone = middlebit.cloneNode(true);
+    spannode.appendChild(middleclone);
+    middlebit.parentNode.replaceChild(spannode, middlebit);
+    skip = 1;
+   }
+  }
+  else if (node.nodeType == 1 && node.childNodes && !/(script|style)/i.test(node.tagName)) {
+   for (var i = 0; i < node.childNodes.length; ++i) {
+    i += innerHighlight(node.childNodes[i], pat);
+   }
+  }
+  return skip;
+ }
+ return this.each(function() {
+  innerHighlight(this, pat.toUpperCase());
+ });
+};
+
+jQuery.fn.removeHighlight = function() {
+ return this.find("span.highlight").each(function() {
+  this.parentNode.firstChild.nodeName;
+  with (this.parentNode) {
+   replaceChild(this.firstChild, this);
+   normalize();
+  }
+ }).end();
+};

libs/jquery/jquery.json-2.2.min.js

+
+(function($){$.toJSON=function(o)
+{if(typeof(JSON)=='object'&&JSON.stringify)
+return JSON.stringify(o);var type=typeof(o);if(o===null)
+return"null";if(type=="undefined")
+return undefined;if(type=="number"||type=="boolean")
+return o+"";if(type=="string")
+return $.quoteString(o);if(type=='object')
+{if(typeof o.toJSON=="function")
+return $.toJSON(o.toJSON());if(o.constructor===Date)
+{var month=o.getUTCMonth()+1;if(month<10)month='0'+month;var day=o.getUTCDate();if(day<10)day='0'+day;var year=o.getUTCFullYear();var hours=o.getUTCHours();if(hours<10)hours='0'+hours;var minutes=o.getUTCMinutes();if(minutes<10)minutes='0'+minutes;var seconds=o.getUTCSeconds();if(seconds<10)seconds='0'+seconds;var milli=o.getUTCMilliseconds();if(milli<100)milli='0'+milli;if(milli<10)milli='0'+milli;return'"'+year+'-'+month+'-'+day+'T'+
+hours+':'+minutes+':'+seconds+'.'+milli+'Z"';}
+if(o.constructor===Array)
+{var ret=[];for(var i=0;i<o.length;i++)
+ret.push($.toJSON(o[i])||"null");return"["+ret.join(",")+"]";}
+var pairs=[];for(var k in o){var name;var type=typeof k;if(type=="number")
+name='"'+k+'"';else if(type=="string")
+name=$.quoteString(k);else
+continue;if(typeof o[k]=="function")
+continue;var val=$.toJSON(o[k]);pairs.push(name+":"+val);}
+return"{"+pairs.join(", ")+"}";}};$.evalJSON=function(src)
+{if(typeof(JSON)=='object'&&JSON.parse)
+return JSON.parse(src);return eval("("+src+")");};$.secureEvalJSON=function(src)
+{if(typeof(JSON)=='object'&&JSON.parse)
+return JSON.parse(src);var filtered=src;filtered=filtered.replace(/\\["\\\/bfnrtu]/g,'@');filtered=filtered.replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,']');filtered=filtered.replace(/(?:^|:|,)(?:\s*\[)+/g,'');if(/^[\],:{}\s]*$/.test(filtered))
+return eval("("+src+")");else
+throw new SyntaxError("Error parsing JSON, source is not valid.");};$.quoteString=function(string)
+{if(string.match(_escapeable))
+{return'"'+string.replace(_escapeable,function(a)
+{var c=_meta[a];if(typeof c==='string')return c;c=a.charCodeAt();return'\\u00'+Math.floor(c/16).toString(16)+(c%16).toString(16);})+'"';}
+return'"'+string+'"';};var _escapeable=/["\\\x00-\x1f\x7f-\x9f]/g;var _meta={'\b':'\\b','\t':'\\t','\n':'\\n','\f':'\\f','\r':'\\r','"':'\\"','\\':'\\\\'};})(jQuery);
\ No newline at end of file

