Big changes in Eigen documentation:

- Organize the documentation into "chapters".
  - Each chapter include many documentation pages, reference pages organized as modules, and a quick reference page.
  - The "Chapters" tree is created using the defgroup/ingroup mechanism, even for the documentation pages (i.e., .dox files for which I added an \eigenManualPage macro that we can switch between \page or \defgroup ).
  - Add a "General topics" entry for all pages that do not fit well in the previous "chapters".
  - The highlevel struture is managed by a new eigendoxy_layout.xml file.
- remove the "index" and quite useless pages (namespace list, class hierarchy, member list, file list, etc.)
- add the javascript search-engine.
- add the "treeview" panel.
- remove \tableofcontents (replace them by a custom \eigenAutoToc macro to be able to easily re-enable if needed).
- add javascript to automatically generate a TOC from the h1/h2 tags of the current page, and put the TOC in the left side panel.
- overload various javascript function generated by doxygen to:
  - remove the root of the treeview
  - remove links to section/subsection from the treeview
  - automatically expand the "Chapters" section
  - automatically expand the current section
  - adjust the height of the treeview to take into account the TOC
- always use the default .css file, eigendoxy.css now only includes our modifications
- use Doxyfile to specify our logo
- remove cross references to unsupported modules (temporarily)

1 files changed, 239 insertions, 0 deletions

diff --git a/doc/eigen_navtree_hacks.js b/doc/eigen_navtree_hacks.js
new file mode 100644
index 000000000..1a09e74fc
--- /dev/null
+++ b/doc/eigen_navtree_hacks.js
@@ -0,0 +1,239 @@
+
+// generate a table of contents in the side-nav based on the h1/h2 tags of the current page.
+function generate_autotoc() {
+  var headers = $("h1, h2");
+  if(headers.length > 1) {
+    var toc = $("#side-nav").append('<div id="nav-toc" class="toc"><h3>Table of contents</h3></div>');
+    toc = $("#nav-toc");
+    var footerHeight = footer.height();
+    toc = toc.append('<ul></ul>');
+    toc = toc.find('ul');
+    var indices = new Array();
+    indices[0] = 0;
+    indices[1] = 0;
+
+    var h1counts = $("h1").length;
+    headers.each(function(i) {
+      var current = $(this);
+      var levelTag = current[0].tagName.charAt(1);
+      if(h1counts==0)
+        levelTag--;
+      var cur_id = current.attr("id");
+
+      indices[levelTag-1]+=1;  
+      var prefix = indices[0];
+      if (levelTag >1) {
+        prefix+="."+indices[1];
+      }
+        
+      current.html(prefix + "   " + current.html());
+      for(var l = levelTag; l < 2; ++l){
+          indices[l] = 0;
+      }
+
+      if(cur_id == undefined) {
+        current.attr('id', 'title' + i);
+        current.addClass('anchor');
+        toc.append("<li class='level" + levelTag + "'><a id='link" + i + "' href='#title" +
+                    i + "' title='" + current.prop("tagName") + "'>" + current.text() + "</a></li>");
+      } else {
+        toc.append("<li class='level" + levelTag + "'><a id='" + cur_id + "' href='#title" +
+                    i + "' title='" + current.prop("tagName") + "'>" + current.text() + "</a></li>");
+      }
+    });
+    resizeHeight();
+  }
+}
+
+
+var global_navtree_object;
+
+// Overloaded to remove links to sections/subsections
+function getNode(o, po)
+{
+  po.childrenVisited = true;
+  var l = po.childrenData.length-1;
+  for (var i in po.childrenData) {
+    var nodeData = po.childrenData[i];
+    if((!nodeData[1]) ||  (nodeData[1].indexOf('#')==-1)) // <- we added this line
+      po.children[i] = newNode(o, po, nodeData[0], nodeData[1], nodeData[2], i==l);
+  }
+}
+
+// Overloaded to adjust the size of the navtree wrt the toc
+function resizeHeight() 
+{
+  var toc = $("#nav-toc");
+  var tocHeight = toc.height();  // <- we added this line
+  var headerHeight = header.height();
+  var footerHeight = footer.height();
+  var windowHeight = $(window).height() - headerHeight - footerHeight;
+  content.css({height:windowHeight + "px"});
+  navtree.css({height:(windowHeight-tocHeight) + "px"}); // <- we modified this line
+  sidenav.css({height:(windowHeight) + "px",top: headerHeight+"px"});
+}
+
+// Overloaded to save the root node into global_navtree_object
+function initNavTree(toroot,relpath)
+{
+  var o = new Object();
+  global_navtree_object = o; // <- we added this line
+  o.toroot = toroot;
+  o.node = new Object();
+  o.node.li = document.getElementById("nav-tree-contents");
+  o.node.childrenData = NAVTREE;
+  o.node.children = new Array();
+  o.node.childrenUL = document.createElement("ul");
+  o.node.getChildrenUL = function() { return o.node.childrenUL; };
+  o.node.li.appendChild(o.node.childrenUL);
+  o.node.depth = 0;
+  o.node.relpath = relpath;
+  o.node.expanded = false;
+  o.node.isLast = true;
