"
Team:Amsterdam/maarten/toolscripts
From 2012.igem.org
(function() {
var ua = navigator.userAgent,
iStuff = ua.match(/iPhone/i) || ua.match(/iPad/i),
typeOfCanvas = typeof HTMLCanvasElement,
nativeCanvasSupport = (typeOfCanvas == 'object' || typeOfCanvas == 'function'),
textSupport = nativeCanvasSupport
&& (typeof document.createElement('canvas').getContext('2d').fillText == 'function');
//I'm setting this based on the fact that ExCanvas provides text support for IE
//and that as of today iPhone/iPad current text support is lame
labelType = (!nativeCanvasSupport || (textSupport && !iStuff))? 'Native' : 'HTML';
nativeTextSupport = labelType == 'Native';
useGradients = nativeCanvasSupport;
animate = !(iStuff || !nativeCanvasSupport);
})();
var Log = {
elem: false,
write: function(text){
if (!this.elem)
this.elem = document.getElementById('log');
this.elem.innerHTML = text;
this.elem.style.left = (500 - this.elem.offsetWidth / 2) + 'px';
}
};
function visualization(number){ $('#readout').empty() $('#inner-details').empty() $('#infovis').empty()
$('#genbankInfo').empty()
json = JSON.parse(unescape($(':input[name=json'+number+']').val()))
//init data
//init Sunburst
var sb = new $jit.Sunburst({
//id container for the visualization
injectInto: 'infovis',
//Distance between levels
levelDistance: 90,
//Change node and edge styles such as
//color, width and dimensions.
Node: {
overridable: true,
type: useGradients? 'gradient-multipie' : 'multipie'
},
//Select canvas labels
//'HTML', 'SVG' and 'Native' are possible options
Label: {
type: labelType
},
//Change styles when hovering and clicking nodes
NodeStyles: {
enable: true,
type: 'Native',
stylesClick: {
'color': '#000000'
},
},
//Add tooltips
Tips: {
enable: true,
onShow: function(tip, node) {
var html = " var data = node.data;
if("length" in data) {
html += "Length of feature: " + data.length + "bp";
}
if("type" in data){
html += "
Type of feature: " + data.type;
}
tip.innerHTML = html;
}
},
//implement event handlers
Events: {
enable: true,
onClick: function(node) {
if(!node) return;
//Build detailed information about the file/folder
//and place it in the right column.
var html = "" + node.name + "
", data = node.data; if("dna" in data) {
html += "Sequence:" + data.dna + "";
}
$jit.id('inner-details').innerHTML = html;
//hide tip
sb.tips.hide();
//rotate
//sb.rotate(node, animate? 'animate' : 'replot', {
//duration: 1000,
//transition: $jit.Trans.Quart.easeInOut
//});
}
},
// Only used when Label type is 'HTML' or 'SVG'
// Add text to the labels.
// This method is only triggered on label creation
onCreateLabel: function(domElement, node){
var labels = sb.config.Label.type,
aw = node.getData('length');
if (labels === 'HTML' && (node._depth < 2 || aw > 2000)) {
domElement.innerHTML = node.name;
} else if (labels === 'SVG' && (node._depth < 2 || aw > 2000)) {
domElement.firstChild.appendChild(document.createTextNode(node.name));
}
},
// Only used when Label type is 'HTML' or 'SVG'
// Change node styles when labels are placed
// or moved.
onPlaceLabel: function(domElement, node){
var labels = sb.config.Label.type;
if (labels === 'SVG') {
var fch = domElement.firstChild;
var style = fch.style;
style.display = ;
style.cursor = 'pointer';
style.fontSize = "0.8em";
fch.setAttribute('fill', "#fff");
} else if (labels === 'HTML') {
var style = domElement.style;
style.display = ;
style.cursor = 'pointer';
style.fontSize = "0.8em";
style.color = "#ddd";
var left = parseInt(style.left);
var w = domElement.offsetWidth;
style.left = (left - w / 2) + 'px';
}
}
});
//load JSON data.
sb.loadJSON(json);
//compute positions and plot.