libs/jquery/jquery.mousewheel.min.js

+/*! Copyright (c) 2011 Brandon Aaron (http://brandonaaron.net)
+ * Licensed under the MIT License (LICENSE.txt).
+ *
+ * Thanks to: http://adomas.org/javascript-mouse-wheel/ for some pointers.
+ * Thanks to: Mathias Bank(http://www.mathias-bank.de) for a scope bug fix.
+ * Thanks to: Seamus Leahy for adding deltaX and deltaY
+ *
+ * Version: 3.0.6
+ * 
+ * Requires: 1.2.2+
+ */
+(function(a){
+    function d(b){
+        var c=b||window.event,d=[].slice.call(arguments,1),e=0,f=!0,g=0,h=0;
+        return b=a.event.fix(c),b.type="mousewheel",c.wheelDelta&&(e=c.wheelDelta/120),c.detail&&(e=-c.detail/3),h=e,c.axis!==undefined&&c.axis===c.HORIZONTAL_AXIS&&(h=0,g=-1*e),c.wheelDeltaY!==undefined&&(h=c.wheelDeltaY/120),c.wheelDeltaX!==undefined&&(g=-1*c.wheelDeltaX/120),d.unshift(b,e,g,h),(a.event.dispatch||a.event.handle).apply(this,d)
+        }
+        var b=["DOMMouseScroll","mousewheel"];
+    if(a.event.fixHooks)for(var c=b.length;c;)a.event.fixHooks[b[--c]]=a.event.mouseHooks;
+    a.event.special.mousewheel={
+        setup:function(){
+            if(this.addEventListener)for(var a=b.length;a;)this.addEventListener(b[--a],d,!1);else this.onmousewheel=d
+                },
+        teardown:function(){
+            if(this.removeEventListener)for(var a=b.length;a;)this.removeEventListener(b[--a],d,!1);else this.onmousewheel=null
+                }
+            },a.fn.extend({
+    mousewheel:function(a){
+        return a?this.bind("mousewheel",a):this.trigger("mousewheel")
+        },
+    unmousewheel:function(a){
+        return this.unbind("mousewheel",a)
+        }
+    })
+})(jQuery)

libs/jquery/jquery.nap-1.0.0.js

+/*	
+ *	jQuery nap 1.0.0
+ *	www.frebsite.nl
+ *	Copyright (c) 2010 Fred Heusschen
+ *	Licensed under the MIT license.
+ *	http://www.opensource.org/licenses/mit-license.php
+ */
+
+
+(function($) {
+	$.fn.nap = function(fallAsleep, wakeUp, standbyTime) {
+		if (typeof(standbyTime) == 'number' && standbyTime > 0) {
+			$.fn.nap.standbyTime = standbyTime;
+			
+			if ($.fn.nap.readySetGo) {
+				$.fn.nap.pressSnooze();
+			}
+		}
+		
+		if (!$.fn.nap.readySetGo) {
+			$.fn.nap.readySetGo = true;
+
+			$(window).mousemove(function() {
+				$.fn.nap.interaction();
+			});
+			$(window).keyup(function() {
+				$.fn.nap.interaction();
+			});
+			$(window).mousedown(function() {
+				$.fn.nap.interaction();
+			});
+
+			$(window).scroll(function() {
+				$.fn.nap.interaction();
+			});
+
+			$.fn.nap.pressSnooze();
+		}
+		
+		return this.each(function() {
+			$.fn.nap.fallAsleepFunctions.push({
+				func: fallAsleep, 
+				napr: $(this)
+			});
+			$.fn.nap.wakeUpFunctions.push({
+				func: wakeUp, 
+				napr: $(this)
+			});		
+		});
+	}
+
+
+	$.fn.nap.standbyTime 	= 60;
+	$.fn.nap.isAwake		= true;
+	$.fn.nap.readySetGo		= false;
+
+	$.fn.nap.fallAsleepFunctions 	= new Array();
+	$.fn.nap.wakeUpFunctions 		= new Array();
+	
+	$.fn.nap.fallAsleep = function() {
+		$.fn.nap.isAwake = false;
+		clearInterval($.fn.nap.alarmClock);
+		$.fn.nap.callFunctions($.fn.nap.fallAsleepFunctions);
+	};
+	$.fn.nap.wakeUp = function() {	
+		$.fn.nap.isAwake = true;
+		$.fn.nap.callFunctions($.fn.nap.wakeUpFunctions);
+	};
+	$.fn.nap.pressSnooze = function() {
+		clearInterval($.fn.nap.alarmClock);
+		$.fn.nap.alarmClock = setInterval(function() {
+			$.fn.nap.fallAsleep();
+		}, $.fn.nap.standbyTime * 1000);
+	}
+	$.fn.nap.interaction = function() {
+		if (!$.fn.nap.isAwake) {
+			$.fn.nap.wakeUp();
+		}
+		$.fn.nap.pressSnooze();
+	}
+	$.fn.nap.callFunctions = function(f) {
+		for (var i in f) {
+			if (typeof(f[i].func) == 'function') {
+				f[i].func();
+
+			} else if (typeof(f[i].func) == 'string' && f[i].func.length > 0) {
+				f[i].napr.trigger(f[i].func);
+
+			} else if (typeof(f[i].func) == 'object') {
+				for (var z in f[i].func) {
+					f[i].napr.trigger(f[i].func[z]);
+				}
+			}
+		}
+	}
+	
+})(jQuery);
\ No newline at end of file

