Team:Heidelberg/js/notebook tree

From 2014.igem.org

(Difference between revisions)
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var Graph = new (function () {
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var self = this;
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var graph;
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var svg;
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self.date = 0;
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var color = d3.scale.category20();
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var firstDate = 1401573600;//1407861000;
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var heightOfSecond = 100 / 86400; // = 300 Pixel per day?!
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var date = firstDate;
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var viewportHeight = 300 / heightOfSecond;
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var bufferHeight = 1000 / heightOfSecond;
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var scrollSpeed = 6000; // = 20 minutes
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var heightOfSecond = 100 / 86400; // = 300 Pixel per day?!
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var width, height;
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var viewportHeight = 300/heightOfSecond;
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var bufferHeight = 1000/heightOfSecond;
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var scrollSpeed = 6000; // = 20 minutes
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var width = 1;
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var height = 1;
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var bigNodes = []; //Contains [{containsDate(), [data]},...]
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"p/3cuNZHSvzbmc5wGLz" : "Make a liquid culture",
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"p/3wt4jvadcLzkvFn9X" : "Make a liquid culture",
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"p/4jCgLAziJ2DSmmcvR" : "Streak bacteria onto an agar plate",
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"p/53yEPDJz7oRihLz3M" : "Dilute DNA",
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"p/5K8vL8t4egnG8SRtc" : "PCA",
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"p/9S64Hy4vyzPvM4aiC" : "DNA purification (\"PCR Purification\")",
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"p/9TiKPrpdykEiSHFcy" : "Make a liquid culture",
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"p/ATv6a4HMeQZMa9WYX" : "Dilute DNA",
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"p/Ae7BXywPx8nNApvPK" : "Golden Gate Assembly",
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"p/CdKqzhX6FqmmHYKdE" : "Maxens neues Protokoll",
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"p/D9hHrT2Ere5rrcuXK" : "Make competent cells",
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"p/E8wraGbztRq8EsET7" : "Make a glycerol stock",
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"p/ENCvtL4jWZQW72hE5" : "Restriction digest",
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"p/F2oNT7tGTyGFCjAB9" : "Make competent cells",
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"p/FY69K4x7xdaJT6Lzk" : "Pick a colony from an agar plate",
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"p/HA9CLF2Z4kgY3J5rE" : "Make a liquid culture",
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"p/JPmjNykwWASQiD9PX" : "Agarose Gel Electrophoresis",
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"p/NgpLzurL2RKFojWWA" : "PCR",
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"p/Nm75fDvHCr38nXJBo" : "Plasmid Preparation",
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"p/P6LsqW4xkJYaXHFJN" : "Heat shock transformation",
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"p/PxYonEdgff39dmkhq" : "DNA purification (\"PCR Purification\")",
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"p/TD9txcymCuToDta7x" : "Annealing of complementary oligonucleotides",
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"p/WSMMH3bg6CcrcAJ3x" : "PCR",
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"p/ZuE3NijkBg4WwpzKc" : "Recovery of plasmid DNA from filter paper",
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"p/bSEHCZgLpXJ6nb9ze" : "Streak bacteria onto an agar plate",
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"p/gM7FyZeyNrM4hwxZk" : "Dissolve plasmid DNA from the registry distribution",
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"p/maDx7F6ry8Mw5JmKf" : "Pick a colony from an agar plate",
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"p/ms6uHrB9Fv23Tge2J" : "Make a glycerol stock",
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"p/mzGLz4CZBhmDHNivi" : "Make Medium",
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"p/n4Sg8s8AfhMEtQtFH" : "Ligation",
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"p/oFoQguhSKQKC2Hfms" : "Gather bacteria from an agar plate",
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"p/ojKqKzgeLkvNvLDgw" : "Heat shock transformation",
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"p/pk9LqRH9ot8JiKx23" : "Make a glycerol stock",
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"p/qGNf5sATkiC4P7RqF" : "Gather bacteria from an agar plate",
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"p/v97Nktv4idauP3hYh" : "Make competent cells",
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"p/vB88pigyWbKvmKir6" : "Pick a colony from an agar plate",
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"p/vj752RxeBbHsHi83w" : "Pick a colony from an agar plate",
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"p/xBmBAjXPQntkvc8d5" : "Make a glycerol stock",
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"p/z46dHCjoZpLkNgm4k" : "CPEC"
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self.init = function (project) {
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self.project = project;
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var mapping = {
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$svg = $("#graph");
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    "p/3cuNZHSvzbmc5wGLz" : "Make a liquid culture",
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width = $svg.width();
-
    "p/3wt4jvadcLzkvFn9X" : "Make a liquid culture",
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height = $svg.height();
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    "p/4jCgLAziJ2DSmmcvR" : "Streak bacteria onto an agar plate",
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$svg.bind('DOMMouseScroll mousewheel', handleScrolling);
-
    "p/53yEPDJz7oRihLz3M" : "Dilute DNA",
+
-
    "p/5K8vL8t4egnG8SRtc" : "PCA",
+
-
    "p/9S64Hy4vyzPvM4aiC" : "DNA purification (\"PCR Purification\")",
+
-
    "p/9TiKPrpdykEiSHFcy" : "Make a liquid culture",
+
-
    "p/ATv6a4HMeQZMa9WYX" : "Dilute DNA",
+
-
    "p/Ae7BXywPx8nNApvPK" : "Golden Gate Assembly",
+
-
    "p/CdKqzhX6FqmmHYKdE" : "Maxens neues Protokoll",
+
-
    "p/D9hHrT2Ere5rrcuXK" : "Make competent cells",
+
-
    "p/E8wraGbztRq8EsET7" : "Make a glycerol stock",
+
-
    "p/ENCvtL4jWZQW72hE5" : "Restriction digest",
+
-
    "p/F2oNT7tGTyGFCjAB9" : "Make competent cells",
+
-
    "p/FY69K4x7xdaJT6Lzk" : "Pick a colony from an agar plate",
+
-
    "p/HA9CLF2Z4kgY3J5rE" : "Make a liquid culture",
+
-
    "p/JPmjNykwWASQiD9PX" : "Agarose Gel Electrophoresis",
+
-
    "p/NgpLzurL2RKFojWWA" : "PCR",
+
-
    "p/Nm75fDvHCr38nXJBo" : "Plasmid Preparation",
+
-
    "p/P6LsqW4xkJYaXHFJN" : "Heat shock transformation",
+
-
    "p/PxYonEdgff39dmkhq" : "DNA purification (\"PCR Purification\")",
+
-
    "p/TD9txcymCuToDta7x" : "Annealing of complementary oligonucleotides",
+
-
    "p/WSMMH3bg6CcrcAJ3x" : "PCR",
+
-
    "p/ZuE3NijkBg4WwpzKc" : "Recovery of plasmid DNA from filter paper",
+
-
    "p/bSEHCZgLpXJ6nb9ze" : "Streak bacteria onto an agar plate",
+
-
    "p/gM7FyZeyNrM4hwxZk" : "Dissolve plasmid DNA from the registry distribution",
+
-
    "p/hmhE7AHgjXE8Khw6M" : "Gel extraction",
+
-
    "p/jT9cdZ9T5JgFDEJXe" : "Heat shock transformation",
+
-
    "p/kKiCHxutJLzPKayCC" : "Streak bacteria onto an agar plate",
+
-
    "p/kxBySpW3SnbWuYMRw" : "Streak bacteria onto an agar plate",
+
-
    "p/mJNyMCoEko3JKRv5x" : "Heat shock transformation",
+
-
    "p/maDx7F6ry8Mw5JmKf" : "Pick a colony from an agar plate",
+
-
    "p/ms6uHrB9Fv23Tge2J" : "Make a glycerol stock",
+
-
    "p/mzGLz4CZBhmDHNivi" : "Make Medium",
+
-
    "p/n4Sg8s8AfhMEtQtFH" : "Ligation",
+
-
    "p/oFoQguhSKQKC2Hfms" : "Gather bacteria from an agar plate",
+
-
    "p/ojKqKzgeLkvNvLDgw" : "Heat shock transformation",
+
-
    "p/ovMK2ktEeSommgLa2" : "Heat shock transformation",
+
-
    "p/pk9LqRH9ot8JiKx23" : "Make a glycerol stock",
+
-
    "p/qGNf5sATkiC4P7RqF" : "Gather bacteria from an agar plate",
+
-
    "p/v97Nktv4idauP3hYh" : "Make competent cells",
+
-
    "p/vB88pigyWbKvmKir6" : "Pick a colony from an agar plate",
+
-
    "p/vj752RxeBbHsHi83w" : "Pick a colony from an agar plate",
+
-
    "p/xBmBAjXPQntkvc8d5" : "Make a glycerol stock",
+
-
    "p/z46dHCjoZpLkNgm4k" : "CPEC"
+
-
}
+
-
var colorMapping = {"Make a liquid culture":"#1f77b4","Streak bacteria onto an agar plate":"#aec7e8","Dilute DNA":"#ff7f0e","PCA":"#ffbb78","DNA purification (\"PCR Purification\")":"#2ca02c","Golden Gate Assembly":"#98df8a","Maxens neues Protokoll":"#d62728","Make competent cells":"#ff9896","Make a glycerol stock":"#9467bd","Restriction digest":"#c5b0d5","Pick a colony from an agar plate":"#8c564b","Agarose Gel Electrophoresis":"#c49c94","PCR":"#e377c2","Plasmid Preparation":"#f7b6d2","Heat shock transformation":"#7f7f7f","Annealing of complementary oligonucleotides":"#c7c7c7","Recovery of plasmid DNA from filter paper":"#bcbd22","Dissolve plasmid DNA from the registry distribution":"#dbdb8d","Gel extraction":"#17becf","Make Medium":"#9edae5","Ligation":"#1f77b4","Gather bacteria from an agar plate":"#aec7e8","CPEC":"#ff7f0e"};
+
graph = d3.selectAll("#graph");
 +
nodes = graph.selectAll(".node");
 +
links = graph.selectAll(".link");
 +
force = d3.layout.force()
 +
.charge(-250)
 +
.linkDistance(function (d) {
 +
var dist = getHeight(d.target.date) - getHeight(d.source.date);
 +
var minDist = 15;
 +
if (dist < minDist) dist = minDist;
 +
return dist;
 +
})
 +
.linkStrength(.1)
 +
.gravity(0)
 +
.size([width, height])
 +
.nodes(self.fnodes)
 +
.links(self.flinks)
 +
.on("tick", tick);
-
//var circle;
+
ko.computed(function () {
-
$(document).ready(function(){
+
$.each(self.chunksLoaded, function (key, obj) {
 +
obj.xhr.abort();
 +
});
 +
self.chunksLoaded = { };
 +
var projectName = self.project();
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var date = Math.max(Math.min(self.date, self.chunks[projectName][self.chunks[projectName].length - 1].end - viewportHeight + 50 / heightOfSecond), self.chunks[projectName][0].begin - 50 / heightOfSecond);
 +
setDate(date);
 +
});
 +
};
-
svg = d3.selectAll("#graph");
+
function update () {
-
$svg = $("#graph");
+
var nodeData = [], linkData = [];
-
width = $svg.width();
+
$.each(self.chunksLoaded, function (key, chunk) {
-
height = $svg.height();
+
if (chunk.nodes) nodeData.push.apply(nodeData, chunk.nodes);
 +
if (chunk.links) linkData.push.apply(linkData, chunk.links);
 +
});
-
$svg.bind('DOMMouseScroll mousewheel', handleScrolling);
+
console.log(nodeData, linkData);
-
 