sb.refresh();
//end
}
function addForbiddenSequences(){ forbiddenSequences.addSite('Forbidden-EcoRI','GAATTC') forbiddenSequences.addSite('Forbidden-XbaI','GAATTC') forbiddenSequences.addSite('Forbidden-SpeI','ACTAGT') forbiddenSequences.addSite('Forbidden-PstI','CTGCAG') forbiddenSequences.addSite('Forbidden-NotI','GCGGCCGC') }
var forbiddenSequences = {
forbiddenSequencesArray : {},
addSite : function(name,sequence){ forbiddenSequences.forbiddenSequencesArray[name] = sequence }, }
function checkOccurrence(target,sequence){ if (sequence.length > target.length){
if (sequence.indexOf(target) == -1){
return false
} else{
return true
}
} else{ if (target.indexOf(sequence) == -1){
return false
} else{
return true
}
} }
function randomDNA(length){ chars = 'atgc' inForbiddenSite = true while (inForbiddenSite === true){ sequence = inForbiddenSite = false for (k=0; k<length; k++) { rnum = Math.floor(Math.random() * chars.length); sequence += chars.substring(rnum,rnum+1); } for (item in forbiddenSequences.forbiddenSequencesArray){ if (checkOccurrence(sequence,forbiddenSequences.forbiddenSequencesArray[item].toLowerCase()) === false){ continue } else{ inForbiddenSite = true break } } } return sequence }
function getMethyltransferases(){
methyltransferases = new Array() sca1 = new Object() sca1.target = "AGTACT" sca1.sequence = "tccgggcgggactttggatatgtgatacagtcgtccgctgcactatggaatcgactctctacattctcacagagaggaaaagccttggacaccaggcttgcagacatcaagaaggccctggggaagccgtactacgaaacctcggatgtccttctttaccacggcgacagtcttgagctgctcaagtcaatgcctcagcagattttcgaccttaccgtaactagcccaccttacaatattggcaaagagtacgagggtgtactgtcgatcgaggaatacatttcctggtgcgagacatggatgtcgcgcgttcatagggcgaccagcgcaggcggcgcattttggctcaatgttgggtacgtccctgtcccgaaccaaggaaaagcagtcccgattccttacctcttgtgggacaagagtccgttctacatgatccaggaagttgtctggaattacggggcgggagtggcgtctcgaaaatcgttttccccgcgcaatgaaaagtttctctggtatgtgcgcgacccgctgaattattacttcgacctcgattcggtgcgcgacccaaatgtgaaataccccaaccagaaaaagaatgggaagctcaaatgcaacccgttggggaaaaatcccactgacgtttggcagttccccaaggttacgtcgggcgcgaagagatcaagcgtggagcgcaccgcccatccggcacaattcccgtctgctgtcattgaacgggtcatcaaggcgtgcagcccttccgacggcgtcatcctggacccattcctcggttccggaacgacctcgctgaccgccagaaagcaaggccggtgcagcgtcggtatcgaaatccgcgaagactacctcgacatcgcggtgggacgcctggaggcggaggcgcaatccctcttctag" sca1.description = "M.Sca1"
methyltransferases[0] = sca1 addForbiddenSequence(methyltransferases,'hasTarget')
return methyltransferases
}
function getZincFingers(){
zincFingers = new Array()
rawData = document.plasmidForm.zf.value
rawData = rawData.split('>')
rawData.reverse().pop()
rawData.reverse()
for (zf in rawData){
zfFormatted = rawData[zf].split('\n')
zfDescription = zfFormatted[0]
zfTarget = zfDescription.split('|')[5]
zfSequence =
for (i=1;i<zfFormatted.length;i++){
zfSequence+=zfFormatted[i]
}
zfObject = new Object()
zfObject.target = zfTarget
zfObject.sequence = zfSequence
zfObject.description = zfDescription
zincFingers[zf] = zfObject
}
addForbiddenSequence(zincFingers,'hasTarget')
return zincFingers
}
function getLinkers(){
linkers = new Array() linker1 = new Object() linker1.sequence = "gcacccggc" linker1.description = "Linker 1" linkers[0] = linker1
addForbiddenSequence(linkers,'noTarget')
return linkers
}
function getMycTags(){
mycTags = new Array() mycTag1 = new Object() mycTag1.sequence = "gaacagaaactcatctctgaagaggatctg" mycTag1.description = "Myc Tag 1" mycTags[0] = mycTag1 addForbiddenSequence(mycTags,'noTarget') return mycTags
}
function getTerminators(){
terminators = new Array() terminator1 = new Object() terminator1.sequence = "tcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattattt" terminator1.description = "B0014 containing BOO12 and BOO11 terminators"
terminators[0] = terminator1 addForbiddenSequence(terminators,'noTarget')
return terminators
}
function getRBS(){
rbs = new Array() rbs1 = new Object() rbs1.sequence = "tcacacaggaaag" rbs1.description = "BBa_B0032" rbs[0] = rbs1
addForbiddenSequence(rbs,'noTarget')
return rbs
}
