source: SMC/trunk/SMC/src/web/scripts/js/smc-graph.js @ 3815

var item_li = null;

var svg  = null; // main svg-element
var css; 
var data_all = null; // global holder for all (input) data
var nodes_sel = []; // global holder for selected data (selected nodes)
var data_show = null; // global holder for data to show  closure over nodes_sel 
var nest = {}; 
var detail_data = null; // global holder for detail-data (in html)  
 

var input_prefix = "input-";
var select_rect_min_size = 5;
var first_level_margin = 20;
var min_circle = 4;
var max_circle = 80;

var show_count = 1;
var show_arrows = 0; 

var comp_reg_url = "http://catalog.clarin.eu/ds/ComponentRegistry/?item=";
var mdrepo_url_search = "http://localhost:8680/exist/apps/cr-xq/mdrepo/index.html?operation=searchRetrieve&x-context=&query=";
/*http://localhost:8680/exist/apps/cr-xq/mdrepo/fcs?operation=scan&scanClause=cmd:CountryName&x-context=&x-format=htmlpage*/
var mdrepo_url_scan = "http://localhost:8680/exist/apps/cr-xq/mdrepo/fcs?operation=scan&x-context=&x-format=htmlpage&sort=size&scanClause=";
/*var source_file = "../scripts/cmd-dep-graph-d3_all_svg.json"*/
/*var source_file = "file:/C:/Users/m/3/clarin/_repo/SMC/output/cmd-dep-graph.d3.js"
var detail_file = "file:/C:/Users/m/3/clarin/_repo/SMC/output/smc_stats_detail.html"
*/
/*
var source_file = "/smc/_structure-graph.json";
var source_file = "cmd-dep-graph.d3.js";
var detail_file = "smc_stats_detail.html";
var userdocs_file = "userdocs.html";
*/
//now graph-param is used
//var source_file = "/smc/smc-graph.d3";
/*var source_file = "/smc/cmd-dep-graph.d3.js";*/
var detail_file = "smc_stats_detail.html";
var userdocs_file = "userdocs.html";

var opts = {"graph": {"value":"/smc/data/profiles.js", 
                    "values":[{value: "/smc/data/smc-graph-basic.js", label:"SMC graph basic"},
                              {value: "/smc/data/smc-graph-all.js", label:"SMC graph all"},                              
                              {value: "/smc/data/smc-graph-profiles-datcats.js", label:"only profiles + datcats"},
                              {value: "/smc/data/smc-graph-groups-profiles-datcats-rr.js", label:"profiles+datcats+groups+rr"},
                              {value: "/smc/data/profiles.js", label:"just profiles"}                              
                              
                              /*,
                              {value: "/smc/data/smc-graph-mdrepo-stats.js", label:"instance data"}*/
                              
                             ], "widget":"selectone" },
            "depth-before": {"value":2, "min":0, "max":10, "widget":"slider"}, 
            "depth-after":{"value":2, "min":0, "max":10, "widget":"slider"}, 
            "link-distance": {"value":120, "min":10, "max":300, "widget":"slider" }, 
            "charge":{"value":250, "min":10, "max":1000, "widget":"slider" },
            "friction":{"value":75, "min":1, "max":100, "widget":"slider" },
            "gravity":{"value":20, "min":1, "max":100, "widget":"slider" },
            "node-size": {"value":"count", "values":["1","4","8","16","count"], "widget":"selectone" },
            "labels": {"value":"show", "values":["show","hide"], "widget":"selectone" },                         
            "curve": {"value":"straight", "values":["straight","arc"], "widget":"selectone" },
           "layout": {"value":"force", "values":["vertical-tree", "horizontal-tree", "weak-tree","force","dot", "freeze"], "widget":"selectone" },
            "selected": {"widget":"hidden" },
            "link": {"widget":"link", "label":""},
            "download": {"widget":"link", "label":""},
            "add_profile": {"widget":"link", "label":"Add profile", "widget":""}
            };


/** temporary helper function
to easily get the param-data
*/
function opt(key) {
 var val = $("#navigate").data("qi").getParamValue(key);
 return typeof val == 'undefined' ? "" : val;
}

/**  gets the data for the graph and calls rendering of the lists 
 * @name initGraph
 * @function
 */
 function initGraph (graph_source)
    {