+
-
node = svg.selectAll(".node");
+
-
link = svg.selectAll(".link");
+
-
force = d3.layout.force()
+
-
      .charge(-500)
+
-
      .linkDistance(function (d) {
+
-
      var dist = getHeight(d.target.date) - getHeight(d.source.date);
+
-
      var minDist = 50;
+
-
      if (dist < minDist) dist = minDist;
+
-
      return dist;
+
-
      })
+
-
      .linkStrength(.1)
+
-
      .gravity(0)
+
-
      .size([width, height])
+
-
      .links(flinks)
+
-
      .nodes(fnodes)
+
-
      .on("tick", tick);
+
-
     
+
-
 
+
-
    setSubproject("Lyso", firstDate);
+
-
+
 +
nodes = nodes.data(nodeData, function (d) { return d.id; } );
 +
linkData = linkData.filter(function(d) {
 +
return findByID(d.target) !== undefined && findByID(d.source) !== undefined;
});
});
 +
linkData.forEach(function(d) {
 +
d.source = findByID(d.source);
 +
d.target = findByID(d.target);
 +
});
 +
links = links.data(linkData, function (d) { return d.source.id + '/' + d.target.id; });
-
function update(){
+
links
-
if(dataUpdated){
+
.enter()
-
dataUpdated=false;
+
.append("line")
-
var links = flatten(bigLinks);
+
.each(function (d) {
-
var nodes = flatten(bigNodes);
+
self.flinks.push(d);
 +
})
 +
.on("click", function (d){if(d3.event.defaultPrevented) return ; scrollToDate(d.target.date-100000);})
 +
.attr("class", "link");
-
node = node.data(nodes, function(d) { return d.id;});
+
links
-
node.enter()
+
.exit()
-
.append("circle")
+
.each(function (d) {
-
.attr("class", "node")
+
//var index = flinks.indexOf(findByID(d)); if(index >-1) flinks.splice(index, 1);
-
.attr("r", 11)
+
removeLinksByIDs(self.flinks, d.source.id, d.target.id);
-
.attr("fill", function (d) {
+
})
-
return colorMapping[mapping[d.type]];
+
.remove();
-
})
+
-
.on("click", function(){if(d3.event.defaultPrevented) return ; alert("Silvan show Overlay");})
+
-
.call(force.drag)
+
-
.each(function(d) {
+
-
d.y = (d.date - firstDate) * heightOfSecond;
+
-
fnodes.push(d);
+
-
})
+
-
.append("svg:title")
+
-
.text(function(d){return mapping[d.type] + ", " + d.groups;});
+
-
node.exit()
+
nodes
-
.each(function(d) { removeByID(fnodes, d.id); })
+
.enter()
-
.remove();
+
.append("circle")
 +
.attr("class", "node")
 +
.attr("fill", function (d) {
 +
return colorMapping[mapping[d.type]];
 +
})
 +
.on("click", function () {
 +
if (d3.event.defaultPrevented) return;
 +
alert("Silvan show Overlay");
 +
})
 +
.call(force.drag)
 +
.each(function (d) {
 +
d.y = d.date - heightOfSecond;
 +
self.fnodes.push(d);
 +
})
 +
.append("svg:title")
 +
.text(function(d){return mapping[d.type] + ", " + d.groups;})
-
links = links.filter(function(d) {
+
nodes
-
return findByID(d.target) !== undefined && findByID(d.source) !== undefined;
+
.exit()
-
});
+
.each(function (d) {
-
links.forEach(function(d) {  
+
removeByID(self.fnodes, d.id);
-
d.source = findByID(d.source);
+
})
-
d.target = findByID(d.target);
+
.remove();
-
});
+
-
link = link.data(links);
+
force.start();
-
var lines = link.enter()
+
-
.append("line")
+
-
.each(function (d) {
+
-
flinks.push(d);
+
-
})
+
-
.on("click", function (d){if(d3.event.defaultPrevented) return ; scrollToDate(d.target.date-100000);})
+
-
.attr("class", "link");
+
-
//lines.filter(function () { return Math.random() > 0.5; }).attr("opacity", "0");
+
updateVis();
 +
}
-
link.exit()
+
function tick(e) {
-
.each(function(d) {
+
force.nodes().forEach(function(d){
-
var index = flinks.indexOf(findByID(d)); if(index >-1) flinks.splice(index, 1);
+
if(!d.fixed){
-
removeLinksByIDs(flinks, d.source.id, d.target.id);
+
d.y += (getHeight(d.date) - d.y) * e.alpha;
-
})
+
//d.y = getHeight(d.date);
-
.remove();
+
if(d.x > width * 8/10){
-
 
+
d.x += (width*8/10 - d.x) * e.alpha;
-
force.start();
+
}else if(d.x < width * 2/10){
-
 
+
d.x += (width* 2/10 - d.x) * e.alpha;
-
unhighlightData(unhighlightedData);
+
} else{
 +
d.x += (width/2 - d.x) * e.alpha * 0.2 ;
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}
}
}
-
+
});
-
updateVis();
+
updateVis();
 +
}
-
}
 