function addForbiddenSequence(array,type){ if (type == 'hasTarget'){ for (item in array){ forbiddenSequences.addSite(array[item].description,array[item].target) } } else{ for (item in array){ forbiddenSequences.addSite(array[item].description,array[item].sequence) } }
}
function getDate(){
today = new Date()
dd = today.getDate()
mm = today.getMonth()+1
yyyy = today.getFullYear()
if(dd<10){
dd='0'+dd
}
if(mm<10){
mm='0'+mm
}
today = dd+'-'+mm.substring(0,2)+'-'+yyyy;
return today
}
function generateWhiteSpace(amount){
output =
for (i=0;i<amount;i++){
output += ' '
}
return output
}
function staticGenbank(name){ output = 'LOCUS'
output += generateWhiteSpace(16)
output += name
output += generateWhiteSpace(8)
output += memoryPlasmid.dna.length+' bp DNA '
output += generateWhiteSpace(3)
output += 'linear'
output += generateWhiteSpace(7)
output += getDate()+'\n'
output += 'DEFINITION\n'
output += 'ACCESSION\n'
output += 'VERSION\n'
output += 'SOURCE\n'
output += ' ORGANISM\n'
output += 'COMMENT\n'
output += 'FEATURES'
output += generateWhiteSpace(13)
output += 'Location/Qualifiers\n'
return output }
function genbankRestriction(targetSites){ restrictionPlasmidOutput = staticGenbank('restriction_plasmid') restrictionOrigin = memoryPlasmid.features[1].sequence for (key in targetSites){ restrictionOrigin += randomDNA(120) restrictionPlasmidOutput += generateWhiteSpace(5) restrictionPlasmidOutput += 'misc_feature' restrictionPlasmidOutput += generateWhiteSpace(5) restrictionPlasmidOutput += restrictionOrigin.length+1+'...' restrictionOrigin += targetSites[key].zincFinger restrictionPlasmidOutput += restrictionOrigin.length+'\n' restrictionPlasmidOutput += generateWhiteSpace(10) restrictionPlasmidOutput += '/label=Zinc Finger '+targetSites[key].zincFingerDescription.split('|')[0]+' target site\n' restrictionOrigin += randomDNA(120) restrictionPlasmidOutput += generateWhiteSpace(5) restrictionPlasmidOutput += 'misc_feature' restrictionPlasmidOutput += generateWhiteSpace(5) restrictionPlasmidOutput += restrictionOrigin.length+1+'...' restrictionOrigin += targetSites[key].methyltransferase restrictionPlasmidOutput += restrictionOrigin.length+'\n' restrictionPlasmidOutput += generateWhiteSpace(10) restrictionPlasmidOutput += '/label='+targetSites[key].methyltransferaseDescription+'\n' restrictionOrigin += targetSites[key].methyltransferase restrictionOrigin += randomDNA(120) restrictionPlasmidOutput += generateWhiteSpace(5) restrictionPlasmidOutput += 'misc_feature' restrictionPlasmidOutput += generateWhiteSpace(5) restrictionPlasmidOutput += restrictionOrigin.length+1+'...'+restrictionOrigin.length+'\n' restrictionPlasmidOutput += generateWhiteSpace(10) restrictionPlasmidOutput += '/label=Zinc Finger '+targetSites[key].zincFingerDescription.split('|')[0]+' target site\n'
} restrictionOrigin = restrictionOrigin.toLowerCase()
restrictionOrigin = restrictionOrigin.replace(/[atgc]{10}/g,'$& ').replace(/amp;/g,).split(' ')
pos = 1
newString =
restrictionPlasmidOutput += 'ORIGIN\n'
for (i=0;i<restrictionOrigin.length;i++){
newString = newString+' '+restrictionOrigin[i]
if ((i+1)%6===0){
whiteSpace =
for (j=0;j<9-pos.toString().length;j++){
whiteSpace+= ' '
}
newString = whiteSpace+pos + ' ' + newString
restrictionPlasmidOutput+=newString+'\n'
newString =
} else if ((i+1)%6==1){
if (i!=0){
pos+=60
}
}
}
if (restrictionOrigin.length%6 != 0){
newString =
whiteSpace =
for (j=0;j<9-pos.toString().length;j++){
whiteSpace+= ' '
}
newString+=whiteSpace+pos
for (i=0;i<(restrictionOrigin.length%6);i++){
newString+=' '+restrictionOrigin[restrictionOrigin.length-restrictionOrigin.length%6+i]
}
restrictionPlasmidOutput+=newString+'\n'
}
$('#genbankButtons').append('<input type="hidden" name="genbank-1" value="'+restrictionPlasmidOutput+'"/><input class="submit" type="submit" value="Restriction Plasmid Genbank" onclick="genbankOut(-1);return false"/>'); } function genbankOut(number){ $('#readout').empty() $('#inner-details').empty() $('#infovis').empty()
$('#genbankInfo').empty()
