//      This program is free software; you can redistribute it and/or modify 
//      it under the terms of the GNU General Public License as published by 
//      the Free Software Foundation; either version 2 of the License, or 
//      (at your option) any later version. 
// 
//      This program is distributed in the hope that it will be useful, 
//      but WITHOUT ANY WARRANTY; without even the implied warranty of 
//      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the 
//      GNU General Public License for more details. 
// 
//      You should have received a copy of the GNU General Public License 
//      along with this program; if not, write to the Free Software 
//      Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, 
//      MA 02110-1301, USA. 
 
 
var tinaviz = {}; 
 
$(document).ready(function(){ 
 
$("#title").html("<h1>Biases in biomedical research (Chavalarias and Ioannidis, <i>JCE</I> 2010)</h1><a href=\"indexBias1958_1969_1978.html\">1969-1978</a> | <a href=\"indexBias1958_1979_1988.html\">1979-1988</a> | <a href=\"indexBias1958_1989_1998.html\">1989-1998</a> | <a href=\"indexBias1958_1999_2008.html\">1999-2008</a>"); 
 
tinaviz = new Tinaviz({ 
tag: $("#vizdiv"), 
path: "js/tinaviz/" 
}); 
 
$('#appletInfo').effect('pulsate', {}, 'fast'); 
 
$(window).bind('resize', function() { 
var size = resize(); 
tinaviz.size(size.w, size.h); 
}); 
 
tinaviz.ready(function(){ 
 
var infodiv =  InfoDiv('infodiv'); 
tinaviz.infodiv = infodiv; 
tinaviz.infodiv.reset(); 
 
var size = resize(); 
tinaviz.size(size.w, size.h); 
 
$("#infodiv").accordion({ 
fillSpace: true 
}); 
 
var prefs = { 
gexf: "bipartite_map_Bias1958_1999_2008_s.gexf", 
view: "macro", 
category: "Document", 
node_id: "", 
search: "", 
magnify: "0.5", 
cursor_size: "1.0", 
edge_filter_min: "0.0", 
edge_filter_max: "1.0", 
node_filter_min: "0.0", 
node_filter_max: "1.0" 
 
}; 
var urlVars = getUrlVars(); 
for (x in urlVars) { 
prefs[x] = urlVars[x]; 
} 
 
tinaviz.setView(prefs.view); 
 
var session = tinaviz.session(); 
var macro = tinaviz.view("macro"); 
var meso = tinaviz.view("meso"); 
 
session.set("edgeWeight/min", parseFloat(prefs.edge_filter_min)); 
session.set("edgeWeight/max", parseFloat(prefs.edge_filter_max)); 
session.set("nodeWeight/min", parseFloat(prefs.node_filter_min)); 
session.set("nodeWeight/max", parseFloat(prefs.node_filter_max)); 
session.set("category/category", prefs.category); 
session.set("output/nodeSizeMin", 5.0); 
session.set("output/nodeSizeMax", 20.0); 
session.set("output/nodeSizeRatio", parseFloat(prefs.magnify)); 
session.set("selection/radius", parseFloat(prefs.cursor_size)); 
 
 
macro.filter("Category", "category"); 
macro.filter("NodeWeightRange", "nodeWeight"); 
macro.filter("EdgeWeightRange", "edgeWeight"); 
macro.filter("NodeFunction", "radiusByWeight"); 
macro.filter("Output", "output"); 
 
meso.filter("SubGraphCopyStandalone", "category"); 
meso.set("category/source", "macro"); 
meso.set("category/category", "Document"); 
meso.set("category/mode", "keep"); 
 
meso.filter("NodeWeightRangeHack", "nodeWeight"); 
meso.filter("EdgeWeightRangeHack", "edgeWeight"); 
meso.filter("NodeFunction", "radiusByWeight"); 
meso.filter("Output", "output"); 
 
//tinaviz.readGraphJava("macro", "bipartite_graph_bipartite_map_bionet_2004_2007_g.gexf_.gexf"); 
$("#appletInfo").html("Loading graph.."); 
 
tinaviz.open({ 
success: function() { 
// init the node list with ngrams 
tinaviz.updateNodes( prefs.view, prefs.category ); 
 
// cache the document list 
tinaviz.getNodes( prefs.view, "Document" ); 
 
var view = tinaviz.view(); 
 
// initialize the sliders 
$("#sliderNodeSize").slider( "option", "value", 
parseInt(view.get("output/nodeSizeRatio")) *100 
); 
$("#sliderSelectionZone").slider( "option", "value", 
parseInt(view.get("selection/radius")) * 100 
); 
$("#sliderEdgeWeight").slider( "option", "values", [ 
parseInt( view.get("edgeWeight/min") ), 
parseInt(view.get("edgeWeight/max")) *100 
]); 
$("#sliderNodeWeight").slider( "option", "values", [ 
parseInt(view.get("nodeWeight/min") ), 
parseInt(view.get("nodeWeight/max")) *100 
]); 
 
tinaviz.infodiv.display_current_category(); 
tinaviz.infodiv.display_current_view(); 
 
$("#appletInfo").hide(); 
 
if (prefs.node_id != "") { 
tinaviz.selectFromId( prefs.node_id, true ); 
} 
 
if (prefs.search != "") { 
$("#search_input").val(prefs.search); 
tinaviz.searchNodes(prefs.search, "containsIgnoreCase"); 
} 
 
}, 
error: function(msg) { 
$("#appletInfo").html("Error, couldn't load graph: "+msg); 
} 
}); 
 
tinaviz.open({ 
view: prefs.view, 
url: prefs.gexf 
}); 
 
tinaviz.event({ 
 
viewChanged: function(view) { 
 
tinaviz.autoCentering(); 
 
$("#sliderEdgeWeight").slider( "option", "values", [ 
parseInt( view.get("edgeWeight/min") ), 
parseInt(view.get("edgeWeight/max")) *100 
]); 
$("#sliderNodeWeight").slider( "option", "values", [ 
parseInt(view.get("nodeWeight/min") ), 
parseInt(view.get("nodeWeight/max")) *100 
]); 
tinaviz.infodiv.display_current_category(); 
tinaviz.infodiv.display_current_view(); 
 
var showFilter = false; 
 
if (view.name == "meso") { 
 
// TODO check selection 
// if selection has edges with edge of all the same weight, we disable the filter 
var weight = null; 
for (node in view.nodes) { 
//alert("node:"+node); 
for (out in node.outputs) { 
//alert("node weight:"+out.weight); 
if (weight == null) { 
weight = out.weight; 
} 
else { 
if (weight != out.weight) { 
showFilter = true; 
break; 
} 
} 
} 
} 
} 
$("#sliderEdgeWeight").slider( "option", "disabled", false ); 
} 
}); 
 
 
 
}); 
 
});