     // load data
     d3.json(graph_source, 
                function(json) {        
                    // return if data missing
                    if (json==null) { notifyUser("source data missing: " + graph_source ); return null}            
                    data_all = json;
                    data_all.links.forEach(function(d) { 
                                        //resolve numeric index to node references
                                                src_ix = d.source;
                                                d.source = data_all.nodes[src_ix];
                                                d.source.index = src_ix;
                                                trg_ix = d.target;
                                                d.target = data_all.nodes[trg_ix];
                                                d.target.index = trg_ix;
                                                src_key = d.source.key;
                                                trg_key = d.target.key;
                                             });
                // generate lookup hashes for neighbours;                                             
                 add_lookups(data_all);
                 
                 // get min/max on some properties
                 var init_x_arr = [];
                    data_all.nodes.forEach(function(d,i){init_x_arr.push(d.init_x);})
                 data_all.init_x_min = d3.min(init_x_arr);
                 data_all.init_x_max = d3.max(init_x_arr);

                 var init_level = [];
                    data_all.nodes.forEach(function(d,i){init_level.push(+d.level);})
                    data_all.level_min = d3.min(init_level);
                
                 var init_count = [];
                    data_all.nodes.forEach(function(d,i){init_count.push(+d.count);})
                 
                 data_all.count_max = d3.max(init_count);
                 data_all.node_size_ratio = Math.sqrt(data_all.count_max) / max_circle;

                notifyUser("count max: " + data_all.count_max + "; "
                        + "node_size_ratio: " + data_all.node_size_ratio);
                 
                 // should be delivered by the data directly
                   data_all.nodes.forEach(function(d,i) {
                       d.x = d.init_x;
                       d.y = d.init_y;
                     });

                  // get selected nodes (if any) from param
                  selected_ids = opt("selected").split(",");
                  selectNodeByKey(selected_ids);
                  /*var selected_match = 0;
                    for (var i = 0; i < selected_ids.length; i++)
                    {  if (data_all.nodes_index[selected_ids[i]]) {
                             data_all.nodes_index[selected_ids[i]].selected = 1;
                             selected_match ++;
                       }
                    }    
                  // if something was selected, update and render Graph and Detail
                  if (selected_match) { updateSelected();}
                  */  
              renderIndex();
    
                
                });        
}

/** put grouped list of nodes into the target container*/
function renderIndex (data, target_container_selector) {
    data = typeof data !== 'undefined' ? data : data_all.nodes;
    target_container_selector = typeof target_container_selector !== 'undefined' ? target_container_selector : index_container_selector;
    renderNodeList (data, target_container_selector); 
}


/** generate the detail lists
    @param nodes
*/  
function renderDetail (nodes) {    
    renderNodeList (nodes, detail_container_selector); 
}



/** generate a grouped (by type) list of nodes
    @param nodes - accepts an array of nodes (like in data.nodes)
*/  
function renderNodeList (nodes, target_container_selector) {

    nest = d3.nest()
    .key(function(d) { return d.type; })
    .sortValues(function(a, b) { return d3.ascending(a.name, b.name); })
    .entries(nodes);
  
    target_container = d3.select(target_container_selector);
        target_container.selectAll("div.node-detail").remove();
        
        var group_divs = target_container.selectAll("div.node-detail").data(nest)
                        .enter().append("div")
                       .attr("id", function (d) { return "detail-" + d.key })                        
                        .classed("node-detail cmds-ui-block", 1)
                        // collapse groups in index, but expand right away in detail view
                        .classed("init-show", (target_container_selector != index_container_selector)); 
                        
      var group_headers = group_divs.append("div").classed("header", 1)
                        .text(function (d) { return d.key + " |" + d.values.length + "|"});
                        
      var list =  group_divs.append("div").classed("content",1)
                    .append("ul");
      var item_li = list.selectAll(".node-item")        
                    .data(function(d) { return d.values; })
                    .enter().append("li")
                    .attr("class", "node-item");
               item_li.append("span")
/*                     .text(function (d) { return d.name})*/
                    .text(renderItemText)
                    .on("click", function(d) { d.selected= d.selected ? 0 : 1 ; updateSelected() });
          
                    
            /* slightly different behaviour for the main-index and rendering of the selected nodes in the detail-view */
          //  console.log("target_container:" + target_container_selector);
            if (target_container_selector == index_container_selector) {
                index_container = target_container;
                item_li.attr("id", function (d) { return "n-" + d.name })
                        .attr("title", function(d) { return  d.id });
                item_li.classed("highlight", function (d) { return d.selected });
/*                item_li.classed("highlight", liveSelected);*/
                
                
              } else {
                 var item_detail = item_li.append("div");
                                        /*  .classed("node-detail", 1);*/
                            
                 item_detail.append("a")
                            .attr("href",function (d) { if (d.type.toLowerCase()=='datcat') return d.id 
                                                        else return comp_reg_url + d.id })
                            .text(function (d) { return d.id });
                
                profile_item_detail = item_detail.filter(function(d, i) { return d.type.toLowerCase()=='profile' }); 
                profile_item_detail.append("a")
                            .attr("target",'_blank')
                            .attr("href",function (d) { return 'profiles/' + d.key + '.html' })
                            .text(' html-view ');
                