outString = $(':input[name=genbank'+number+']').val()
$('#genbankInfo').append('Genbank file} function genbankMemory(number){
memoryPlasmidOutput = staticGenbank('memory_plasmid')
for (item in memoryPlasmid.memoryObjects){
for (key in memoryPlasmid.memoryObjects[item]){ memoryPlasmidOutput += generateWhiteSpace(5) memoryPlasmidOutput += 'misc_feature' memoryPlasmidOutput += generateWhiteSpace(5) memoryPlasmidOutput += memoryPlasmid.memoryObjects[item][key].start+'...'+memoryPlasmid.memoryObjects[item][key].end+'\n' memoryPlasmidOutput += generateWhiteSpace(10) memoryPlasmidOutput += '/label='+memoryPlasmid.memoryObjects[item][key].description+'\n' }
}
origin = memoryPlasmid.dna
origin = origin.replace(/[atgc]{10}/g,'$& ').replace(/amp;/g,).split(' ')
pos = 1
newString =
memoryPlasmidOutput += 'ORIGIN\n'
for (i=0;i<origin.length;i++){
newString = newString+' '+origin[i]
if ((i+1)%6===0){
whiteSpace =
for (j=0;j<9-pos.toString().length;j++){
whiteSpace+= ' '
}
newString = whiteSpace+pos + ' ' + newString
memoryPlasmidOutput+=newString+'\n'
newString =
} else if ((i+1)%6==1){
if (i!=0){
pos+=60
}
}
}
if (origin.length%6 != 0){
newString =
whiteSpace =
for (j=0;j<9-pos.toString().length;j++){
whiteSpace+= ' '
}
newString+=whiteSpace+pos
for (i=0;i<(origin.length%6);i++){
newString+=' '+origin[origin.length-origin.length%6+i]
}
memoryPlasmidOutput+=newString+'\n'
}
$('#genbankButtons').append('<input type="hidden" name="genbank'+number+'" value="'+memoryPlasmidOutput+'"/><input class="submit" type="submit" value="Sensory Plasmid Genbank '+(number+1)+'" onclick="genbankOut('+number+');return false"/>');
}
function formatPlasmidInput(backbone){
backbone = backbone.split('\n')
originBoolean = false
backboneName =
sequence =
if (backbone[0].toLowerCase().indexOf('locus') != -1){
for (i=0;i<backbone.length;i++){
if (originBoolean === true){
if (backbone[i].indexOf('//') == -1){
appendThis = backbone[i].replace(/[0-9]|\s|\n|\t/g,)
sequence = sequence+appendThis
} else{
originalBoolean = false
}
}
if (backbone[i].indexOf('locus') != -1){
backboneName = backbone[i].split(/\s+|\t+/g)[1]
}
if (backbone[i].indexOf('origin') != -1){
originBoolean = true
}
}
} else if (backbone[0][0] == '>'){
for (i=0;i<backbone.length;i++){
if (backbone[i][0] != '>'){
appendThis = backbone[i].replace(/[0-9]|\s|\n|\t/g,)
sequence = sequence+appendThis
} else{
backboneName = backbone[i].replace('>',)
}
}
}
memoryPlasmid.addFeature(1,sequence.length,'Backbone',sequence,backboneName,)
return sequence
}
function feature(start,end,type,sequence,description,featureObject){ this.start = start; this.end = end; this.type = type;
this.sequence = sequence; this.description = description;
this.featureObject = featureObject }
var restrictionPlasmid = { backboneName : , dna : , features : {},
setBackboneName : function(backboneName){
restrictionlasmid.backboneName = backboneName
},
setDNA : function(dna){ restrictionPlasmid.dna = dna }, addFeature : function(start,end,type,sequence,description){ restrictionPlasmid.features[start] = new feature(start,end,type,sequence,description) }, addRecognitionAreaObject : function(zfTarget,mtaseTarget){
recognitionPlasmid.zfTarget = zfTarget recognitionPlasmid.mtaseTarget = mtaseTarget } }
var memoryPlasmid = {
backboneName : ,
dna : , features : {}, memoryObjects : {},
setBackboneName : function(backboneName){
memoryPlasmid.backboneName = backboneName
},
setDNA : function(dna){ memoryPlasmid.dna = dna }, addMemoryObject : function(sensor,rbs,zincFinger,linker,mycTag,methyltransferase,terminator){ memoryObject = new Object() memoryObject.sensor = sensor memoryObject.rbs = rbs memoryObject.zincFinger = zincFinger memoryObject.linker = linker memoryObject.mycTag = mycTag memoryObject.methyltransferase = methyltransferase memoryObject.terminator = terminator memoryPlasmid.memoryObjects[sensor.start] = memoryObject }, addFeature : function(start,end,type,sequence,description){ memoryPlasmid.features[start] = new feature(start,end,type,sequence,description) } }