libs/jquery/jquery.notify.min.js

+/*
+ * jQuery Notify UI Widget 1.4
+ * Copyright (c) 2010 Eric Hynds
+ *
+ * http://www.erichynds.com/jquery/a-jquery-ui-growl-ubuntu-notification-widget/
+ *
+ * Depends:
+ *   - jQuery 1.4
+ *   - jQuery UI 1.8 widget factory
+ *
+ * Dual licensed under the MIT and GPL licenses:
+ *   http://www.opensource.org/licenses/mit-license.php
+ *   http://www.gnu.org/licenses/gpl.html
+ *
+*/
+(function(d){d.widget("ech.notify",{options:{speed:500,expires:5E3,stack:"below",custom:false},_create:function(){var a=this;this.templates={};this.keys=[];this.element.addClass("ui-notify").children().addClass("ui-notify-message ui-notify-message-style").each(function(b){b=this.id||b;a.keys.push(b);a.templates[b]=d(this).removeAttr("id").wrap("<div></div>").parent().html()}).end().empty().show()},create:function(a,b,c){if(typeof a==="object"){c=b;b=a;a=null}a=this.templates[a||this.keys[0]];if(c&&c.custom)a=d(a).removeClass("ui-notify-message-style").wrap("<div></div>").parent().html();return(new d.ech.notify.instance(this))._create(b,d.extend({},this.options,c),a)}});d.extend(d.ech.notify,{instance:function(a){this.parent=a;this.isOpen=false}});d.extend(d.ech.notify.instance.prototype,{_create:function(a,b,c){this.options=b;var e=this;c=c.replace(/#(?:\{|%7B)(.*?)(?:\}|%7D)/g,function(f,g){return g in a?a[g]:""});c=this.element=d(c);var h=c.find(".ui-notify-close");typeof this.options.click==="function"&&c.addClass("ui-notify-click").bind("click",function(f){e._trigger("click",f,e)});h.length&&h.bind("click",function(){e.close();return false});this.open();typeof b.expires==="number"&&window.setTimeout(function(){e.close()},b.expires);return this},close:function(){var a=this,b=this.options.speed;this.isOpen=false;this.element.fadeTo(b,0).slideUp(b,function(){a._trigger("close")});return this},open:function(){if(this.isOpen||this._trigger("beforeopen")===false)return this;var a=this;this.isOpen=true;this.element[this.options.stack==="above"?"prependTo":"appendTo"](this.parent.element).css({display:"none",opacity:""}).fadeIn(this.options.speed,function(){a._trigger("open")});return this},widget:function(){return this.element},_trigger:function(a,b,c){return this.parent._trigger.call(this,a,b,c)}})})(jQuery);