-
function tick(e) {
+
function updateVis(){
-
force.nodes().forEach(function(d){
+
nodes
-
if(!d.fixed){
+
.attr("cx", function(d) { return d.x; })
-
              d.y += (getHeight(d.date) - d.y)  * e.alpha;
+
.attr("cy", function(d) { return d.y - self.date * heightOfSecond; });
-
              //d.y = getHeight(d.date);
+
-
              if(d.x > width * 8/10){
+
-
              d.x += (width*8/10 - d.x)  * e.alpha;
+
-
              }else if(d.x < width * 2/10){
+
-
              d.x += (width* 2/10 - d.x) * e.alpha;
+
-
              } else{
+
-
              d.x += (width/2 - d.x) * e.alpha * 0.2 ;
+
-
              }
+
-
            }
+
-
});
+
-
updateVis();
+
links
-
}
+
.attr("x1", function(d) {  if(d.source !== undefined) return d.source.x; else return d.target.x; })
 +
.attr("y1", function(d) {  if(d.source !== undefined) return d.source.y - self.date * heightOfSecond; else return 0;})
 +
.attr("x2", function(d) {  if(d.target !== undefined) return d.target.x; else return d.source.x; })
 +
.attr("y2", function(d) {  if(d.target !== undefined) return d.target.y - self.date * heightOfSecond; else return viewportHeight * heightOfSecond;});
 +
}
 +
function setDate(d){
 +
self.date = d;
 +
setDateRange(d - bufferHeight, d + viewportHeight + bufferHeight);
 +
}
-
function updateVis(){
+
function scrollToDate (d) {
-
node.attr("cx", function(d) { return d.x; })
+
var dif = d - self.date;
-
.attr("cy", function(d) { return d.y - (date - firstDate) * heightOfSecond; });
+
console.log(dif);
 +
var smoothness = 60; //30 FPS
 +
var i = 0;
 +
var max = 1 * smoothness; //1 sec.
 +
var interval = setInterval(function(){
 +
i=i+1;
 +
if(i > max){
 +
clearInterval(interval);
 +
}
 +
setDate(self.date+ dif/max)
 +
}, max*1000/smoothness/smoothness);
 +
}
-
link
+
function highlightData(typeName){
-
.attr("x1", function(d) { if(d.source !== undefined) return d.source.x; else return d.target.x; })
+
var array = [].concat(typeName);
-
.attr("y1", function(d) { if(d.source !== undefined) return d.source.y - (date - firstDate) * heightOfSecond; else return 0;})
+
console.log(array);
-
.attr("x2", function(d) { if(d.target !== undefined) return d.target.x; else return d.source.x; })
+
nodes.attr("opacity", function(d){
-
.attr("y2", function(d) {  if(d.target !== undefined) return d.target.y - (date - firstDate) * heightOfSecond; else return viewportHeight * heightOfSecond;});
+
var h = false;
-
}
+
for(var g = 0; g < array.length; g=g+1) {
 +
h = h || d.groups.indexOf(array[g]) !== -1;
 +
}
 +
if(h) return 1.0;
 +
else return 0.1;
 +
});
 +
links.attr("opacity", function(d){
 +
var h = false;
 +
for(var g = 0; g < array.length; g=g+1) {
 +
h = h || (d.target && d.target.groups.indexOf(array[g]) !== -1 && d.source && d.source.groups.indexOf(array[g]) !== -1);
 +
}
-
function setSubproject(project, d){
+
if(h) return 1;
-
dateJSONMatchingList = undefined;
+
else return 0.1;
-
if(d === undefined) d = date;
+
});
-
this.selectedProject = project;
+
}
-
unhighlightedData = [];
+
-
unloadGreaterDate(firstDate-1);
+
-
loadDate(d-bufferHeight);
+
function unhighlightData(typeName){
-
    loadDate(d);
+
var array = [].concat(typeName);
-
    loadDate(d+viewportHeight);
+
console.log(array);
-
    loadDate(d+viewportHeight+bufferHeight);
+
nodes.attr("opacity", function(d){
-
    setDate(d);
+
var h = false;
-
}
+
for(var g = 0; g < array.length; g=g+1) {
 +
h = h || d.groups.indexOf(array[g]) !== -1;
 +
}
 +
if(h) return 0.1;
 +
else return 1.0;
 +
});
 +
links.attr("opacity", function(d){
 +
var h = false;
 +
for(var g = 0; g < array.length; g=g+1) {
 +
h = h || ((d.target && d.target.groups.indexOf(array[g]) !== -1) || (d.source && d.source.groups.indexOf(array[g]) !== -1));
 +
}
-
function setDate(date){
+
if(h) return 0.1;
-
/*if(date < firstDate){
+
else return 1.0;
-
date = firstDate;
+
});
-
}*/
+
for(i = 0; i < array.length; i=i+1){
-
var lastDateDisplayed = date + viewportHeight;
+
if(unhighlightedData.indexOf(array[i]) === -1) unhighlightedData.push(array[i]);
-
loadDate(date - bufferHeight);
+
-
loadDate(lastDateDisplayed + bufferHeight);
+
-
unloadSmallerDate(date - bufferHeight);
+
-
unloadGreaterDate(lastDateDisplayed + bufferHeight);
+
-
this.date = date;
+
-
update();
+
}
}
 +
}
-
/*function animateFlow(){
 
-
var links = flatten(bigLinks);
 
-
var x = Math.floor(links.length * Math.random());
 
-
xs.push(x);
 
-
var l = links[x];
 
-
svg.append("ellipse")
 
-
.attr("fill", "#33CC33")
 
-
.attr("rx", ( l.target.x -  l.source.x)/100)
 
-
.attr("ry", ( l.target.y -  l.source.y)/100)
 
-
.attr("cx", l.source.x)
 
-
.attr("cy", l.source.y)
 
-
  .transition()
 
-
.duration(1000000/(( l.target.x -  l.source.x) + ( l.target.y -  l.source.y)))
 
-
.ease("linear")
 
-
.attr("cx", l.target.x)
 
-
.attr("cy", l.target.y)
 
-
.remove();
 
-
}*/
+
//////***************************************Helper Function*************************************/
-
function scrollToDate(d){
+
function findByID(id){
-
var currentDate = date;
+
return $.grep(self.fnodes, function(e){return e === id || e.id === id;})[0];
-
var dif = d - currentDate;
+
}
-
console.log(dif);
+
-
var smoothness = 60; //30 FPS
+
-
var i = 0;
+
-
var max = 1 * smoothness; //1 sec.
+
-
var interval = setInterval(function(){
+
-
i=i+1;
+
-
if(i > max){
+
-
clearInterval(interval);
+
-
}
+
-
setDate(date+ dif/max)
+
-
}, max*1000/smoothness/smoothness);
+
-
}
+
-
function highlightData(typeName){
+
function removeByID(array, id){
-
var array = [].concat(typeName);
+
var index = -1;
-
node.attr("opacity", function(d){
+
for(i = 0; i<array.length; i=i+1){
-
var h = false;
+
if(array[i].id === id){
-
for(var g = 0; g < array.length; g=g+1) {
+
index = i;
-
h = h || d.groups.indexOf(array[g]) !== -1;
+
break;
-
}
+
-
if(h) return 1.0;
+
-
else return 0.1;
+
-
});
+
-
link.attr("opacity", function(d){
+
-
var h = false;
+
-
for(var g = 0; g < array.length; g=g+1) {
+
-
h = h || (d.target && d.target.groups.indexOf(array[g]) !== -1 && d.source && d.source.groups.indexOf(array[g]) !== -1);
+
-
}
+
-
 
+
-
if(h) return 1;
+
-
else return 0.1;
+
-
});
+
-
}
+
-
 
+
-
function unhighlightData(typeName){
+
-
var array = [].concat(typeName);
+
-
node.attr("opacity", function(d){
+
-
var h = false;
+
-
for(var g = 0; g < array.length; g=g+1) {
+
-
h = h || d.groups.indexOf(array[g]) !== -1;
+
-
}
+
-
if(h) return 0.1;
+
-
else return 1.0;
+
-
});
+
-
link.attr("opacity", function(d){
+
-
var h = false;
+
-
for(var g = 0; g < array.length; g=g+1) {
+
-
h = h || ((d.target && d.target.groups.indexOf(array[g]) !== -1) || (d.source && d.source.groups.indexOf(array[g]) !== -1));
+
-
}
+
-
 
+
-
if(h) return 0.1;
+
-
else return 1.0;
+
-
});
+
-
for(i = 0; i < array.length; i=i+1){
+
-
if(unhighlightedData.indexOf(array[i]) === -1) unhighlightedData.push(array[i]);
+
}
}
}
}
 +
array.splice(index, 1);
 +
}
-
 
+
function removeLinksByIDs(array, sourceId, targetId){
-
//////***************************************Helper Function*************************************/
+
var index = -1;
-
 