function sensorObject(name,sequence){
this.name = name
this.sequence = sequence
}
function formatSensors(sensors){
sensorArray = new Array()
if (sensors.indexOf('LOCUS') != -1){
sensors = sensors.split('LOCUS')
sensors.reverse().pop()
for (i=0;i<sensors.length;i++){
originBoolean = false
sensorName =
sequence =
sensor = sensors[i].split('\n')
for (j=0;j<sensor.length;j++){
if (j===0){
sensorName = sensor[j]
}
if (originBoolean === true){
if (sensor[j].indexOf('//') == -1){
appendThis = sensor[j].replace(/[0-9]|\s|\n|\t/g,)
sequence += appendThis
} else {
originBoolean = false
}
}
if (sensor[j].indexOf('ORIGIN') != -1){
originBoolean = true
}
}
sensorArray[i] = new sensorObject(sensorName,sequence)
}
} else if (sensors[0] == '>'){
sensors = sensors.split('//')
sensors.pop()
sensorName =
for (i=0;i<sensors.length;i++){
sensor = sensors[i].split('\n')
sequence =
for (j=0;j<sensor.length;j++){
if (sensor[j][0] != '>'){
appendThis = sensor[j].replace(/[0-9]|\s|\n|\t/g,)
sequence = sequence+appendThis
} else if (sensor[j][0] == '>'){
sensorName = sensor[j].replace('>',)
}
}
sensorArray[i] = new sensorObject(sensorName,sequence)
}
}
return sensorArray
}
function reset(){
$('#readout').empty()
$('#inner-details').empty() $('#infovis').empty()
$('#genbankInfo').empty()
$('#genbankButtons').empty()
$('#visualizationButtons').empty()
$('input[type=checkbox]').each(function() {
this.checked = false;
});
} function formatPartsregistryPromoters(){
promoters = new Array()
$("input:checkbox[name=promoter]:checked").each(function(){
promoter = $(this).val().split(':')
promoters.push(new sensorObject(promoter[0],promoter[2]))
})
return promoters
}
function configuratePlasmid(sensorArray,number){ memoryPlasmid.features = {} memoryPlasmid.memoryObjects = {}
backbone = document.plasmidForm.plasmid.value.toLowerCase()
methyltransferases = getMethyltransferases()
zincFingers = getZincFingers()
linkers = getLinkers()
mycTags = getMycTags()
rbs = getRBS()
terminators = getTerminators()
plasmidSequence = formatPlasmidInput(backbone)
memoryPlasmid.setDNA(plasmidSequence)
for (i=0;i<sensorArray.length;i++){
featureArray = new Array() featureArray[0] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+sensorArray[i].sequence.length,'Sensor',sensorArray[i].sequence,sensorArray[i].name,sensorArray[i])
memoryPlasmid.setDNA(memoryPlasmid.dna+sensorArray[i].sequence)
j = Math.floor((Math.random()*rbs.length))
featureArray[1] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+rbs[j].sequence.length,'RBS',rbs[j].sequence,rbs[j].description,rbs[j])
memoryPlasmid.setDNA(memoryPlasmid.dna+rbs[j].sequence+randomDNA(3))
memoryPlasmid.setDNA(memoryPlasmid.dna+'atg'+randomDNA(10))
for (j=0;j<zincFingers.length;j++){
if (checkOccurrence(zincFingers[j].target.toLowerCase(),memoryPlasmid.dna) === true || checkOccurrence(zincFingers[j].sequence.toLowerCase(),memoryPlasmid.dna) === true){
continue
} else{
featureArray[2] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+zincFingers[j].sequence.length,'Zinc Finger',zincFingers[j].sequence,'Zinc Finger '+zincFingers[j].description.split('|')[0],zincFingers[j])
memoryPlasmid.setDNA(memoryPlasmid.dna+zincFingers[j].sequence)
break
}
}
j = Math.floor((Math.random()*linkers.length))
featureArray[3] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+linkers[j].sequence.length,'Linker',linkers[j].sequence,linkers[j].description,linkers[j])
memoryPlasmid.setDNA(memoryPlasmid.dna+linkers[j].sequence)
j = Math.floor((Math.random()*mycTags.length))
featureArray[4] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+mycTags[j].sequence.length,'Myc Tag',mycTags[j].sequence,mycTags[j].description,mycTags[j])
memoryPlasmid.setDNA(memoryPlasmid.dna+mycTags[j].sequence)
j = Math.floor((Math.random()*methyltransferases.length))
featureArray[5] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+methyltransferases[j].sequence.length,'Methyltransferase',methyltransferases[j].sequence,methyltransferases[j].description,methyltransferases[j])