/*                profile_item_detail.append("a")*/
/*                item_detail.append("a")
                            .classed("scan", function (d) {  return !(d.type=='Profile') } )
                            .attr("target",'_blank')
                            .attr("href",function (d) { if (d.type=='Profile') { return mdrepo_url_search +  'cmd.profile=%22' + d.id + '%22'; }
                                                          else { return mdrepo_url_scan +  'cmd:' +  d.name; }   }  )
                            .text(' mdrepo-view ');*/
                
                 item_detail_detail = item_detail.append("div").html(
                                 function (d) { 
                                    var detail_info_div = getDetailInfo(d.type.toLowerCase(), d.key);
                                    if (detail_info_div) {
                                        return detail_info_div 
                                    } else { 
                                        return  "<div>No detail</div>"; 
                                    }
                          });
                          
                 item_detail_detail.classed("node-detail", 1);
                           
              }
                        
   handleUIBlock($(target_container_selector).find(".node-detail.cmds-ui-block"));
  
}

function renderItemText(d) { 
    if (show_count) {
        return d.name + ' |' + d.count + '|'; 
      }
    else {
        return d.name;
        }
 }

function filterIndex (search_string){
    var filtered_index_nodes = data_all.nodes.filter(function(d, i) { 
     //   console.log(d.name.indexOf(search_string));
        return d.name.toLowerCase().indexOf(search_string.toLowerCase()) > -1; 
    });
    
   renderIndex(filtered_index_nodes, index_container_selector);
}


/** render data (data_show) as graph  into target-container (graph_container) */
function renderGraph (data, target_container) {
// setting defaults 
// for now, ignore the params, as they are always the same
    
    //data = typeof data !== 'undefined' ? data : dataToShow(nodes_sel);
    
    if ($(this).is('#input-graph')) {        
        console.log("graph-source changed! reinitializing graph");
        initGraph(data);
    }
    
    data = dataToShow(nodes_sel);
  
      target_container = graph_container ;
    
    if (data == null) { 
       $(target_container).text("no data to show"); 
       return;
     } else {
       $(target_container).text("");
     }
  
  // compute the maximum number, but only if it will be needed (i.e. node-size=count)
    if (opt("node-size")=="count") {
        var init_count = [];
            data.nodes.forEach(function(d,i){init_count.push(+d.count);})
            data.count_max = d3.max(init_count);
            data.node_size_ratio = Math.sqrt(data.count_max) / max_circle;
        }

  // information about the displayed data 
        notifyUser("show nodes: " + data_show.nodes.length + "; "
                        + "show links: " + data_show.links.length + "; " 
                        + "max count:" + data.count_max + "; " 
                        + "node_size_ration:" + data.node_size_ratio);
        
  
  
  
   var w = $(target_container).width(),
        h = $(target_container).height(); 
     
     var ratio = w / (data_all.init_x_max - data_all.init_x_min); 
    var node_size_int = parseInt(opt("node-size"));
 var link_distance = parseInt(opt("link-distance"))
 
        // console.log (w + '-' + h);
     var force = d3.layout.force()
            .nodes(data.nodes)
            .links(data.links)
            .size([w, h])

            .friction(parseInt(opt("friction")) / 100 )
            
            .gravity(parseInt(opt("gravity")) / 100 )
            
/*            .linkDistance(parseInt(opt("link-distance")))*/
            
            .linkDistance(function(d){return link_distance / (d.weight * d.value) })
            /* Profiles:           
            
            
            .linkStrength(function(d){return d.weight})*/
            //.charge(parseInt(opt("charge")) * -1)
          
          if (parseInt(opt("charge"))==0) {
            force.charge(0);
          } else {
            force.charge(function(d) { if (opt("node-size")=="count")
                            {var node_charge = (Math.sqrt(d.count)<=min_circle) ?  min_circle  : Math.sqrt(d.count) / data.node_size_ratio;
                            //console.log (node_charge + ':' + d.count);
                            return node_charge * -1 * parseInt(opt("charge"));
                                }
                              //{ return -d.count * parseInt(opt("charge"));  }
                            else { return parseInt(opt("charge")) * -1} })
          }
         
         force.on("tick", tick)
            .start();
        
        if (opt("layout")=='freeze') {
               data.nodes.forEach(function(d) { d.fixed=true });     
        } else {
                 data.nodes.forEach(function(d) { d.fixed=false});
        }
               