+
for(i = 0; i<array.length; i=i+1){
-
function findByID(id){
+
if(array[i].source.id === sourceId && array[i].target.id === targetId){
-
return $.grep(fnodes, function(e){return e === id || e.id === id;})[0];
+
index = i;
-
}
+
break;
-
 
+
-
function removeByID(array, id){
+
-
var index = -1;
+
-
for(i = 0; i<array.length; i=i+1){
+
-
if(array[i].id === id){
+
-
index = i;
+
-
break;
+
-
}
+
}
}
-
array.splice(index, 1);
 
}
}
 +
array.splice(index, 1);
 +
}
-
function removeLinksByIDs(array, sourceId, targetId){
+
function getHeight(date){
-
var index = -1;
+
return date * heightOfSecond;
-
for(i = 0; i<array.length; i=i+1){
+
-
if(array[i].source.id === sourceId && array[i].target.id === targetId){
+
-
index = i;
+
-
break;
+
-
}
+
-
}
+
-
array.splice(index, 1);
+
-
}
+
-
function getHeight(date){
+
}
-
return (date - firstDate)*heightOfSecond;
+
-
}
+
/***************************************************************************************************/
-
/***************************************************************************************************/
+
/************************************Scrolling and JSON loading stuff*******************************/
-
/************************************Scrolling and JSON loading stuff*******************************/
+
var dataUpdated = false;
-
+
-
+
-
/*var loadedJSONFiles = [];
+
-
var lastLoadedJSON = -1;
+
-
var firstLoadedJSON = 0;*/
+
-
var dateJSONMatchingList;
+
var loadingData = false;
-
var dataUpdated = false;
+
-
var loadingData = false;
+
function extractAndMergeData(a, b){
-
 
+
return a.concat(b.data);
-
function flatten(a){
+
}
-
return a.reduce(extractAndMergeData, []);
+
-
}
+
-
 
+
-
function extractAndMergeData(a, b){
+
-
return a.concat(b.data);
+
-
}
+
function getFileURL(file) {
function getFileURL(file) {
Line 378: Line 326:
}
}
-
function getJSONForDate(date){
+
function setDateRange(startDate, endDate) {
-
if(dateJSONMatchingList === undefined){
+
var projectName = self.project();
-
dateJSONMatchingList = [];
+
for (var ii = 0; ii < self.chunks[projectName].length; ii++) {
-
for(i = 0; i < jsonFiles[selectedProject].length; i=i+1){
+
var chunk = self.chunks[projectName][ii];
-
var file = jsonFiles[selectedProject][i];
+
var key = '' + chunk.begin + '-' + chunk.end;
-
var f = (function (file) {  
+
if (chunk.end >= startDate) {
-
return function(d){
+
if (chunk.begin < endDate) {
-
return d >= file.begin && d <= file.end;
+
if (!self.chunksLoaded[key]) {
 +
var test = false;
 +
self.chunksLoaded[key] = {
 +
xhr: d3.json(getFileURL('Heidelberg_Notebook_Data_' + projectName + '_summary_' + chunk.begin + '_' + chunk.end + '.txt'), function (error, data) { window.setTimeout(function () {
 +
if (error) {
 +
console.warn(error);
 +
} else {
 +
self.chunksLoaded[key].nodes = data.nodes;
 +
self.chunksLoaded[key].links = data.links;
 +
update();
 +
}
 +
}, 0); }),
};
};
-
})(file);
+
test = true;
-
dateJSONMatchingList.push({
+
}
-
fun: f,
+
continue;
-
file: getFileURL('Heidelberg_Notebook_Data_' + selectedProject + '_summary_' + file.begin + '_' + file.end + '.txt'),
+
-
begin: file.begin,
+
-
end: file.end,
+
-
});
+
}
}
}
}
-
for(j = 0; j < dateJSONMatchingList.length; j=j+1){
 
-
if(dateJSONMatchingList[j].fun(date)) return dateJSONMatchingList[j];
 
-
}
 
-
return -1;
 
-
}
 
-
function loadDate(date){
+
if (self.chunksLoaded[key]) {
-
 
+
self.chunksLoaded[key].xhr.abort();
-
//Check if date is already loaded
+
delete self.chunksLoaded[key];
-
if(!isDateLoaded(date)){
+
update();
-
//Load new date
+
-
var json = getJSONForDate(date);
+
-
if(json !== -1){
+
-
d3.json(json.file, function(error, data){
+
-
if(error) console.warn(error);
+
-
var containsFnc = json.fun;
+
-
var smallerFnc = (function(l1, l2){
+
-
return function(d){
+
-
return d < l1 && d < l2;
+
-
};
+
-
})(json.begin, json.end);
+
-
var greaterFnc = (function(l1, l2){
+
-
return function(d){
+
-
return d > l1 && d > l2;
+
-
};
+
-
})(json.begin, json.end);
+
-
if(!isDateLoaded(date)){ //Attention this could lead due to the asynchronous nature of d3.json to a race condition and double adding of the nodes and links...
+
-
bigNodes.push({
+
-
contains: containsFnc,
+
-
greater: greaterFnc,
+
-
smaller: smallerFnc,
+
-
data: data.nodes
+
-
});
+
-
bigLinks.push({
+
-
contains: containsFnc,
+
-
greater: greaterFnc,
+
-
smaller: smallerFnc,
+
-
data: data.links
+
-
});
+
-
dataUpdated = true;
+
-
}
+
-
update();
+
-
});
+
-
}
+
}
}
-
 
}
}
 +
}
-
function unloadSmallerDate(date){
+
function handleScrolling(e) {
-
if(bigNodes.reduce(function(a, b){return a || b.greater(date);}, false)){
+
var scrollTo = 0;
-
bigNodes = bigNodes.filter(function(d){return !d.greater(date);});
+
e.preventDefault();
-
bigLinks = bigLinks.filter(function(d){return !d.greater(date);});
+
if (e.type == 'mousewheel') {
-
dataUpdated = true;
+
scrollTo = (e.originalEvent.wheelDelta * -scrollSpeed/100);
-
 
