Team:Amsterdam/maarten/

From 2012.igem.org

(Difference between revisions)

Revision as of 18:39, 3 September 2012

Parts registry sensors: Madras
BBa_K086017	BBa_K086018	BBa_K086019	BBa_K086020	BBa_K086021
BBa_K086022	BBa_K086023	BBa_K086024	BBa_K086025	BBa_K086026
BBa_K086027	BBa_K086028	BBa_K086029	BBa_K086030	BBa_K086031
BBa_K086032	BBa_K086033

Parts registry sensors: Phage
BBa_I712074	BBa_I719005	BBa_J34814	BBa_J64997	BBa_J64998
BBa_K113010	BBa_K113011	BBa_K113012	BBa_K525998	BBa_R0085
BBa_R0180	BBa_R0181	BBa_R0182	BBa_R0183	BBa_R0184
BBa_R0185	BBa_R0186	BBa_R0187	BBa_Z0251	BBa_Z0252
BBa_Z0253

Parts registry sensors: Metal sensitive
BBa_I721001	BBa_I731004	BBa_I760005	BBa_I765000	BBa_I765007
BBa_J3902

Parts registry sensors: Cell signalling
BBa_I1051	BBa_I14015	BBa_I14016	BBa_I14017	BBa_I739105
BBa_I746104	BBa_I751501	BBa_I751502	BBa_I761011	BBa_J06403
BBa_J102001	BBa_J64000	BBa_J64010	BBa_J64067	BBa_J64712
BBa_K091107	BBa_K091117	BBa_K091143	BBa_K091146	BBa_K091156
BBa_K091157	BBa_K145150	BBa_K266000	BBa_K266005	BBa_K266006
BBa_K266007	BBa_K658006	BBa_K658007	BBa_K658008	BBa_R0061
BBa_R0062	BBa_R0063	BBa_R0071	BBa_R0078	BBa_R0079
BBa_R1062