memoryPlasmid.setDNA(memoryPlasmid.dna+methyltransferases[j].sequence)
j = Math.floor((Math.random()*terminators.length))
featureArray[6] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+terminators[j].sequence.length,'Terminator',terminators[j].sequence,terminators[j].description,terminators[j])
memoryPlasmid.setDNA(memoryPlasmid.dna+terminators[j].sequence+randomDNA(10))
memoryPlasmid.addMemoryObject(featureArray[0],featureArray[1],featureArray[2],featureArray[3],featureArray[4],featureArray[5],featureArray[6])
} restrictionPlasmid.setDNA(memoryPlasmid.features[1].sequence) for (item in memoryPlasmid.memoryObjects){ featureArray = new Array() mtaseStart = restrictionPlasmid.dna.length+1 mtaseEnd = restrictionPlasmid.dna.length+memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.target.length mtaseType = 'Restriction Site' mtaseTarget = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.target.toLowerCase() mtaseDescription = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.description+' restriction site' featureArray[0] = new feature(mtaseStart,mtaseEnd,mtaseType,mtaseTarget,mtaseDescription) restrictionPlasmid.setDNA(restrictionPlasmid.dna+mtaseTarget) zfStart = restrictionPlasmid.dna.length+1 zfEnd = restrictionPlasmid.dna.length+memoryPlasmid.memoryObjects[item].zincFinger.featureObject.target.length zfType = 'Restriction Site' zfTarget = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.target zfDescription = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.description+' restriction site' featureArray[1] = new feature(zfStart,zfEnd,zfType,zfTarget,zfDescription) restrictionPlasmid.setDNA(restrictionPlasmid.dna+mtaseTarget) restrictionPlasmid.mtaseTarget = featureArray[0] restrictionPlasmid.zfTarget = featureArray[1] } json = createJSONMemory(number) genbankMemory(number) $('#visualizationButtons').append('<input type="hidden" name="json'+number+'" value="'+escape(JSON.stringify(json))+'"/><input class="submit" type="submit" value="Sensory Plasmid Visualization '+(number+1)+'" onclick="visualization('+number+');return false"/>'); }
function setup(){ $('#visualizationButtons').empty() $('#infovis').empty() $('#readout').empty() $('#genbankButtons').empty() $('#inner-details').empty()
$('#genbankInfo').empty()
addForbiddenSequences() sensors = document.plasmidForm.sensors.value.toLowerCase() sensorArray = formatSensors(sensors)
promoters = formatPartsregistryPromoters()
sensorArray = promoters.concat(sensorArray)
tempArray = new Array() j = 0 number = 0 targetSites = new Array() for (sensor in sensorArray){ tempArray[j] = sensorArray[sensor] j++ if (j%5 === 0 && j !== 0){
configuratePlasmid(tempArray,number) number++ tempArray = new Array() j = 0 for (item in memoryPlasmid.memoryObjects){ site = new Object() site.zincFingerDescription = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.description site.zincFinger = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.target site.zincFingerLength = site.zincFinger.length site.methyltransferaseDescription = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.description site.methyltransferase = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.target site.methyltransferaseLength = site.methyltransferase.length site.sensor = memoryPlasmid.memoryObjects[item].sensor.description targetSites.push(site)
}
}
}
if (j%5 !== 0){
configuratePlasmid(tempArray,number)
for (item in memoryPlasmid.memoryObjects){
site = new Object()
site.zincFingerDescription = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.description
site.zincFinger = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.target
site.zincFingerLength = site.zincFinger.length
site.methyltransferaseDescription = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.description
site.methyltransferase = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.target
site.methyltransferaseLength = site.methyltransferase.length