+
}else if (e.type == 'DOMMouseScroll') {
-
}
+
scrollTo = e.originalEvent.detail * scrollSpeed;
}
}
 +
setDate(self.date+scrollTo);
 +
}
-
function unloadGreaterDate(date){
+
function md5cycle(e,t){var n=e[0],r=e[1],i=e[2],s=e[3];n=ff(n,r,i,s,t[0],7,-680876936);s=ff(s,n,r,i,t[1],12,-389564586);i=ff(i,s,n,r,t[2],17,606105819);r=ff(r,i,s,n,t[3],22,-1044525330);n=ff(n,r,i,s,t[4],7,-176418897);s=ff(s,n,r,i,t[5],12,1200080426);i=ff(i,s,n,r,t[6],17,-1473231341);r=ff(r,i,s,n,t[7],22,-45705983);n=ff(n,r,i,s,t[8],7,1770035416);s=ff(s,n,r,i,t[9],12,-1958414417);i=ff(i,s,n,r,t[10],17,-42063);r=ff(r,i,s,n,t[11],22,-1990404162);n=ff(n,r,i,s,t[12],7,1804603682);s=ff(s,n,r,i,t[13],12,-40341101);i=ff(i,s,n,r,t[14],17,-1502002290);r=ff(r,i,s,n,t[15],22,1236535329);n=gg(n,r,i,s,t[1],5,-165796510);s=gg(s,n,r,i,t[6],9,-1069501632);i=gg(i,s,n,r,t[11],14,643717713);r=gg(r,i,s,n,t[0],20,-373897302);n=gg(n,r,i,s,t[5],5,-701558691);s=gg(s,n,r,i,t[10],9,38016083);i=gg(i,s,n,r,t[15],14,-660478335);r=gg(r,i,s,n,t[4],20,-405537848);n=gg(n,r,i,s,t[9],5,568446438);s=gg(s,n,r,i,t[14],9,-1019803690);i=gg(i,s,n,r,t[3],14,-187363961);r=gg(r,i,s,n,t[8],20,1163531501);n=gg(n,r,i,s,t[13],5,-1444681467);s=gg(s,n,r,i,t[2],9,-51403784);i=gg(i,s,n,r,t[7],14,1735328473);r=gg(r,i,s,n,t[12],20,-1926607734);n=hh(n,r,i,s,t[5],4,-378558);s=hh(s,n,r,i,t[8],11,-2022574463);i=hh(i,s,n,r,t[11],16,1839030562);r=hh(r,i,s,n,t[14],23,-35309556);n=hh(n,r,i,s,t[1],4,-1530992060);s=hh(s,n,r,i,t[4],11,1272893353);i=hh(i,s,n,r,t[7],16,-155497632);r=hh(r,i,s,n,t[10],23,-1094730640);n=hh(n,r,i,s,t[13],4,681279174);s=hh(s,n,r,i,t[0],11,-358537222);i=hh(i,s,n,r,t[3],16,-722521979);r=hh(r,i,s,n,t[6],23,76029189);n=hh(n,r,i,s,t[9],4,-640364487);s=hh(s,n,r,i,t[12],11,-421815835);i=hh(i,s,n,r,t[15],16,530742520);r=hh(r,i,s,n,t[2],23,-995338651);n=ii(n,r,i,s,t[0],6,-198630844);s=ii(s,n,r,i,t[7],10,1126891415);i=ii(i,s,n,r,t[14],15,-1416354905);r=ii(r,i,s,n,t[5],21,-57434055);n=ii(n,r,i,s,t[12],6,1700485571);s=ii(s,n,r,i,t[3],10,-1894986606);i=ii(i,s,n,r,t[10],15,-1051523);r=ii(r,i,s,n,t[1],21,-2054922799);n=ii(n,r,i,s,t[8],6,1873313359);s=ii(s,n,r,i,t[15],10,-30611744);i=ii(i,s,n,r,t[6],15,-1560198380);r=ii(r,i,s,n,t[13],21,1309151649);n=ii(n,r,i,s,t[4],6,-145523070);s=ii(s,n,r,i,t[11],10,-1120210379);i=ii(i,s,n,r,t[2],15,718787259);r=ii(r,i,s,n,t[9],21,-343485551);e[0]=add32(n,e[0]);e[1]=add32(r,e[1]);e[2]=add32(i,e[2]);e[3]=add32(s,e[3])}function cmn(e,t,n,r,i,s){t=add32(add32(t,e),add32(r,s));return add32(t<<i|t>>>32-i,n)}function ff(e,t,n,r,i,s,o){return cmn(t&n|~t&r,e,t,i,s,o)}function gg(e,t,n,r,i,s,o){return cmn(t&r|n&~r,e,t,i,s,o)}function hh(e,t,n,r,i,s,o){return cmn(t^n^r,e,t,i,s,o)}function ii(e,t,n,r,i,s,o){return cmn(n^(t|~r),e,t,i,s,o)}function md51(e){txt="";var t=e.length,n=[1732584193,-271733879,-1732584194,271733878],r;for(r=64;r<=e.length;r+=64){md5cycle(n,md5blk(e.substring(r-64,r)))}e=e.substring(r-64);var i=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0];for(r=0;r<e.length;r++)i[r>>2]|=e.charCodeAt(r)<<(r%4<<3);i[r>>2]|=128<<(r%4<<3);if(r>55){md5cycle(n,i);for(r=0;r<16;r++)i[r]=0}i[14]=t*8;md5cycle(n,i);return n}function md5blk(e){var t=[],n;for(n=0;n<64;n+=4){t[n>>2]=e.charCodeAt(n)+(e.charCodeAt(n+1)<<8)+(e.charCodeAt(n+2)<<16)+(e.charCodeAt(n+3)<<24)}return t}function rhex(e){var t="",n=0;for(;n<4;n++)t+=hex_chr[e>>n*8+4&15]+hex_chr[e>>n*8&15];return t}function hex(e){for(var t=0;t<e.length;t++)e[t]=rhex(e[t]);return e.join("")}function md5(e){return hex(md51(e))}function add32(e,t){return e+t&4294967295}var hex_chr="0123456789abcdef".split("");if(md5("hello")!="5d41402abc4b2a76b9719d911017c592"){function add32(e,t){var n=(e&65535)+(t&65535),r=(e>>16)+(t>>16)+(n>>16);return r<<16|n&65535}}
-
if(bigNodes.reduce(function(a, b){return a || b.smaller(date);}, false)){
+
})();
-
bigNodes = bigNodes.filter(function(d){return !d.smaller(date);});
+
-
bigLinks = bigLinks.filter(function(d){return !d.smaller(date);});
+
-
dataUpdated = true;
+
-
}
+
-
}
+
-
 
+
-
function parseFileName(name){
+
-
var l = name.substring(0, name.length-4).split("_");
+
-
if(l === undefined || l.length !== 2) console.warn("erroneous file name", name, l);
+
-
return l;
+
-
}
+
-
 
+
-
function parseFileNameToContainsFnc(name){
+
-
var l = parseFileName(name);
+
-
var f = function(l1, l2){
+
-
return function(d){
+
-
return d >= l1 && d <= l2;
+
-
};
+
-
}(l[0], l[1]);
+
-
return f;
+
-
}
+
-
 
+
-
function parseFileNameToSmallerFnc(name){
+
-
var l  = parseFileName(name);
+
-
var f = function(l1, l2){
+
-
return function(d){
+
-
return d < l1 && d < l2;
+
-
};
+
-
}(l[0], l[1]);
+
-
return f;
+
-
}
+
-
function parseFileNameToGreaterFnc(name){
+
-
var l = parseFileName(name);
+
-
var f = function(l1, l2){
+
-
return function(d){
+
-
return d > l1 && d > l2;
+
-
};
+
-
}(l[0], l[1]);
+
-
return f;
+
-
}
+
-
 
+
-
function isDateLoaded(date){
+
-
for(i = 0; i < bigNodes.length; i=i+1){
+
-
if(bigNodes[i].contains(date)){
+
-
return true;
+
-
}
+
-
}
+
-
return false;
+
-
}
+
-
 
+
-
function handleScrolling(e) {
+
-
var scrollTo = 0;
+
-
    e.preventDefault();
+
-
    if (e.type == 'mousewheel') {
+
-
        scrollTo = (e.originalEvent.wheelDelta * -scrollSpeed/100);
+
-
    }else if (e.type == 'DOMMouseScroll') {
+
-
        scrollTo = e.originalEvent.detail * scrollSpeed;
+
-
    }
+
-
    setDate(date+scrollTo);
+
-
}
+

Revision as of 20:27, 17 October 2014

var Graph = new (function () { var self = this; var graph;

self.date = 0;

var heightOfSecond = 100 / 86400; // = 300 Pixel per day?! var viewportHeight = 300 / heightOfSecond; var bufferHeight = 1000 / heightOfSecond; var scrollSpeed = 6000; // = 20 minutes

var width, height;

var nodes, links;

var force; self.fnodes = []; self.flinks = [];