            
//    console.log ("gravity: " + force.gravity() );              
  
       // remove old render:
          d3.select(graph_container_selector).selectAll("svg").remove();
                 
        svg = d3.select(graph_container_selector).append("svg:svg")
            .attr("width", w)        .attr("height", h);
        
        // Per-type markers, as they don't inherit styles.
      if (show_arrows)  {
        svg.append("svg:defs").selectAll("marker")
          .data(["uses"])
          .enter().append("svg:marker")
            .attr("id", String)
            .attr("viewBox", "0 -5 10 10")
            .attr("refX", 15)
            .attr("refY", -1.5)
            .attr("markerWidth", 6)
            .attr("markerHeight", 6)
            .attr("orient", "auto")
          .append("svg:path")
            .attr("d", "M0,-3L10,0L0,3");
       }
        
        var path = svg.append("svg:g").selectAll("path")
            .data(force.links())
            .enter().append("svg:path")
/*            .attr("class", function(d) { return "link uses"; })*/
            .classed("link", 1)
            .classed("uses", 1)
            .classed("highlight", function(d) { d.highlight } )
            .attr("marker-end", function(d) { return "url(#uses)"; })
            .style("stroke-width", function(d) { return Math.sqrt(d.value); });
/*             .style("stroke-width", function(d) { return d.value });*/

           path.append("title").text(function(d){ return d.value });
            
         var gnodes = svg.append("svg:g")
                      .selectAll("g.node")
                      .data(force.nodes())
                      .enter().append("g")
                      .attr("class", function(d) { return "node type-" + d.type.toLowerCase()})
                      .classed("selected", function(d) { return d.selected; })
                      .call(force.drag);
                      
          // dragging of all selected nodes on freeze layout
          // this does not work yet
          /*if (opt("layout")=="freeze") {
                      gnodes.on("mousedown", function() {
                            var m0 = d3.mouse(this);
                
                       gnodes.on("mousemove", function() {
                            var m1 = d3.mouse(this),
                        x0 = Math.min(w, m0[0], m1[0]),
                        y0 = Math.min(w, m0[1], m1[1]),
                        x1 = Math.max(0, m0[0], m1[0]),
                        y1 = Math.max(0, m0[1], m1[1]);
                        // console.log("DEBUG: mousedown: " + (x1-x0) + ( y1-y0));
                            x_d = (x1 - x0);
                            y_d = (y1 - y0);
                               // y_d = d.y - d.py;
                               // x_d = d.x - d.px;
                        
                            nodes_sel.forEach(function (d) {
                                d.x += x_d;
                                d.y += y_d;
                            });
                            
                  });
                
                    gnodes.on("mouseup", function() {
                        gnodes.on("mousemove", null).on("mouseup", null);
                  });
                
                  d3.event.preventDefault();
                });     
            }          
          */  
            gnodes.append("svg:circle")
/*            .attr("r", 6)*/
                    .on("click", function(d) {d.selected= d.selected ? 0 : 1; updateSelected() })
                      .on("mouseover", highlight()).on("mouseout", unhighlight())
            .attr("r", function(d) { if (opt("node-size")=="count") 
                                        {return (Math.sqrt(d.count)<=min_circle) ?  min_circle  : Math.sqrt(d.count) / data.node_size_ratio;                                        
                                        }
                                        else { return node_size_int; }
                                    })    
            
            gnodes.append("title")
/*                .text(function (d) { return d.name + ' |' + d.count + '|' })*/
                  .text(renderItemText);
                  
                  
      
         
        /*
       svg.selectAll("circle")
            .attr("class", function(d) { return "type-" + d.type.toLowerCase()})
            .classed("selected", function(d) { return d.selected; })
          .on("click", function(d) {d.selected= d.selected ? 0 : 1; updateSelected() })
          .on("mouseover", highlight("in")).on("mouseout", highlight("out"));
        */
        
        // A copy of the text with a thick white stroke for legibility.
        //if (opt("labels") =='show') {
           gnodes.append("svg:text")
                 .attr("x", 8)
                 .attr("y", ".31em")
                 .attr("class", "shadow")
                 .classed("hide", opt("labels")=='hide')
                 .text(function(d) { return d.name; });
           gnodes.append("svg:text")
                 .attr("x", 8)
                 .attr("y", ".31em")
                 .classed("hide", function(d) { return !d.selected && opt("labels")=='hide'})
                 .text(function(d) { return d.name; });
        //}
        
  
  var tick_counter=0;
   function tick(e) {
    var link_distance_int = parseInt(opt("link-distance"));      
    var k =  10 * e.alpha;
          if (opt("layout")=='dot') {
            var offset = data_all.init_x_min;
            /*data.links.forEach(function(d, i) {
              d.source.x = (d.source.init_x / 150 * link_distance_int) ;
              d.target.x = (d.target.init_x / 150 * link_distance_int);
            