site.sensor = memoryPlasmid.memoryObjects[item].sensor.description
targetSites.push(site)
}
}
genbankRestriction(targetSites)
json = createJSONRestriction(targetSites)
$('#visualizationButtons').append('<input type="hidden" name="json-1" value="'+escape(JSON.stringify(json))+'"/><input class="submit" type="submit" value="Restriction Plasmid Visualization" onclick="visualization(-1);return false"/>');
$('#visualizationButtons').append('
Fill in the underlying form with your band sizes, seperated by a comma, to see which sensor-specific methyltransferases have been cut
<input type="textfield" name="readout" value=""/><input class="submit" type="submit" value="Readout" onClick="getReadout();return false"/>');
}
function getReadout(){ $('#readout').empty() $('#inner-details').empty() $('#infovis').empty()
$('#genbankInfo').empty()
inputArray = new Array() json = JSON.parse(unescape($(':input[name=json-1]').val())) inputs = $(':input[name=readout]').val() inputArray = inputs.split(',') totalLength = json.children[0].data.length uncutArray = new Array() i = 0 for (child in json.children){ if (child != 0){ totalLength+=json.children[child].data.length if (json.children[child].data.description.indexOf('Methyltransferase') != -1){ uncutArray[i] = [json.children[child].id,totalLength] i++ } } } bandsArray = new Array () j = 0 for (item in uncutArray){ i = 0 tempBandArray = new Array() tempBandArray[i] = [uncutArray[item][1],uncutArray[item][0]]
i++ for (bandArray in bandsArray){ for (band in bandsArray[bandArray]){ tempBandArray[i] = [uncutArray[item][1] - bandsArray[bandArray][band][0],uncutArray[item][0]] i++ } } bandsArray[j] = tempBandArray j++ } matchingBands = new Array() i = 0 for (input in inputArray){ difference = 100000000000 bandSize = inputArray[input] for (bandArray in bandsArray){ for (band in bandsArray[bandArray]){ if (bandSize > bandsArray[bandArray][band][0]){ tempDifference = bandSize - bandsArray[bandArray][band][0] } else{ tempDifference = bandsArray[bandArray][band][0] - bandSize } if (tempDifference < difference){ matchingBand = bandsArray[bandArray][band][1] difference = tempDifference } } } matchingBands[i] = matchingBand i++ } i = 0 sensedSignals = new Array() for (matchingBand in matchingBands){ for (child in json.children){ if (json.children[child].id == matchingBands[matchingBand]){ sensedSignals[i] = json.children[child].data.sensor i++ } }
}
outString =
for (signal in sensedSignals){
outString += sensedSignals[signal]+'
'
}
if (outString != ){
<font size="3">'+outString+'</font>')
}
}
function createJSONRestriction(targetSites){ json = {
"children": [],
"data": {
"$type": "none",
},
"id": "Source",
"name": "Memory Plasmid"
};
json.children[0] = {} json.children[0].data = {} json.children[0].data.description = memoryPlasmid.features[1].description json.children[0].data.$color = '#B2ABF4' json.children[0].data.length = memoryPlasmid.features[1].end - memoryPlasmid.features[1].start json.children[0].data.$angularWidth = 10000 json.children[0].data.type = memoryPlasmid.features[1].type json.children[0].data.dna = memoryPlasmid.dna json.children[0].children = [] json.children[0].name = memoryPlasmid.features[1].description json.children[0].id = memoryPlasmid.features[1].description totalLength = memoryPlasmid.dna.length i = 1 for (item in targetSites){ site = targetSites[item] json.children[i] = {} json.children[i].data = {} json.children[i].children = [] json.children[i].data.description = '120bp random DNA' json.children[i].data.$color = '#FFFF00' json.children[i].data.length = 120 json.children[i].data.$angularWidth = 1000 json.children[i].data.dna = randomDNA(120+i*10) json.children[i].name = '120bp DNA' json.children[i].id = i i++ json.children[i] = {} json.children[i].data = {} json.children[i].children = [] json.children[i].data.description = site.zincFingerDescription json.children[i].data.$color = '#FF0000' json.children[i].data.length = site.zincFingerLength json.children[i].data.