self.chunks = {"Toolbox":[{"begin":1388527200,"end":1388530800},{"begin":1392040800,"end":1392072300},{"begin":1396947600,"end":1396951200},{"begin":1401804000,"end":1402056000},{"begin":1402070400,"end":1402234200},{"begin":1402567200,"end":1402825080},{"begin":1403030400,"end":1403172000},{"begin":1403301600,"end":1403390400},{"begin":1403598600,"end":1403789400},{"begin":1403859600,"end":1403958600},{"begin":1404134400,"end":1404388800},{"begin":1404403680,"end":1404660346},{"begin":1404664800,"end":1404849600},{"begin":1404932400,"end":1405186800},{"begin":1405193400,"end":1405447200},{"begin":1405458000,"end":1405641000},{"begin":1405720800,"end":1405980000},{"begin":1406021160,"end":1406278800},{"begin":1406282400,"end":1406539200},{"begin":1406543880,"end":1406757600},{"begin":1406808000,"end":1407067200},{"begin":1407070800,"end":1407330000},{"begin":1407330600,"end":1407580200},{"begin":1407596700,"end":1407855600},{"begin":1407857400,"end":1408115700},{"begin":1408117620,"end":1408376700},{"begin":1408377600,"end":1408636800},{"begin":1408642200,"end":1408901220},{"begin":1408911600,"end":1409170200},{"begin":1409173200,"end":1409432400},{"begin":1409436000,"end":1409695200},{"begin":1409697000,"end":1409955000},{"begin":1409957940,"end":1410215400},{"begin":1410220800,"end":1410453000},{"begin":1410512400,"end":1410771600},{"begin":1410775200,"end":1411034400},{"begin":1411036200,"end":1411295400},{"begin":1411336800,"end":1411596000},{"begin":1411598280,"end":1411855200},{"begin":1411863840,"end":1412114700},{"begin":1412134500,"end":1412380800},{"begin":1412414880,"end":1412655300},{"begin":1412681400,"end":1412905020},{"begin":1412995020,"end":1413085020},],"LOV":[{"begin":1388530800,"end":1388530800},{"begin":1392040800,"end":1392044400},{"begin":1401804000,"end":1402000800},{"begin":1402070400,"end":1402234200},{"begin":1402567200,"end":1402825080},{"begin":1403030400,"end":1403172000},{"begin":1403301600,"end":1403301600},{"begin":1403604000,"end":1403863200},{"begin":1403866800,"end":1404064800},{"begin":1404203520,"end":1404424800},{"begin":1404511200,"end":1404770400},{"begin":1404807600,"end":1404938700},{"begin":1405112400,"end":1405371600},{"begin":1405447200,"end":1405641000},{"begin":1405720800,"end":1405871100},{"begin":1406021160,"end":1406278800},{"begin":1406282400,"end":1406500200},{"begin":1406543880,"end":1406757600},{"begin":1406808000,"end":1407024000},{"begin":1407070800,"end":1407323460},{"begin":1407369600,"end":1407623400},{"begin":1407630600,"end":1407841200},{"begin":1407960000,"end":1408140000},{"begin":1408277700,"end":1408536000},{"begin":1408541400,"end":1408744800},{"begin":1408809600,"end":1409065200},{"begin":1409070600,"end":1409329800},{"begin":1409332800,"end":1409589000},{"begin":1409601600,"end":1409847600},{"begin":1409941800,"end":1410192000},{"begin":1410210000,"end":1410469200},{"begin":1410472800,"end":1410732000},{"begin":1410749400,"end":1410991200},{"begin":1411016280,"end":1411252200},{"begin":1411279200,"end":1411531500},{"begin":1411542000,"end":1411794960},{"begin":1411826400,"end":1412082000},{"begin":1412088480,"end":1412345340},{"begin":1412348940,"end":1412577300},{"begin":1412624700,"end":1412877600},{"begin":1412887800,"end":1412953200},],"DNMT1":[{"begin":1388527200,"end":1388530800},{"begin":1401804000,"end":1402000800},{"begin":1402131600,"end":1402174800},{"begin":1402567200,"end":1402581600},{"begin":1403096400,"end":1403096400},{"begin":1403604000,"end":1403820000},{"begin":1403891280,"end":1403953200},{"begin":1404230400,"end":1404424800},{"begin":1404640800,"end":1404722700},{"begin":1405461600,"end":1405615500},{"begin":1406154600,"end":1406293200},{"begin":1406656800,"end":1406656800},{"begin":1406930400,"end":1407024000},{"begin":1407226500,"end":1407321900},{"begin":1407623400,"end":1407841200},{"begin":1408314600,"end":1408399800},{"begin":1408635300,"end":1408821780},{"begin":1409349600,"end":1409349600},{"begin":1409683500,"end":1409841600},{"begin":1409956140,"end":1410199200},{"begin":1410253200,"end":1410420600},{"begin":1410523200,"end":1410781200},{"begin":1410793200,"end":1411036200},{"begin":1411054380,"end":1411232400},{"begin":1411395300,"end":1411601100},{"begin":1411657200,"end":1411916400},{"begin":1411922700,"end":1411922700},{"begin":1412575200,"end":1412699400},],"Lyso":[{"begin":1388530800,"end":1388530800},{"begin":1396947600,"end":1396951200},{"begin":1401804000,"end":1401984600},{"begin":1402567200,"end":1402825080},{"begin":1403030400,"end":1403101800},{"begin":1403301600,"end":1403301600},{"begin":1405447200,"end":1405447200},{"begin":1405814400,"end":1405871100},{"begin":1406494800,"end":1406642400},{"begin":1406757600,"end":1407016800},{"begin":1407020400,"end":1407263400},{"begin":1407289200,"end":1407518100},{"begin":1407589200,"end":1407799800},{"begin":1407857400,"end":1408115700},{"begin":1408140000,"end":1408312800},{"begin":1408447800,"end":1408656240},{"begin":1408744800,"end":1408834560},{"begin":1409065200,"end":1409320800},{"begin":1409349600,"end":1409603400},{"begin":1409662800,"end":1409768100},{"begin":1410037200,"end":1410213600},{"begin":1410364800,"end":1410618600},{"begin":1410683400,"end":1410904800},{"begin":1410946200,"end":1411153200},{"begin":1411308000,"end":1411558200},{"begin":1411639200,"end":1411855200},{"begin":1411909200,"end":1412164800},{"begin":1412182800,"end":1412442000},{"begin":1412449200,"end":1412546400},],"Xyla":[{"begin":1388530800,"end":1388530800},{"begin":1401804000,"end":1401973800},{"begin":1402825080,"end":1402825080},{"begin":1405371600,"end":1405371600},{"begin":1405641000,"end":1405871100},{"begin":1406021160,"end":1406278800},{"begin":1406282400,"end":1406500200},{"begin":1407623400,"end":1407799800},{"begin":1407960000,"end":1408217040},{"begin":1408226400,"end":1408484700},{"begin":1408490760,"end":1408744800},{"begin":1408802400,"end":1408834560},{"begin":1409243400,"end":1409429700},{"begin":1409603400,"end":1409781600},{"begin":1410159600,"end":1410418800},{"begin":1410444000,"end":1410688800},{"begin":1410775200,"end":1410962400},{"begin":1411072200,"end":1411320600},{"begin":1411489800,"end":1411742700},{"begin":1411754400,"end":1411941600},{"begin":1412017200,"end":1412269200},{"begin":1412287200,"end":1412380800},],"General":[{"begin":1388530800,"end":1388530800},{"begin":1401804000,"end":1402056000},{"begin":1402070400,"end":1402261200},{"begin":1402567200,"end":1402825080},{"begin":1403030400,"end":1403172000},{"begin":1403301600,"end":1403390400},{"begin":1403611200,"end":1403856000},{"begin":1403892000,"end":1404043200},{"begin":1404319200,"end":1404576000},{"begin":1404587400,"end":1404832260},{"begin":1404897720,"end":1405066500},{"begin":1405814400,"end":1406047200},{"begin":1406106000,"end":1406235600},{"begin":1406448000,"end":1406671200},{"begin":1406752200,"end":1406934000},{"begin":1407020400,"end":1407257040},{"begin":1407283200,"end":1407512700},{"begin":1407596700,"end":1407794400},{"begin":1407888900,"end":1408130100},{"begin":1408234500,"end":1408476000},{"begin":1408618800,"end":1408626000},{"begin":1408881600,"end":1409058000},{"begin":1409176740,"end":1409405580},{"begin":1409439600,"end":1409486400},{"begin":1409925600,"end":1410159600},{"begin":1410206400,"end":1410264000},{"begin":1410606000,"end":1410825240},{"begin":1410931800,"end":1411088400},{"begin":1411421400,"end":1411421400},{"begin":1411754400,"end":1411992000},{"begin":1412164800,"end":1412377200},{"begin":1412449200,"end":1412637600},],}; self.chunksLoaded = { };