libs/jquery/jquery.vticker-min.js

+/*
+* vertical news ticker
+* Tadas Juozapaitis ( kasp3rito@gmail.com )
+* http://plugins.jquery.com/project/vTicker
+*/
+(function(a){a.fn.vTicker=function(b){var c={speed:700,pause:4000,showItems:3,animation:"",mousePause:true,isPaused:false,direction:"up",height:0};var b=a.extend(c,b);moveUp=function(g,d,e){if(e.isPaused){return}var f=g.children("ul");var h=f.children("li:first").clone(true);if(e.height>0){d=f.children("li:first").height()}f.animate({top:"-="+d+"px"},e.speed,function(){a(this).children("li:first").remove();a(this).css("top","0px")});if(e.animation=="fade"){f.children("li:first").fadeOut(e.speed);if(e.height==0){f.children("li:eq("+e.showItems+")").hide().fadeIn(e.speed)}}h.appendTo(f)};moveDown=function(g,d,e){if(e.isPaused){return}var f=g.children("ul");var h=f.children("li:last").clone(true);if(e.height>0){d=f.children("li:first").height()}f.css("top","-"+d+"px").prepend(h);f.animate({top:0},e.speed,function(){a(this).children("li:last").remove()});if(e.animation=="fade"){if(e.height==0){f.children("li:eq("+e.showItems+")").fadeOut(e.speed)}f.children("li:first").hide().fadeIn(e.speed)}};return this.each(function(){var f=a(this);var e=0;f.css({overflow:"hidden",position:"relative"}).children("ul").css({position:"absolute",margin:0,padding:0}).children("li").css({margin:0,padding:0});if(b.height==0){f.children("ul").children("li").each(function(){if(a(this).height()>e){e=a(this).height()}});f.children("ul").children("li").each(function(){a(this).height(e)});f.height(e*b.showItems)}else{f.height(b.height)}var d=setInterval(function(){if(b.direction=="up"){moveUp(f,e,b)}else{moveDown(f,e,b)}},b.pause);if(b.mousePause){f.bind("mouseenter",function(){b.isPaused=true}).bind("mouseleave",function(){b.isPaused=false})}})}})(jQuery);
\ No newline at end of file