@@ Line 5: / Line 5: @@
 <html>
 <head>
-<link rel="stylesheet" type="text/css" href="style.css" />
 <script type="text/javascript" src="jquery-1.2.3.min.js"></script>
-<link type="text/css" href="css/base.css" rel="stylesheet" />
-<link type="text/css" href="css/Sunburst.css" rel="stylesheet" />
-<script language="javascript" type="text/javascript" src="jit.js"></script>
 <script type='text/javascript'>
@@ Line 37: / Line 33: @@
 };
-function visualization(number){
-	$('#infovis').empty()
+function init(json){
-	json = JSON.parse(unescape($(':input[name=json'+number+']').val()))
      //init data
      //init Sunburst
@@ Line 63: / Line 58: @@
            type: 'Native',
            stylesClick: {
-             'color': '#000000'
+             'color': '#33dddd'
            },
          },
@@ Line 70: / Line 65: @@
            enable: true,
            onShow: function(tip, node) {
-             var html = "<div class=\"tip-title\">" + node.data.description + "</div>";
+             var html = "<div class=\"tip-title\">" + node.name + "</div>";
              var data = node.data;
              if("length" in data) {
@@ Line 89: / Line 84: @@
              //and place it in the right column.
              var html = "<h4>" + node.name + "</h4>", data = node.data;
-             if("dna" in data) {
-               html += "<br /><br /><b>Sequence:</b><br /><pre>" + data.dna + "</pre>";
+             if("description" in data) {
+               html += "<br /><br /><b>Last commit was:</b><br /><pre>" + data.description + "</pre>";
              }
              $jit.id('inner-details').innerHTML = html;
@@ Line 96: / Line 92: @@
              sb.tips.hide();
              //rotate
-             //sb.rotate(node, animate? 'animate' : 'replot', {
+             sb.rotate(node, animate? 'animate' : 'replot', {
-               //duration: 1000,
+               duration: 1000,
-               //transition: $jit.Trans.Quart.easeInOut
+               transition: $jit.Trans.Quart.easeInOut
-             //});
+             });
            }
          },
@@ Line 107: / Line 103: @@
          onCreateLabel: function(domElement, node){
            var labels = sb.config.Label.type,
-               aw = node.getData('length');
+               aw = node.getData('angularWidth');
            if (labels === 'HTML' && (node._depth < 2 || aw > 2000)) {
              domElement.innerHTML = node.name;
@@ Line 353: / Line 349: @@
 }
-function genbankRestriction(targetSites){
+function genbank(){
+        memoryPlasmidOutput = staticGenbank('memory_plasmid')
+        for (item in memoryPlasmid.memoryObjects){
+		    for (key in memoryPlasmid.memoryObjects[item]){
+				memoryPlasmidOutput += generateWhiteSpace(5)
+				memoryPlasmidOutput += 'misc_feature'
+				memoryPlasmidOutput += generateWhiteSpace(5)
+				memoryPlasmidOutput += memoryPlasmid.memoryObjects[item][key].start+'...'+memoryPlasmid.memoryObjects[item][key].end+'<br>'
+				memoryPlasmidOutput += generateWhiteSpace(10)
+				memoryPlasmidOutput += '/label='+memoryPlasmid.memoryObjects[item][key].description+'<br>'
+			}
+        }
+        origin = memoryPlasmid.dna
+        origin = origin.replace(/[atgc]{10}/g,'$& ').replace(/amp;/g,'').split(' ')
+        pos = 1
+        newString = ''
+        memoryPlasmidOutput += 'ORIGIN<br>'
+        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+= '&nbsp;'
+                 }
+                 newString = whiteSpace+pos + ' ' + newString
+                 memoryPlasmidOutput+=newString+'<br>'
+                 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+= '&nbsp;'
+            }
+            newString+=whiteSpace+pos
+            for (i=0;i<(origin.length%6);i++){
+                newString+=' '+origin[origin.length-origin.length%6+i]
+            }
+            memoryPlasmidOutput+=newString+'<br>'
+        }
 		restrictionPlasmidOutput = staticGenbank('restriction_plasmid')
+		targetSites = new Array()
+		for (item in memoryPlasmid.memoryObjects){
+		    site = new Object()
+			site.zincFinger = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.target
+			site.methyltransferase = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.target
+            targetSites[item-1] = site
+        }
 		restrictionOrigin = memoryPlasmid.features[1].sequence
 		for (key in targetSites){
@@ Line 406: / Line 454: @@
              restrictionPlasmidOutput+=newString+'<br>'
          }
+        myWindow=window.open()
+        myWindow.document.write(memoryPlasmidOutput)
+        myWindow.focus()
 		restrictionSiteWindow = window.open()
 		restrictionSiteWindow.document.write(restrictionPlasmidOutput)
 		restrictionSiteWindow.focus()
-}
-function genbankMemory(){
-        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+'<br>'
-				memoryPlasmidOutput += generateWhiteSpace(10)
-				memoryPlasmidOutput += '/label='+memoryPlasmid.memoryObjects[item][key].description+'<br>'
-			}
-        }
-        origin = memoryPlasmid.dna
-        origin = origin.replace(/[atgc]{10}/g,'$& ').replace(/amp;/g,'').split(' ')
-        pos = 1
-        newString = ''
-        memoryPlasmidOutput += 'ORIGIN<br>'
-        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+= '&nbsp;'
-                 }
-                 newString = whiteSpace+pos + ' ' + newString
-                 memoryPlasmidOutput+=newString+'<br>'