            });*/
            
            data.nodes.forEach (function(d,i) {
                d.x = d.init_x * ratio - link_distance_int;  
            });
            
          } else if (opt("layout")=='weak-tree') {
              data.links.forEach(function(d, i) {
              d.source.x -= k;
                d.target.x += k;
                });
          } else if (opt("layout")=='vertical-tree') {
                   var ky= 1.4 * e.alpha, kx = .4 * e.alpha;
                   data.links.forEach(function(d, i) {
                     if (d.source.level==data_all.level_min) { d.source.y = first_level_margin };
                   //  d.target.x += (d.source.x - d.target.x)  * kx;
                     d.target.y += (d.source.y - d.target.y + link_distance_int) * ky;
                    });
           } else if (opt("layout")=='horizontal-tree') {
                   var kx= 1.4 * e.alpha, ky = .4 * e.alpha;
                   data.links.forEach(function(d, i) {
                       if (d.source.level==data_all.level_min) { d.source.x = first_level_margin };
                       //d.target.y += (d.source.y - d.target.y)  * ky;
                       d.target.x += (d.source.x - d.target.x + link_distance_int  ) * kx;
                  });
           }
           /*  parent foci 
                  var kx = 1.2 * e.alpha;
    data.links.forEach(function(d, i) {
      d.target.x += (d.target.level * link_distance  - d.target.x) * kx;
      });*/
      
      tick_counter ++;   
       if (tick_counter % 2 == 0) {transform(); }
   } // end  tick()


    function transform () { 
         
       path.attr("d", function(d) {
             // links as elliptical arc path segments
            if (opt("curve")=="arc") 
            {   var dx = d.target.x - d.source.x,
                    dy = d.target.y - d.source.y,
                    dr = Math.sqrt(dx * dx + dy * dy);
                return "M" + d.source.x + "," + d.source.y + "A" + dr + "," + dr + " 0 0,1 " + d.target.x + "," + d.target.y;
            } else { 
            // or straight
                return "M" + d.source.x + "," + d.source.y + "L" + d.target.x + "," + d.target.y;
            }  
       });
         
         /*circle.attr("cx", function(d) {return d.x;})
                .attr("cy", function(d) {return d.y;});*/
       gnodes.attr("transform", function(d) {
            return "translate(" + d.x + "," + d.y + ")";
       });
        
  /*     textgroup.attr("transform", function(d) {
            return "translate(" + d.x + "," + d.y + ")";
       });*/
    }
        
        // Highlight selected nodes using the quadtree.
        svg.on("mousedown", function() {
          var m0 = d3.mouse(this);
        
          var rect = d3.select(this).append("rect")
              .style("fill", "#999")
              .style("fill-opacity", .5);
        
          d3.select(window).on("mousemove", function() {
            var m1 = d3.mouse(rect.node()),
                x0 = Math.min(w, m0[0], m1[0]),
                y0 = Math.min(w, m0[1], m1[1]),
                x1 = Math.max(0, m0[0], m1[0]),
                y1 = Math.max(0, m0[1], m1[1]);
                // console.log("DEBUG: mousedown: " + (x1-x0) + ( y1-y0));       
                    selectNodes(data.nodes, x0, y0, x1, y1);                    
                    rect.attr("x", x0).attr("y", y0).attr("width", x1 - x0).attr("height", y1 - y0);
                    
          });
        
          d3.select(window).on("mouseup", function() {
            // only change selection, if the rectangle was big enough 
            // (mainly to prevent clearing of the graph on clicks that look like mousemoves to the system)
            if (rect.attr("width") > select_rect_min_size && rect.attr("height") > select_rect_min_size) {
                updateSelected();
            }
            rect.remove();
            d3.select(window).on("mousemove", null).on("mouseup", null);
          });
        
          d3.event.preventDefault();
        });
}  // end renderGraph


/** loads detail info about individual nodes (in html) from separate file  
later used in renderDetail() 
invoked during the (jquery-)initalization */
function loadDetailInfo () {
     
  $(detail_info_holder_selector).load(detail_file,function(data) {
     $(detail_container_selector).find("h3").after(
     '<div id="detail-summary-overall" class="cmds-ui-block init-show" ><div class="header">Overview</div><div class="content">'
     + getDetailInfo("summary", "overall") + '</div></div>');
     
     handleUIBlock($(detail_container_selector).find(".cmds-ui-block"));
     