php/PySQlite/FA2.py

+from Region import Region
+import ForceFactory
+import math
+import random
+import sys
+import pprint
+
+class ForceAtlas2:
+	def __init__(self,graph):
+		self.graph = graph
+		self.nodesIndex = {}
+		self.p={
+			"linLogMode": False,
+			"outboundAttractionDistribution": False,
+			"adjustSizes": False,
+			"edgeWeightInfluence": 0,
+			"scalingRatio": 1,
+			"strongGravityMode": False,
+			"gravity": 1,
+			"jitterTolerance": 1,
+			"barnesHutOptimize": False,
+			"barnesHutTheta": 1.2,
+			"speed": 1,
+			"outboundAttCompensation": 1,
+			"totalSwinging": 0,
+			"swingVSnode1": 0,
+			"totalEffectiveTraction": 0,
+			"complexIntervals": 500,
+			"simpleIntervals": 1000
+		}
+		self.state = {"step": 0, "index": 0}
+		self.rootRegion = 0
+
+	def init(self):
+		self.setAutoSettings()
+		nds = self.graph["nodes"]
+		for i in range(len(nds)):
+
+			if not nds[i].has_key("fixed"):
+				nds[i]['fixed'] = False
+
+			if not nds[i].has_key("x"):
+				nds[i]['x'] = random.uniform(0,1)
+
+			if not nds[i].has_key("y"):
+				nds[i]['y'] = random.uniform(0,1)
+
+			self.nodesIndex[nds[i]['id']] = i
+			nds[i]["fa2"] = {
+				"mass": 1+nds[i]["degree"],
+				"old_dx": 0,
+				"old_dy": 0,
+				"dx": 0,
+				"dy": 0
+			}
+		return self
+
+	def go(self):
+		while (self.atomicGo()):
+			print "something"
+
+	def printNodesFA2(self):
+		for i in self.graph["nodes"]:
+			print i
+
+	def setAutoSettings(self):
+		# Tuning
+		lenNodes = len(self.graph["nodes"])
+		if (lenNodes >= 100):
+			self.p["scalingRatio"] = 2.0
+		else:
+			self.p["scalingRatio"] = 10.0
+
+		self.p["strongGravityMode"] = False
+		self.p["gravity"] = 1
+
+		# Behavior
+		self.p["outboundAttractionDistribution"] = False
+		self.p["linLogMode"] = False
+		self.p["adjustSizes"] = False
+		self.p["edgeWeightInfluence"] = 1
+
+		# Performance
+		if (lenNodes >= 50000):
+			self.p["jitterTolerance"] = 10
+		elif (lenNodes >= 5000):
+			self.p["jitterTolerance"] = 1
+		else:
+			self.p["jitterTolerance"] = 0.1
+
+		if (lenNodes >= 1000):
+			self.p["barnesHutOptimize"] = True
+		else:
+			self.p["barnesHutOptimize"] = False
+
+		self.p["barnesHutTheta"] = 1.2
+
+
+
+
+	def atomicGo(self):
+		graph = self.graph
+		nodes = graph["nodes"]
+		edges = graph["edges"]
+
+		cInt = self.p["complexIntervals"]
+		sInt = self.p["simpleIntervals"]
+		
+		case = self.state["step"]
+
+		if   case==0:
+								# Initialise layout data
+			print "the case 0"
+			for i in range(len(nodes)):
+				if nodes[i]["fa2"]:
+					nodes[i]["fa2"]["mass"] = 1 + nodes[i]["degree"]
+					nodes[i]["fa2"]["old_dx"] = nodes[i]["fa2"]["dx"]
+					nodes[i]["fa2"]["old_dy"] = nodes[i]["fa2"]["dy"]
+					nodes[i]["fa2"]["dx"] = 0
+					nodes[i]["fa2"]["dy"] = 0
+				else:
+					nodes[i]["fa2"] = {
+						"mass": 1 + nodes[i]["degree"],
+						"old_dx": 0,
+						"old_dy": 0,
+						"dx": 0,
+						"dy": 0
+					}
+			
+			# If Barnes Hut active, initialize root region
+			if self.p["barnesHutOptimize"]:
+				print '\tcase 0 -> ["barnesHutOptimize"]'
+				self.rootRegion = Region(nodes, 0)
+				self.rootRegion.buildSubRegions()
+
+
+			# If outboundAttractionDistribution active, compensate.
+			if self.p["outboundAttractionDistribution"]:
+				print '\tcase 0 -> ["outboundAttractionDistribution"]'
+				self.p["outboundAttCompensation"] = 0
+				for i in range(len(nodes)):
+					self.p["outboundAttCompensation"] += nodes[i]["fa2"]["mass"]
+				self.p["outboundAttCompensation"] /= len(nodes)
+
+			self.state["step"] = 1
+			self.state["index"] = 0
+			return True
+
+
+		elif case==1:
+								# Repulsion
+			print "the case 1: Repulsion"
+			Repulsion = ForceFactory.buildRepulsion(self.p["adjustSizes"],self.p["scalingRatio"])
+			print "\tprinting what it is inside of Repulsion variable"
+			print Repulsion
+			if self.p["barnesHutOptimize"]:
+				rootRegion = self.rootRegion
+				barnesHutTheta = self.p["barnesHutTheta"]
+				i = self.state["index"]
+				while (i < len(nodes) and i < self.state["index"] + cInt):
+					n = nodes[i]
+					i+=1
+					if n["fa2"]:
+						rootRegion.applyForce(n, Repulsion, barnesHutTheta)
+				if (i == len(nodes)):
+					self.state["step"] = 2
+					self.state["index"] = 0
+				else:
+					self.state["index"] = i
+			else:
+				i1 = self.state["index"]
+				while (i1 < len(nodes) and i1 < self.state["index"] + cInt):
+					n1 = nodes[i1]
+					i1+=1
+					if n1["fa2"]:
+						for i2 in range(len(nodes)):
+							if i2 < i1 and nodes[i2]["fa2"]:
+								Repulsion.apply_nn(n1, nodes[i2])
+				if (i1 == len(nodes)):
+					self.state["step"] = 2
+					self.state["index"] = 0
+				else:
+					self.state["index"] = i1
+			return True
+
+
+		elif case==2:
+								# Gravity
+			print "the case 2: Gravity"
+			Gravity=""
+			if self.p["strongGravityMode"]:
+				Gravity = ForceFactory.getStrongGravity(self.p["scalingRatio"])
+			else:
+				Gravity = ForceFactory.buildRepulsion(self.p["adjustSizes"],self.p["scalingRatio"])
+			gravity = self.p["gravity"]