var mapping = { "p/3cuNZHSvzbmc5wGLz" : "Make a liquid culture", "p/3wt4jvadcLzkvFn9X" : "Make a liquid culture", "p/4jCgLAziJ2DSmmcvR" : "Streak bacteria onto an agar plate", "p/53yEPDJz7oRihLz3M" : "Dilute DNA", "p/5K8vL8t4egnG8SRtc" : "PCA", "p/9S64Hy4vyzPvM4aiC" : "DNA purification (\"PCR Purification\")", "p/9TiKPrpdykEiSHFcy" : "Make a liquid culture", "p/ATv6a4HMeQZMa9WYX" : "Dilute DNA", "p/Ae7BXywPx8nNApvPK" : "Golden Gate Assembly", "p/CdKqzhX6FqmmHYKdE" : "Maxens neues Protokoll", "p/D9hHrT2Ere5rrcuXK" : "Make competent cells", "p/E8wraGbztRq8EsET7" : "Make a glycerol stock", "p/ENCvtL4jWZQW72hE5" : "Restriction digest", "p/F2oNT7tGTyGFCjAB9" : "Make competent cells", "p/FY69K4x7xdaJT6Lzk" : "Pick a colony from an agar plate", "p/HA9CLF2Z4kgY3J5rE" : "Make a liquid culture", "p/JPmjNykwWASQiD9PX" : "Agarose Gel Electrophoresis", "p/NgpLzurL2RKFojWWA" : "PCR", "p/Nm75fDvHCr38nXJBo" : "Plasmid Preparation", "p/P6LsqW4xkJYaXHFJN" : "Heat shock transformation", "p/PxYonEdgff39dmkhq" : "DNA purification (\"PCR Purification\")", "p/TD9txcymCuToDta7x" : "Annealing of complementary oligonucleotides", "p/WSMMH3bg6CcrcAJ3x" : "PCR", "p/ZuE3NijkBg4WwpzKc" : "Recovery of plasmid DNA from filter paper", "p/bSEHCZgLpXJ6nb9ze" : "Streak bacteria onto an agar plate", "p/gM7FyZeyNrM4hwxZk" : "Dissolve plasmid DNA from the registry distribution", "p/hmhE7AHgjXE8Khw6M" : "Gel extraction", "p/jT9cdZ9T5JgFDEJXe" : "Heat shock transformation", "p/kKiCHxutJLzPKayCC" : "Streak bacteria onto an agar plate", "p/kxBySpW3SnbWuYMRw" : "Streak bacteria onto an agar plate", "p/mJNyMCoEko3JKRv5x" : "Heat shock transformation", "p/maDx7F6ry8Mw5JmKf" : "Pick a colony from an agar plate", "p/ms6uHrB9Fv23Tge2J" : "Make a glycerol stock", "p/mzGLz4CZBhmDHNivi" : "Make Medium", "p/n4Sg8s8AfhMEtQtFH" : "Ligation", "p/oFoQguhSKQKC2Hfms" : "Gather bacteria from an agar plate", "p/ojKqKzgeLkvNvLDgw" : "Heat shock transformation", "p/ovMK2ktEeSommgLa2" : "Heat shock transformation", "p/pk9LqRH9ot8JiKx23" : "Make a glycerol stock", "p/qGNf5sATkiC4P7RqF" : "Gather bacteria from an agar plate", "p/v97Nktv4idauP3hYh" : "Make competent cells", "p/vB88pigyWbKvmKir6" : "Pick a colony from an agar plate", "p/vj752RxeBbHsHi83w" : "Pick a colony from an agar plate", "p/xBmBAjXPQntkvc8d5" : "Make a glycerol stock", "p/z46dHCjoZpLkNgm4k" : "CPEC" }

var colorMapping = {"Make a liquid culture":"#1f77b4","Streak bacteria onto an agar plate":"#aec7e8","Dilute DNA":"#ff7f0e","PCA":"#ffbb78","DNA purification (\"PCR Purification\")":"#2ca02c","Golden Gate Assembly":"#98df8a","Maxens neues Protokoll":"#d62728","Make competent cells":"#ff9896","Make a glycerol stock":"#9467bd","Restriction digest":"#c5b0d5","Pick a colony from an agar plate":"#8c564b","Agarose Gel Electrophoresis":"#c49c94","PCR":"#e377c2","Plasmid Preparation":"#f7b6d2","Heat shock transformation":"#7f7f7f","Annealing of complementary oligonucleotides":"#c7c7c7","Recovery of plasmid DNA from filter paper":"#bcbd22","Dissolve plasmid DNA from the registry distribution":"#dbdb8d","Gel extraction":"#17becf","Make Medium":"#9edae5","Ligation":"#1f77b4","Gather bacteria from an agar plate":"#aec7e8","CPEC":"#ff7f0e"};

self.init = function (project) { self.project = project;

$svg = $("#graph"); width = $svg.width(); height = $svg.height(); $svg.bind('DOMMouseScroll mousewheel', handleScrolling);

graph = d3.selectAll("#graph");

nodes = graph.selectAll(".node"); links = graph.selectAll(".link"); force = d3.layout.force() .charge(-250) .linkDistance(function (d) { var dist = getHeight(d.target.date) - getHeight(d.source.date); var minDist = 15; if (dist < minDist) dist = minDist; return dist; }) .linkStrength(.1) .gravity(0) .size([width, height]) .nodes(self.fnodes) .links(self.flinks) .on("tick", tick);

ko.computed(function () { $.each(self.chunksLoaded, function (key, obj) { obj.xhr.abort(); }); self.chunksLoaded = { }; var projectName = self.project(); var date = Math.max(Math.min(self.date, self.chunks[projectName][self.chunks[projectName].length - 1].end - viewportHeight + 50 / heightOfSecond), self.chunks[projectName][0].begin - 50 / heightOfSecond); setDate(date); }); };

function update () { var nodeData = [], linkData = []; $.each(self.chunksLoaded, function (key, chunk) { if (chunk.nodes) nodeData.push.apply(nodeData, chunk.nodes); if (chunk.links) linkData.push.apply(linkData, chunk.links); });

console.log(nodeData, linkData);

nodes = nodes.data(nodeData, function (d) { return d.id; } ); linkData = linkData.filter(function(d) { return findByID(d.target) !== undefined && findByID(d.source) !== undefined; }); linkData.forEach(function(d) { d.source = findByID(d.source); d.target = findByID(d.target); }); links = links.data(linkData, function (d) { return d.source.id + '/' + d.target.id; });

links .enter() .append("line") .each(function (d) { self.flinks.push(d); }) .on("click", function (d){if(d3.event.defaultPrevented) return ; scrollToDate(d.target.date-100000);}) .attr("class", "link");

links .exit() .each(function (d) { //var index = flinks.indexOf(findByID(d)); if(index >-1) flinks.splice(index, 1); removeLinksByIDs(self.flinks, d.source.id, d.target.id); }) .remove();

nodes .enter() .append("circle") .attr("class", "node") .attr("fill", function (d) { return colorMapping[mapping[d.type]]; }) .on("click", function () { if (d3.event.defaultPrevented) return; alert("Silvan show Overlay"); }) .call(force.drag) .each(function (d) { d.y = d.date - heightOfSecond; self.fnodes.push(d); }) .append("svg:title") .text(function(d){return mapping[d.type] + ", " + d.groups;})

nodes .exit() .each(function (d) { removeByID(self.fnodes, d.id); }) .remove();

force.start();

updateVis(); }

function tick(e) { force.nodes().forEach(function(d){ if(!d.fixed){ d.y += (getHeight(d.date) - d.y) * e.alpha; //d.y = getHeight(d.date); if(d.x > width * 8/10){ d.x += (width*8/10 - d.x) * e.alpha; }else if(d.x < width * 2/10){ d.x += (width* 2/10 - d.x) * e.alpha; } else{ d.x += (width/2 - d.x) * e.alpha * 0.2 ; } } });

updateVis(); }


function updateVis(){ nodes .attr("cx", function(d) { return d.x; }) .attr("cy", function(d) { return d.y - self.date * heightOfSecond; });

links .attr("x1", function(d) { if(d.source !== undefined) return d.source.x; else return d.target.x; }) .attr("y1", function(d) { if(d.source !== undefined) return d.source.y - self.date * heightOfSecond; else return 0;}) .attr("x2", function(d) { if(d.target !== undefined) return d.target.x; else return d.source.x; }) .attr("y2", function(d) { if(d.target !== undefined) return d.target.y - self.date * heightOfSecond; else return viewportHeight * heightOfSecond;}); }

function setDate(d){ self.date = d; setDateRange(d - bufferHeight, d + viewportHeight + bufferHeight); }

function scrollToDate (d) { var dif = d - self.date; console.log(dif); var smoothness = 60; //30 FPS var i = 0; var max = 1 * smoothness; //1 sec. var interval = setInterval(function(){ i=i+1; if(i > max){ clearInterval(interval); } setDate(self.date+ dif/max) }, max*1000/smoothness/smoothness); }

function highlightData(typeName){ var array = [].concat(typeName); console.log(array); nodes.attr("opacity", function(d){ var h = false; for(var g = 0; g < array.length; g=g+1) { h = h || d.groups.indexOf(array[g]) !== -1; } if(h) return 1.0; else return 0.1; }); links.attr("opacity", function(d){ var h = false; for(var g = 0; g < array.length; g=g+1) { h = h || (d.target && d.target.groups.indexOf(array[g]) !== -1 && d.source && d.source.groups.indexOf(array[g]) !== -1); }

if(h) return 1; else return 0.1; }); }

function unhighlightData(typeName){ var array = [].concat(typeName); console.log(array); nodes.attr("opacity", function(d){ var h = false; for(var g = 0; g < array.length; g=g+1) { h = h || d.groups.indexOf(array[g]) !== -1; } if(h) return 0.1; else return 1.0; }); links.attr("opacity", function(d){ var h = false; for(var g = 0; g < array.length; g=g+1) { h = h || ((d.target && d.target.groups.indexOf(array[g]) !== -1) || (d.source && d.source.groups.indexOf(array[g]) !== -1)); }

if(h) return 0.1; else return 1.0; }); for(i = 0; i < array.length; i=i+1){ if(unhighlightedData.indexOf(array[i]) === -1) unhighlightedData.push(array[i]); } }