     // only render detail for initially selected nodes, after the detail info has been loaded 
     if (nodes_sel) { renderDetail(nodes_sel) };
     
  });
  
  // loading css to store in extra variable, for later use = injecting into exported SVG 
  $.get("scripts/style/smc-graph.css", function(data) {
 //  console.log(data)
    css = data
  });
  
}

function getDetailInfo(type, id) {
    //notify("getDetailInfo: #" + type + "-" + id );
    var d = $(detail_info_holder_selector).find("#" + type + "-" + id );
    // notify(d);
    return d.html();
}

/** generates a base64-data encoded url out of the current svg
does some preprocessing: injects the css and sets the @viewBox, @width and @height attributes to ensure, 
that everything is visible in the exported svg.
later perhaps even exporting to server, for rendering to PNG, PDF
http://d3export.cancan.cshl.edu/
called on mousedown of the download-link, so assumes the <a>-element as this
*/
function genDownload (event) {
//console.log("genDownload:" + this);

    var svg_w = svg.attr("width");
    var svg_h = svg.attr("height");
    var bounds = graphBounds();
    var margin = 30;
    var link_dist = parseInt(opt("link-distance"));
    
    var x, y, w, h;
    x = Math.floor(bounds["x-min"]) - margin 
    y = Math.floor(bounds["y-min"]) - margin
    // add extra space to the right, because of the possible labels 
    w = (bounds["width"] > svg_w) ? bounds["width"] + 2 * margin + link_dist : svg_w + link_dist;  
    h = (bounds["height"] > svg_h) ? bounds["height"] + 2 * margin : svg_h;
       
    var viewBox = x + " " + y + " " + w + " " + h;

  svg.attr("title", "SMC Browser - export")
        .attr("version", 1.1)
        .attr("viewBox", viewBox)
        .attr("width", w)
        .attr("height", h)
        .attr("xmlns", "http://www.w3.org/2000/svg");
      var style = svg.append("style" );
        style.attr("type", 'text/css');
        style.text(css);

var html = svg.node().parentNode.innerHTML;

/*    $(html).append("<style type='text/css'><![CDATA[" + css + "]]> </style>" );*/
     
        
    //console.log(html);

    $(this).attr("title", "smc-browser-export.svg")
      .attr("target", "_blank")
      .attr("href-lang", "image/svg+xml")
      .attr("href", "data:image/svg+xml;base64,\n" + btoa(html));
      
}


/**  select the nodes within the specified rectangle. */
function selectNodes(nodes, x0, y0, x3, y3) {
    
  var points = [];
  nodes.forEach(function(n) {    
    if (n && (n.x >= x0) && (n.x < x3) && (n.y >= y0) && (n.y < y3)) {
            points.push(n);
            n.selected = 1;
        } else {
            n.selected = 0;
        }
/*    return x1 >= x3 || y1 >= y3 || x2 < x0 || y2 < y0;*/
  });
  return points;
}

function selectNodeByKey(nodes_keys) {

    // get selected nodes (if any) from param
      var selected_match = 0;
        for (var i = 0; i < nodes_keys.length; i++)
        {  if (data_all.nodes_index[nodes_keys[i]]) {
                 data_all.nodes_index[nodes_keys[i]].selected = 1;
                 selected_match ++;
           }
        }    
      // if something was selected, update and render Graph and Detail
      if (selected_match) { updateSelected();}
}

function updateSelected () {

    // don't change the selected nodes on freeze-layout
if (opt("layout")!='freeze') {
    nodes_sel = data_all.nodes.filter(function (d) { return d.selected });
    
    // update param
      var selected = [];
      nodes_sel.forEach(function(d) { selected.push(d.key) });
    $("#navigate").data("qi").setParamValue("selected",selected.join());
    renderDetail(nodes_sel);
    
  }
    
    renderGraph();
    
 // just need to highlight the selected nodes
    d3.select(index_container_selector).selectAll("li").classed("highlight", function (d) { return d.selected });
 //   renderIndex(); - this would be unnecessary and too expensive   
}