+			scalingRatio = self.p["scalingRatio"]
+			i = self.state["index"]
+			while (i < len(nodes) and i < self.state["index"] + sInt):
+				n = nodes[i]
+				i+=1
+				if n["fa2"]:
+					Gravity.apply_g(n, gravity / scalingRatio)
+
+			if (i == len(nodes)):
+				self.state["step"] = 3
+				self.state["index"] = 0
+			else:
+				self.state["index"] = i
+			return True
+
+		elif case==3:
+								# Attraction
+			print "the case 3: Attraction"
+			field=""
+			if self.p["outboundAttractionDistribution"]:
+				field = self.p["outboundAttCompensation"]
+			else:
+				field = 1
+			Attraction = ForceFactory.buildAttraction(self.p["linLogMode"],self.p["outboundAttractionDistribution"],self.p["adjustSizes"],1*field)
+			i = self.state["index"]
+			if self.p["edgeWeightInfluence"] == 0:
+				while (i < len(edges) and i < self.state["index"] + cInt):
+					e = edges[i]
+					i+=1
+					s = nodes[self.nodesIndex[e["source"]]]
+					t = nodes[self.nodesIndex[e["target"]]]
+					Attraction.apply_nn(s, t, 1)
+			elif self.p["edgeWeightInfluence"] == 1:
+				while (i < len(edges) and i < self.state["index"] + cInt):
+					e = edges[i]
+					i+=1
+					s = nodes[self.nodesIndex[e["source"]]]
+					t = nodes[self.nodesIndex[e["target"]]]
+					Attraction.apply_nn(s, t, (e["weight"] or 1))
+			else:
+				while (i < len(edges) and i < self.state["index"] + cInt):
+					e = edges[i]
+					i+=1
+					t = nodes[self.nodesIndex[e["target"]]]
+					Attraction.apply_nn(t,(math.pow(e["weight"] or 1), self.p["edgeWeightInfluence"]))
+			if (i == len(edges)):
+				self.state["step"] = 4
+				self.state["index"] = 0
+			else:
+				self.state["index"] = i
+			return True
+
+		elif case==4:
+								# Auto adjust speed
+			print "the case 4: Auto-adjust speed"
+			totalSwinging=0# How much irregular movement
+			totalEffectiveTraction = 0  # Hom much useful movement
+			swingingSum=0
+			promdxdy=0
+			for i in range(len(nodes)):
+				n = nodes[i]
+				fixed = n["fixed"] or False
+				if not fixed and n["fa2"]:
+					swinging = math.sqrt(math.pow(n["fa2"]["old_dx"] - n["fa2"]["dx"], 2)+math.pow(n["fa2"]["old_dy"] - n["fa2"]["dy"], 2))
+					totalSwinging+=n["fa2"]["mass"]*swinging
+					totalEffectiveTraction +=n["fa2"]["mass"]*0.5*math.sqrt(math.pow(n["fa2"]["old_dx"] + n["fa2"]["dx"], 2)+math.pow(n["fa2"]["old_dy"] + n["fa2"]["dy"], 2))
+			self.p["totalSwinging"] = totalSwinging
+			self.p["totalEffectiveTraction"] = totalEffectiveTraction
+			#We want that swingingMovement < tolerance * convergenceMovement
+			targetSpeed = math.pow(self.p["jitterTolerance"], 2)*self.p["totalEffectiveTraction"]/self.p["totalSwinging"]
+			#But the speed shoudn't rise too much too quickly,
+			#since it would make the convergence drop dramatically.
+			maxRise = 0.5
+			self.p["speed"] = self.p["speed"]+min(targetSpeed-self.p["speed"],maxRise * self.p["speed"])
+
+			#Save old coordinates
+			for i in range(len(nodes)):
+				nodes[i]["old_x"] = +nodes[i]["x"]
+				nodes[i]["old_y"] = +nodes[i]["y"]
+			self.state["step"] = 5
+			return True
+
+		elif case==5:
+								# Apply forces
+			print "the case 5: Apply forces"
+
+			i = self.state["index"]
+			if self.p["adjustSizes"]:
+				speed = self.p["speed"]
+				while (i < len(nodes) and i < self.state["index"] + sInt):
+					n = nodes[i]
+					i+=1
+					fixed = n["fixed"] or False
+					if not fixed and n["fa2"]:
+						swinging = math.sqrt((n["fa2"]["old_dx"] - n["fa2"]["dx"])*(n["fa2"]["old_dx"] - n["fa2"]["dx"]) +(n["fa2"]["old_dy"] - n["fa2"]["dy"])*(n["fa2"]["old_dy"] - n["fa2"]["dy"]))
+						factor = 0.1 * speed / (1 + speed * math.sqrt(swinging))
+						df = math.sqrt(math.pow(n["fa2"]["dx"], 2)+math.pow(n["fa2"]["dy"], 2))
+						factor = min(factor * df, 10) / df
+						n["x"] += n["fa2"]["dx"] * factor
+						n["y"] += n["fa2"]["dy"] * factor
+			else:
+				speed = self.p["speed"]
+				while (i < len(nodes) and i < self.state["index"] + sInt):
+					n = nodes[i]
+					i+=1
+					fixed = n["fixed"] or False
+					if not fixed and n["fa2"]:
+					#Adaptive auto-speed: the speed of each node is lowered
+					#when the node swings.
+						swinging = math.sqrt((n["fa2"]["old_dx"] - n["fa2"]["dx"])*(n["fa2"]["old_dx"] - n["fa2"]["dx"]) +(n["fa2"]["old_dy"] - n["fa2"]["dy"])*(n["fa2"]["old_dy"] - n["fa2"]["dy"]))
+						factor = speed / (1 + speed * math.sqrt(swinging))
+						n["x"] += n["fa2"]["dx"] * factor
+						n["y"] += n["fa2"]["dy"] * factor
+			if (i == len(edges)):
+				self.state["step"] = 0
+				self.state["index"] = 0
+				return False
+			else:
+				self.state["index"] = i
+				return True
+
+		else:
+								# Do the default
+			print "Error"
+			return False
+
+	def getGraph(self):
+		nds = self.graph['nodes']
+		justNodes = []
+		for i in range(len(nds)):
+			n = {
+				"id":i,
+				"sID":nds[i]["id"],
+				"x":nds[i]["x"],
+				"y":nds[i]["y"],
+				"occ":nds[i]["degree"]
+			}
+			justNodes.append(n)
+		return justNodes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