//////***************************************Helper Function*************************************/

function findByID(id){ return $.grep(self.fnodes, function(e){return e === id || e.id === id;})[0]; }

function removeByID(array, id){ var index = -1; for(i = 0; i<array.length; i=i+1){ if(array[i].id === id){ index = i; break; } } array.splice(index, 1); }

function removeLinksByIDs(array, sourceId, targetId){ var index = -1; for(i = 0; i<array.length; i=i+1){ if(array[i].source.id === sourceId && array[i].target.id === targetId){ index = i; break; } } array.splice(index, 1); }

function getHeight(date){ return date * heightOfSecond;

}

/***************************************************************************************************/

/************************************Scrolling and JSON loading stuff*******************************/

var dataUpdated = false;

var loadingData = false;


function extractAndMergeData(a, b){ return a.concat(b.data); }

function getFileURL(file) { var md5Name = md5(file); return '/wiki/images/' + md5Name.substr(0, 1) + '/' + md5Name.substr(0, 2) + '/' + file; }

function setDateRange(startDate, endDate) { var projectName = self.project(); for (var ii = 0; ii < self.chunks[projectName].length; ii++) { var chunk = self.chunks[projectName][ii]; var key = + chunk.begin + '-' + chunk.end; if (chunk.end >= startDate) { if (chunk.begin < endDate) { if (!self.chunksLoaded[key]) { var test = false; self.chunksLoaded[key] = { xhr: d3.json(getFileURL('Heidelberg_Notebook_Data_' + projectName + '_summary_' + chunk.begin + '_' + chunk.end + '.txt'), function (error, data) { window.setTimeout(function () { if (error) { console.warn(error); } else { self.chunksLoaded[key].nodes = data.nodes; self.chunksLoaded[key].links = data.links; update(); } }, 0); }), }; test = true; } continue; } }

if (self.chunksLoaded[key]) { self.chunksLoaded[key].xhr.abort(); delete self.chunksLoaded[key]; update(); } } }

function handleScrolling(e) { var scrollTo = 0; e.preventDefault(); if (e.type == 'mousewheel') { scrollTo = (e.originalEvent.wheelDelta * -scrollSpeed/100); }else if (e.type == 'DOMMouseScroll') { scrollTo = e.originalEvent.detail * scrollSpeed; } setDate(self.date+scrollTo); }

function md5cycle(e,t){var n=e[0],r=e[1],i=e[2],s=e[3];n=ff(n,r,i,s,t[0],7,-680876936);s=ff(s,n,r,i,t[1],12,-389564586);i=ff(i,s,n,r,t[2],17,606105819);r=ff(r,i,s,n,t[3],22,-1044525330);n=ff(n,r,i,s,t[4],7,-176418897);s=ff(s,n,r,i,t[5],12,1200080426);i=ff(i,s,n,r,t[6],17,-1473231341);r=ff(r,i,s,n,t[7],22,-45705983);n=ff(n,r,i,s,t[8],7,1770035416);s=ff(s,n,r,i,t[9],12,-1958414417);i=ff(i,s,n,r,t[10],17,-42063);r=ff(r,i,s,n,t[11],22,-1990404162);n=ff(n,r,i,s,t[12],7,1804603682);s=ff(s,n,r,i,t[13],12,-40341101);i=ff(i,s,n,r,t[14],17,-1502002290);r=ff(r,i,s,n,t[15],22,1236535329);n=gg(n,r,i,s,t[1],5,-165796510);s=gg(s,n,r,i,t[6],9,-1069501632);i=gg(i,s,n,r,t[11],14,643717713);r=gg(r,i,s,n,t[0],20,-373897302);n=gg(n,r,i,s,t[5],5,-701558691);s=gg(s,n,r,i,t[10],9,38016083);i=gg(i,s,n,r,t[15],14,-660478335);r=gg(r,i,s,n,t[4],20,-405537848);n=gg(n,r,i,s,t[9],5,568446438);s=gg(s,n,r,i,t[14],9,-1019803690);i=gg(i,s,n,r,t[3],14,-187363961);r=gg(r,i,s,n,t[8],20,1163531501);n=gg(n,r,i,s,t[13],5,-1444681467);s=gg(s,n,r,i,t[2],9,-51403784);i=gg(i,s,n,r,t[7],14,1735328473);r=gg(r,i,s,n,t[12],20,-1926607734);n=hh(n,r,i,s,t[5],4,-378558);s=hh(s,n,r,i,t[8],11,-2022574463);i=hh(i,s,n,r,t[11],16,1839030562);r=hh(r,i,s,n,t[14],23,-35309556);n=hh(n,r,i,s,t[1],4,-1530992060);s=hh(s,n,r,i,t[4],11,1272893353);i=hh(i,s,n,r,t[7],16,-155497632);r=hh(r,i,s,n,t[10],23,-1094730640);n=hh(n,r,i,s,t[13],4,681279174);s=hh(s,n,r,i,t[0],11,-358537222);i=hh(i,s,n,r,t[3],16,-722521979);r=hh(r,i,s,n,t[6],23,76029189);n=hh(n,r,i,s,t[9],4,-640364487);s=hh(s,n,r,i,t[12],11,-421815835);i=hh(i,s,n,r,t[15],16,530742520);r=hh(r,i,s,n,t[2],23,-995338651);n=ii(n,r,i,s,t[0],6,-198630844);s=ii(s,n,r,i,t[7],10,1126891415);i=ii(i,s,n,r,t[14],15,-1416354905);r=ii(r,i,s,n,t[5],21,-57434055);n=ii(n,r,i,s,t[12],6,1700485571);s=ii(s,n,r,i,t[3],10,-1894986606);i=ii(i,s,n,r,t[10],15,-1051523);r=ii(r,i,s,n,t[1],21,-2054922799);n=ii(n,r,i,s,t[8],6,1873313359);s=ii(s,n,r,i,t[15],10,-30611744);i=ii(i,s,n,r,t[6],15,-1560198380);r=ii(r,i,s,n,t[13],21,1309151649);n=ii(n,r,i,s,t[4],6,-145523070);s=ii(s,n,r,i,t[11],10,-1120210379);i=ii(i,s,n,r,t[2],15,718787259);r=ii(r,i,s,n,t[9],21,-343485551);e[0]=add32(n,e[0]);e[1]=add32(r,e[1]);e[2]=add32(i,e[2]);e[3]=add32(s,e[3])}function cmn(e,t,n,r,i,s){t=add32(add32(t,e),add32(r,s));return add32(t<>>32-i,n)}function ff(e,t,n,r,i,s,o){return cmn(t&n|~t&r,e,t,i,s,o)}function gg(e,t,n,r,i,s,o){return cmn(t&r|n&~r,e,t,i,s,o)}function hh(e,t,n,r,i,s,o){return cmn(t^n^r,e,t,i,s,o)}function ii(e,t,n,r,i,s,o){return cmn(n^(t|~r),e,t,i,s,o)}function md51(e){txt="";var t=e.length,n=[1732584193,-271733879,-1732584194,271733878],r;for(r=64;r<=e.length;r+=64){md5cycle(n,md5blk(e.substring(r-64,r)))}e=e.substring(r-64);var i=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0];for(r=0;r<e.length;r++)i[r>>2]|=e.charCodeAt(r)<<(r%4<<3);i[r>>2]|=128<<(r%4<<3);if(r>55){md5cycle(n,i);for(r=0;r<16;r++)i[r]=0}i[14]=t*8;md5cycle(n,i);return n}function md5blk(e){var t=[],n;for(n=0;n<64;n+=4){t[n>>2]=e.charCodeAt(n)+(e.charCodeAt(n+1)<<8)+(e.charCodeAt(n+2)<<16)+(e.charCodeAt(n+3)<<24)}return t}function rhex(e){var t="",n=0;for(;n<4;n++)t+=hex_chr[e>>n*8+4&15]+hex_chr[e>>n*8&15];return t}function hex(e){for(var t=0;t<e.length;t++)e[t]=rhex(e[t]);return e.join("")}function md5(e){return hex(md51(e))}function add32(e,t){return e+t&4294967295}var hex_chr="0123456789abcdef".split("");if(md5("hello")!="5d41402abc4b2a76b9719d911017c592"){function add32(e,t){var n=(e&65535)+(t&65535),r=(e>>16)+(t>>16)+(n>>16);return r<<16|n&65535}} })();

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