/** Returns an event handler for highlighting the path of selected (mouseover) node.
*/
function highlight() {
  return function(d, i) {
    // console.log ("fade:" + d.key);
    var connected_subgraph_in = neighboursWithLinks(data_show, d,'in', -1);
    var connected_subgraph_out = neighboursWithLinks(data_show, d,'out', -1);
    var connected_subgraph = {"nodes": [], "links": []};
        connected_subgraph.nodes = connected_subgraph.nodes.concat(connected_subgraph_in.nodes).concat(connected_subgraph_out.nodes);
        connected_subgraph.links = connected_subgraph.links.concat(connected_subgraph_in.links).concat(connected_subgraph_out.links);
       add_lookups(connected_subgraph);                 
    svg.selectAll("path.link")
/*        .filter( d.source.index != i && d.target.index != i; })*/
/*      .transition()*/
        .classed("highlight", function(p) { return connected_subgraph.links_index[p.source.key + ',' + p.target.key] })
        .classed("fade", function(p) { return !(connected_subgraph.links_index[p.source.key + ',' + p.target.key]) });
    
    connected = svg.selectAll("g.node").filter(function(d) { 
                    return  connected_subgraph.nodes_in[d.key]  || connected_subgraph.nodes_out[d.key]  
                    })
                .classed("highlight", 1)
                .classed("fade", 0);
                
    connected.selectAll("text").classed("hide",0);                 
     not_connected = svg.selectAll("g.node").filter(function(d) { 
                    return  !(connected_subgraph.nodes_in[d.key]  || connected_subgraph.nodes_out[d.key])  
                    })
                    .classed("highlight",0)
                    .classed("fade",1);
    not_connected.selectAll("text").classed("hide",1);                    
                    
    /*svg.selectAll("circle")
/\*        .filter( d.source.index != i && d.target.index != i; })*\/
/\*      .transition()*\/
        .classed("highlight", function(d) { return connected_subgraph.nodes_in[d.key]  || connected_subgraph.nodes_out[d.key]  })
        .classed("fade", function(d) { return !(connected_subgraph.nodes_in[d.key] || connected_subgraph.nodes_out[d.key])   });*/
/*
   if (opt("labels") =='show') {
           gnodes.append("svg:text")
                 .attr("x", 8)
                 .attr("y", ".31em")
                 .attr("class", "shadow")
                 .text(function(d) { return d.name; });
           gnodes.append("svg:text")
                 .attr("x", 8)
                 .attr("y", ".31em")
                 .text(function(d) { return d.name; });
        }
    */
  };
}

function unhighlight() {
  return function(d, i) {
                     
    svg.selectAll("path.link")
        .classed("highlight", 0 )
        .classed("fade", 0 );
    
     var gnodes = svg.selectAll("g.node")
        .classed("highlight", 0)
        .classed("fade", 0);
        
        gnodes.selectAll("text").classed("hide",function(d) { return !d.selected && opt("labels")=='hide'});
        
  };
}


/**  generates the subset of data to display (based on selected nodes + options) 
fills global variable: data_show ! 
*/
function dataToShow (nodes) {
     data_show = {};
     data_show.nodes = nodes;
        var data_show_collect = {nodes:[],links:[]};
        
        nodes.forEach(function(n) {
                        var data_add_in = neighboursWithLinks(data_all, n,'in', opt("depth-before"));
                        var data_add_out = neighboursWithLinks(data_all, n,'out', opt("depth-after"));
                        data_show_collect.nodes = data_show_collect.nodes.concat(data_add_in.nodes).concat(data_add_out.nodes);
                        data_show_collect.links = data_show_collect.links.concat(data_add_in.links).concat(data_add_out.links);
                    });
            
/*         deduplicate nodes and edges */
     data_show.nodes = unique_nodes(nodes.concat(data_show_collect.nodes));
     data_show.links = unique_links(data_show_collect.links);
     
     // extend the object, with some lookup hashes on neighbourhood
     add_lookups(data_show);
  
     return data_show;
    }

/** generate lookup hashes for neighbours;
    for faster/simpler neighborhood lookup
from: http://stackoverflow.com/questions/8739072/highlight-selected-node-its-links-and-its-children-in-a-d3-js-force-directed-g
*/
function add_lookups(data) {

    var links = data.links;
    var neighbours = {"links_index": {}, "nodes_index": {}, 
                      "nodes_in": {}, "nodes_out": {},
                      "links_in": {}, "links_out": {}};
        
        data.nodes.forEach(function(d){
            neighbours.nodes_index[d.key] = d;
        });
        
        links.forEach(function(d) { 
                            src_key = d.source.key;
                            trg_key = d.target.key;
                         // generate lookup hashes for neighbours;
                            neighbours.links_index[src_key + "," + trg_key] = d;
                            if (d.source) { 
                                    if (! neighbours.nodes_in[trg_key]) { 
                                        neighbours.nodes_in[trg_key] = [d.source];
                                        neighbours.links_in[trg_key] = [d];
                                     }  else {
                                        neighbours.nodes_in[trg_key].push(d.source);
                                        neighbours.links_in[trg_key].push(d);
                                     }
                             }
                            if (d.target) { 
                                    if (! neighbours.nodes_out[src_key]) { 
                                        neighbours.nodes_out[src_key] = [d.target];
                                        neighbours.links_out[src_key] = [d];
                                    } else { 
                                        neighbours.nodes_out[src_key].push(d.target);
                                        neighbours.links_out[src_key].push(d) ;
                                    }
                             }
                       });
                       