php/PySQlite/FA2.py_old

+#! /usr/bin/python
+
+import networkx as nx
+import scipy as sp
+import numpy as np
+import random
+import threading
+
+import matplotlib.pyplot as plt
+
+## Read a food web with > 100 nodes
+'''
+FW = nx.read_edgelist('web.edges', create_using= nx.DiGraph())
+'''
+
+## Plotting using the FR layout
+#nx.draw_spring(FW,iterations=500)
+#plt.show()
+
+
+
+class FA2:
+
+	def eucl_dist(self,a,b):
+	    """
+	    Euclidean distance
+	    """
+	    Di = [(a[i]-b[i])**2 for i in xrange(len(a))]
+	    return np.sqrt(np.sum(Di))
+
+	## Now the layout function
+	def forceatlas2_layout(self,G, iterations = 10, linlog = False, pos = None, nohubs = False, kr = 0.001, k = None, dim = 2):
+	    """
+	    Options values are
+
+	    g                The graph to layout
+	    iterations       Number of iterations to do
+	    linlog           Whether to use linear or log repulsion
+	    random_init      Start with a random position
+		             If false, start with FR
+	    avoidoverlap     Whether to avoid overlap of points
+	    degreebased      Degree based repulsion
+	    """
+	    # We add attributes to store the current and previous convergence speed
+	    for n in G:
+		G.node[n]['prevcs'] = 0
+		G.node[n]['currcs'] = 0
+	    # To numpy matrix
+	    # This comes from the spares FR layout in nx
+	    A=nx.to_scipy_sparse_matrix(G,dtype='f')
+	    nnodes,_=A.shape
+	    from scipy.sparse import spdiags,coo_matrix
+	    try:
+		A=A.tolil()
+	    except:
+		A=(coo_matrix(A)).tolil()
+	    if pos==None:
+		pos=np.asarray(np.random.random((nnodes,dim)),dtype=A.dtype)
+	    else:
+		pos=pos.astype(A.dtype)
+	    if k is None:
+		k=np.sqrt(1.0/nnodes)
+	    # Iterations
+	    # the initial "temperature" is about .1 of domain area (=1x1)
+	    # this is the largest step allowed in the dynamics.
+	    t=0.1
+	    # simple cooling scheme.
+	    # linearly step down by dt on each iteration so last iteration is size dt.
+	    dt=t/float(iterations+1)
+	    displacement=np.zeros((dim,nnodes))
+	    for iteration in range(iterations):
+		displacement*=0
+		# loop over rows
+		for i in range(A.shape[0]):
+		    # difference between this row's node position and all others
+		    delta=(pos[i]-pos).T
+		    # distance between points
+		    distance=np.sqrt((delta**2).sum(axis=0))
+		    # enforce minimum distance of 0.01
+		    distance=np.where(distance<0.01,0.01,distance)
+		    # the adjacency matrix row
+		    Ai=np.asarray(A.getrowview(i).toarray())
+		    # displacement "force"
+		    Dist = k*k/distance**2
+		    if nohubs:
+		        Dist = Dist/float(Ai.sum(axis=1)+1)
+		    if linlog:
+		        Dist = np.log(Dist+1)
+		    displacement[:,i]+=\
+		        (delta*(Dist-Ai*distance/k)).sum(axis=1)
+		# update positions
+		length=np.sqrt((displacement**2).sum(axis=0))
+		length=np.where(length<0.01,0.1,length)
+		pos+=(displacement*t/length).T
+		# cool temperature
+		t-=dt
+	    # Return the layout
+	    return dict(zip(G,pos))
+
+#nx.draw(G, forceatlas2_layout(G,linlog=False,nohubs=False,iterations=100))
+#plt.show()