$angularWidth = 1000 json.children[i].data.dna = site.zincFinger json.children[i].name = site.zincFingerDescription.split('|')[0]+'|'+site.zincFingerDescription.split('|')[1] json.children[i].id = i i++ json.children[i] = {} json.children[i].data = {} json.children[i].children = [] json.children[i].data.description = '120bp random DNA' json.children[i].data.$color = '#FFFF00' json.children[i].data.length = 120 json.children[i].data.$angularWidth = 1000 json.children[i].data.dna = randomDNA(120) json.children[i].name = '120bp DNA' json.children[i].id = i i++ json.children[i] = {} json.children[i].data = {} json.children[i].children = [] json.children[i].data.description = 'Methyltransferase: '+site.methyltransferaseDescription json.children[i].data.$color = '#0000CD' json.children[i].data.length = site.methyltransferaseLength json.children[i].data.$angularWidth = 1000 json.children[i].data.dna = site.methyltransferase json.children[i].data.sensor = site.sensor json.children[i].name = site.methyltransferaseDescription.split('|')[0] json.children[i].id = i i++ json.children[i] = {} json.children[i].data = {} json.children[i].children = [] json.children[i].data.description = '120bp random DNA' json.children[i].data.$color = '#FFFF00' json.children[i].data.length = 120 json.children[i].data.$angularWidth = 1000 json.children[i].data.dna = randomDNA(120) json.children[i].name = '120bp DNA' json.children[i].id = i i++ json.children[i] = {} json.children[i].data = {} json.children[i].children = [] json.children[i].data.description = site.zincFingerDescription json.children[i].data.$color = '#FF0000' json.children[i].data.length = site.zincFingerLength json.children[i].data.$angularWidth = 1000 json.children[i].data.dna = site.zincFinger json.children[i].name = site.zincFingerDescription.split('|')[0]+'|'+site.zincFingerDescription.split('|')[1] json.children[i].id = i i++ } return json }
function createJSONMemory(number){ var json = {} json = {
"children": [],
"data": {
"$type": "none",
},
"id": "Source",
"name": "Sensory Plasmid"
};
json.children[0] = {} json.children[0].data = {} json.children[0].data.description = memoryPlasmid.features[1].description json.children[0].data.$color = '#B2ABF4' json.children[0].data.length = memoryPlasmid.features[1].end - memoryPlasmid.features[1].start json.children[0].data.$angularWidth = 10000 json.children[0].data.type = memoryPlasmid.features[1].type json.children[0].data.dna = memoryPlasmid.dna json.children[0].children = [] json.children[0].name = memoryPlasmid.features[1].description json.children[0].id = memoryPlasmid.features[1].description
i = 1
for (memoryObject in memoryPlasmid.memoryObjects){
for (item in memoryPlasmid.memoryObjects[memoryObject]){ json.children[i] = {} json.children[i].children = [] json.children[i].data = {} json.children[i].data.description = memoryPlasmid.memoryObjects[memoryObject][item].description type = memoryPlasmid.memoryObjects[memoryObject][item].type if (type == 'Sensor'){ color = '#00FFFF' } else if (type == 'RBS'){ color = '#FFFF00' } else if (type == 'Zinc Finger'){ color = '#800080' } else if (type == 'Linker'){ color = '#00FF00' } else if (type == 'Myc Tag'){ color = '#FF00FF' } else if (type == 'Methyltransferase'){ color = '#FFA500' } else if (type == 'Terminator'){ color = '#FF0000' } else{ color = '#B2ABF4' } json.children[i].data.$color = color json.children[i].data.length = memoryPlasmid.memoryObjects[memoryObject][item].end - memoryPlasmid.memoryObjects[memoryObject][item].start json.children[i].data.$angularWidth = 1000 json.children[i].data.type = type json.children[i].data.dna = memoryPlasmid.memoryObjects[memoryObject][item].sequence json.children[i].id = i if (memoryPlasmid.memoryObjects[memoryObject][item].description.length > 14){ json.children[i].name = memoryPlasmid.memoryObjects[memoryObject][item].description.substring(0,14) } else{ json.children[i].name = memoryPlasmid.memoryObjects[memoryObject][item].description } i++ } } return json
//end
}