    data = $.extend(data, neighbours);
    return data; 
}



/*                        item_detail.text(function (d) { return "links_in: " +  dataShowCount(d.key, "links_in") +  "; links_out: " +  dataShowCount(d.key, "links_out") ;
                                                       })*/
function dataShowCount(n_key, info_type) { 

    if (data_show[info_type][n_key]) {
        return data_show[info_type][n_key].length;
       } else {
        return 0
       }
}

/** determines the min/max x/y position of the visible nodes
 ! neglects the labels!
 
 @returns array of [x_min, y_min, x_max, y_max, (x_max - x_min), (y_max - y_min)]
 */
function graphBounds () {

var  x_arr = [], y_arr =[];

data_show.nodes.forEach(function(d,i){x_arr.push(d.x); y_arr.push(d.y)})

    x_min = d3.min(x_arr);
    x_max = d3.max(x_arr);
    y_min = d3.min(y_arr);
    y_max = d3.max(y_arr);
                 
   return {"x-min": x_min, "y-min": y_min, "x-max": x_max, "x-max": y_max, "width": (x_max - x_min), "height":(y_max - y_min)}
}                 
                 
/** returns appropriate link
*/
function neighboring(a, b) {
  return linkedByIndex[a.index + "," + b.index];
}


/** access function to retrieve the neighbours from the hashes
@param data base data to search for links (default: data_all)
@param dir in|out|any  - but "any" branches in unexpected ways (because it goes in and out on every level = it takes all the children of the parent) 
@param depth 0-n - go depth-levels; negative depth := no depth restriction = go to the end of the paths;
@returns a sub-graph
*/
function neighboursWithLinks (data, n, dir, depth) {
// setting defaults
       depth = typeof depth !== 'undefined' ? depth : 1;
       data = typeof data !== 'undefined' ? data : data_all;

    if (depth==0) { return {nodes:[], links:[]};}

        var n_in = data.nodes_in[n.key] ? data.nodes_in[n.key] : [] ;
        var n_out = data.nodes_out[n.key] ? data.nodes_out[n.key] : [] ;
        var l_in = data.links_in[n.key] ? data.links_in[n.key] : [] ;
        var l_out = data.links_out[n.key] ? data.links_out[n.key] : [] ;
        
        var result_n = {nodes:[], links:[]};
        if (dir == 'in' ) { result_n.nodes = n_in; result_n.links = l_in; }
                   else if (dir == 'out' ) { result_n.nodes = n_out; result_n.links = l_out; }
                   else { result_n.nodes = n_out.concat(n_in); result_n.links = l_out.concat(l_in);  }
        var n_nextlevel = {nodes:[], links:[]};
        if (depth > 0 || depth < 0) { 
         result_n.nodes.forEach (function(n) 
                     { var n_neighbours = neighboursWithLinks(data, n, dir, depth - 1);
                     n_nextlevel.nodes = n_nextlevel.nodes.concat(n_neighbours.nodes); 
                     n_nextlevel.links = n_nextlevel.links.concat(n_neighbours.links);
                     })
         }
         result_n.nodes = result_n.nodes.concat(n_nextlevel.nodes);
         result_n.links = result_n.links.concat(n_nextlevel.links);
        
        return result_n;
        
}

/** deduplicates based on index-property */
function unique_nodes(nodes) 
{
    var hash = {}, result = [];
    for ( var i = 0, l = nodes.length; i < l; ++i ) {
           n_key = nodes[i].key;
        if ( !hash[n_key] ) { //it works with objects! in FF, at least
            hash[ n_key ] = true;
            result.push(nodes[i]);
        }
    }
    return result;
}

/** deduplicates links (based on source-target-index
based on: http://stackoverflow.com/questions/1890203/unique-for-arrays-in-javascript
*/
function unique_links(links) 
{
    var hash = {}, result = [];
    for ( var i = 0, l = links.length; i < l; ++i ) {
            src_key = links[i].source.key;
            trg_key = links[i].target.key;
            key = src_key + "," + trg_key;
        if ( !hash[key] ) {
            hash[ key] = true;
            result.push(links[i]);
        }
    }
    return result;
}