php/PySQlite/RV-Uniform.py

+class RVUniformC:
+	def __init__(self,seed):
+		self.a=16807
+		self.b=0
+		self.m=2147483647
+		self.u=0
+		self.semilla=seed
+		self.x = self.semilla
+
+
+	def getRandom(self):
+		x = ((self.x*self.a)+self.b)%self.m
+		self.x = x
+		self.u = self.x/float(self.m)
+		return self.u
+
+
+#instancia = RVUniformC(100000000)
+#instancia.getUniform()

php/PySQlite/__init__.py

+# -*- coding: utf-8 -*-

php/PySQlite/main.py

+# -*- coding: utf-8 -*-
+
+from FA2 import ForceAtlas2
+from extractData import extract as SQLite
+
+import sys
+reload(sys)
+sys.setdefaultencoding('utf-8')
+
+from flask import Flask
+from flask import request
+import simplejson as json
+app = Flask(__name__)
+
+
+@app.route("/getJSON")
+def main():
+	#query = request.args['query']
+	#{"categorya"%3A"Keywords"%2C"categoryb"%3A"Scholars"%2C"keywords"%3A[]%2C"countries"%3A["Chile"]%2C"laboratories"%3A[]%2C"coloredby"%3A[]%2C"tags"%3A[]%2C"organizations"%3A[]}
+
+#	i=int(sys.argv[2])
+#	unique_id = sys.argv[1]
+#	db=SQLite(unique_id)
+#	db.extract()
+
+
+
+	# < Data Extraction > #
+	i = int(request.args['it'])
+
+	if request.args.has_key("query"):
+		db=SQLite("")
+		print request.args['query']
+		print i
+		db.extract2(request.args['query'])
+	else:
+		unique_id = request.args['unique_id']
+		db=SQLite(unique_id)
+		db.extract()
+	# < / Data Extraction > #
+
+
+	tempGraph = db.buildSimpleJSONFinal(db.Graph)
+	spatialized = ForceAtlas2(tempGraph)
+	spatialized.init()
+
+	spatialized.getGraph()
+
+#	for i in range(0,i):
+#		spatialized.atomicGo()
+	
+
+	graphArray = db.buildJSON_sansfa2(db.Graph,spatialized.getGraph())
+
+	return json.dumps(graphArray)
+
+
+    
+
+if __name__ == "__main__":
+#	main()
+	app.run(port=8080)

php/PySQlite/test2.py

+# -*- coding: utf-8 -*-
+
+from extractData import extract as SQLite
+import time
+import sys
+reload(sys)
+sys.setdefaultencoding('utf-8')
+
+
+def main():
+
+	db=SQLite("")
+	print "Start"
+	start = time.time()
+	db.extract2('SELECT * FROM scholars where   country = "'+sys.argv[1]+'"')
+	end = time.time()  
+	seconds1=end-start
+	print "End"
+	print "\ttotal: "+str(seconds1)+"[s]"
+	
+	#return queryFromFilter#json.dumps(graphArray)
+
+
+    
+
+if __name__ == "__main__":
+	main()
+	#app.run(port=8080)