+  o.node.plus_img = document.createElement("img");
+  o.node.plus_img.src = relpath+"ftv2pnode.png";
+  o.node.plus_img.width = 16;
+  o.node.plus_img.height = 22;
+
+  navTo(o,toroot,window.location.hash,relpath);
+
+  $(window).bind('hashchange', function(){
+     if (window.location.hash && window.location.hash.length>1){
+       var a;
+       if ($(location).attr('hash')){
+         var clslink=stripPath($(location).attr('pathname'))+':'+
+                               $(location).attr('hash').substring(1);
+         a=$('.item a[class$="'+clslink+'"]');
+       }
+       if (a==null || !$(a).parent().parent().hasClass('selected')){
+         $('.item').removeClass('selected');
+         $('.item').removeAttr('id');
+       }
+       var link=stripPath2($(location).attr('pathname'));
+       navTo(o,link,$(location).attr('hash'),relpath);
+     }
+  })
+
+  $(window).load(showRoot);
+}
+
+// return false if the the node has no children at all, or has only section/subsection children
+function checkChildrenData(node) {
+  if (!(typeof(node.childrenData)==='string')) {
+    for (var i in node.childrenData) {
+      var url = node.childrenData[i][1];
+      if(url.indexOf("#")==-1)
+        return true;
+    }
+    return false;
+  }
+  return (node.childrenData);
+}
+
+// Modified to:
+// 1 - remove the root node (added && node.parentNode.parentNode.parentNode)
+// 2 - remove the section/subsection children
+function createIndent(o,domNode,node,level)
+{
+  if (node.parentNode && node.parentNode.parentNode
+      && node.parentNode.parentNode.parentNode    // <- we added this line
+     ) {
+    createIndent(o,domNode,node.parentNode,level+1);
+  }
+  var imgNode = document.createElement("img");
+  imgNode.width = 16;
+  imgNode.height = 22;
+  
+  if (level==0 && checkChildrenData(node)) {  // <- we modified this line to use checkChildrenData(node) instead of node.childrenData
+    node.plus_img = imgNode;
+    node.expandToggle = document.createElement("a");
+    node.expandToggle.href = "javascript:void(0)";
+    node.expandToggle.onclick = function() {
+      if (node.expanded) {
+        $(node.getChildrenUL()).slideUp("fast");
+        if (node.isLast) {
+          node.plus_img.src = node.relpath+"ftv2plastnode.png";
+        } else {
+          node.plus_img.src = node.relpath+"ftv2pnode.png";
+        }
+        node.expanded = false;
+      } else {
+        expandNode(o, node, false, false);
+      }
+    }
+    node.expandToggle.appendChild(imgNode);
+    domNode.appendChild(node.expandToggle);
+  } else {
+    domNode.appendChild(imgNode);
+  }
+  if (level==0) {
+    if (node.isLast) {
+      if (checkChildrenData(node)) {  // <- we modified this line to use checkChildrenData(node) instead of node.childrenData
+        imgNode.src = node.relpath+"ftv2plastnode.png";
+      } else {
+        imgNode.src = node.relpath+"ftv2lastnode.png";
+        domNode.appendChild(imgNode);
+      }
+    } else {
+      if (checkChildrenData(node)) {  // <- we modified this line to use checkChildrenData(node) instead of node.childrenData
+        imgNode.src = node.relpath+"ftv2pnode.png";
+      } else {
+        imgNode.src = node.relpath+"ftv2node.png";
+        domNode.appendChild(imgNode);
+      }
+    }
+  } else {
+    if (node.isLast) {
+      imgNode.src = node.relpath+"ftv2blank.png";
+    } else {
+      imgNode.src = node.relpath+"ftv2vertline.png";
+    }
+  }
+  imgNode.border = "0";
+}
+
+// Overloaded to automatically expand the selected node
+function selectAndHighlight(n)
+{
+  var a;
+  if ($(location).attr('hash')) {
+    var link=stripPath($(location).attr('pathname'))+':'+
+      $(location).attr('hash').substring(1);
+    a=$('.item a[class$="'+link+'"]');
+  }
+  if (a && a.length) {
+    a.parent().parent().addClass('selected');
+    a.parent().parent().attr('id','selected');
+    highlightAnchor();
+  } else if (n) {
+    $(n.itemDiv).addClass('selected');
+    $(n.itemDiv).attr('id','selected');
+  }
+  expandNode(global_navtree_object, n, true, true); // <- we added this line
+  showRoot();
+}
+
+
+$(document).ready(function() {
+  
+  generate_autotoc();
+  
+  (function (){ // wait until the first "selected" element has been created
+    try {
+      
+      // this line will triger an exception if there is no #selected element, i.e., before the tree structure is complete.
+      document.getElementById("selected").className = "item selected";
+      
+      // ok, the default tree has been created, we can keep going...
+      
+      // expand the "Chapters" node
+      expandNode(global_navtree_object, global_navtree_object.node.children[0].children[2], true, true);
+      
+      // Hide the root node "Eigen"
+      $(document.getElementsByClassName('index.html')[0]).parent().parent().css({display:"none"});
+      
+    } catch (err) {
+      setTimeout(arguments.callee, 10);
+    }
+  })();
+});