-                 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+= '&nbsp;'
-            }
-            newString+=whiteSpace+pos
-            for (i=0;i<(origin.length%6);i++){
-                newString+=' '+origin[origin.length-origin.length%6+i]
-            }
-            memoryPlasmidOutput+=newString+'<br>'
-        }
-        myWindow=window.open()
-        myWindow.document.write(memoryPlasmidOutput)
-        myWindow.focus()
 }
@@ Line 643: / Line 642: @@
                      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])
+                     featureArray[2] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+zincFingers[j].sequence.length,'Zinc Finger',zincFingers[j].sequence,zincFingers[j].description,zincFingers[j])
                      memoryPlasmid.setDNA(memoryPlasmid.dna+zincFingers[j].sequence)
                      break
@@ Line 682: / Line 681: @@
 			restrictionPlasmid.zfTarget = featureArray[1]
 		}
-		json = createJSONMemory(number)
+		//genbank()
-		//genbankMemory()
+		json = createJSON()
-		$('#visualizationButtons').append('<input type="hidden" name="json'+number+'" value="'+escape(JSON.stringify(json))+'"/><input class="submit" type="submit" value="Memory Plasmid '+(number+1)+'" onclick="visualization('+number+');return false"/>');
+		init(json)
 		}
 function setup(){
-		$('#visualizationButtons').empty()
-		$('#infovis').empty()
-		$('#readout').empty()
 		addForbiddenSequences()
 		sensors = document.plasmidForm.sensors.value.toLowerCase()
@@ Line 699: / Line 695: @@
 		j = 0
 		number = 0
-		targetSites = new Array()
 		for (sensor in sensorArray){
 			tempArray[j] = sensorArray[sensor]
@@ Line 708: / Line 703: @@
 				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" onclick="visualization(-1);return false"/>');
-		$('#readout').append('<input type="textfield" name="readout" value=""/><input class="submit" type="submit" value="Submit" onClick="getReadout();return false"/>');
 }
-function getReadout(){
+function createJSON(){
-	inputArray = new Array()
+	var json = {
-	json = JSON.parse(unescape($(':input[name=json-1]').val()))
+    "children": [
-	inputs = $(':input[name=readout]').val()
+       {
-	inputArray = inputs.split(',')
+         "children": [],
-	totalLength = json.children[0].data.length
+         "data": {
-	uncutArray = new Array()
+           "description": "Fixed polar interpolation problem when theta = pi",
-	i = 0
+           "$color": "#B0AAF6",
-	for (child in json.children){
+           "$angularWidth": 1000,
-		totalLength+=json.children[child].data.length
+         },
-		if (json.children[child].data.description.indexOf('Methyltransferase') != -1){
+         "id": "Source/Coordinates",
-			uncutArray[i] = [json.children[child].id,totalLength]
+         "name": "Backbone"
-			i++
+       },
-		}
+       {
-	}
+         "children": [],
-	bandsArray = new Array ()
+         "data": {
-	j = 0
+           "description": "Memory part",
-	for (item in uncutArray){
+           "$color": "#B2ABF4",
-		i = 0
+           "$angularWidth": 1000,
-		tempBandArray = new Array()
+         },
-		tempBandArray[i] = [uncutArray[item][1],uncutArray[item][0]]
+         "id": "Source/Core",
-		i++
+         "name": "Memory part"
-		for (bandArray in bandsArray){
+       },
-			for (band in bandsArray[bandArray]){
-				tempBandArray[i] = [uncutArray[item][1] - bandsArray[bandArray][band][0],uncutArray[item][0]]
+     ],
-				i++
+     "data": {
-			}
+       "$type": "none"
-		}
+     },
-		bandsArray[j] = tempBandArray
+     "id": "Source",
-		j++
+     "name": "Plasmid"
-	}
+   };
-	matchingBands = new Array()
+	json.children[0].children[0] = {}
-	i = 0
+	json.children[0].children[0].data = {}
-	for (input in inputArray){
+	json.children[0].children[0].data.description = memoryPlasmid.features[1].description
-		difference = 100000000000
+	json.children[0].children[0].data.$color = '#B2ABF4'
-		bandSize = inputArray[input]
+	json.children[0].children[0].data.length = memoryPlasmid.features[1].end - memoryPlasmid.features[1].start
-		for (bandArray in bandsArray){
+	json.children[0].children[0].data.$angularWidth = 1000
-			for (band in bandsArray[bandArray]){
+	json.children[0].children[0].data.type = memoryPlasmid.features[1].type
-				if (bandSize > bandsArray[bandArray][band][0]){
+	json.children[0].children[0].children = []
-					tempDifference = bandSize - bandsArray[bandArray][band][0]
+	json.children[0].children[0].name = memoryPlasmid.features[1].description
-				} else{
+	json.children[0].children[0].id = memoryPlasmid.features[1].description
-					tempDifference = bandsArray[bandArray][band][0] - bandSize
+     i = 0
-				}
+   for (memoryObject in memoryPlasmid.memoryObjects){
-				if (tempDifference < difference){
+		for (feature in memoryPlasmid.memoryObjects[memoryObject]){
-					matchingBand = bandsArray[bandArray][band][1]
+			json.children[1].children[i] = []
-					difference = tempDifference
+			json.children[1].children[i].data = {}
-				}
+			json.children[1].children[i].data.description = memoryPlasmid.memoryObjects[memoryObject][feature].description
-			}
+			type = memoryPlasmid.memoryObjects[memoryObject][feature].type
-		}
+			color = '#B2ABF4'
-		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++
-			}
-		}
-	}
-	for (signal in sensedSignals){
-		$('#readout').append('<br>'+sensedSignals[signal])
-	}
-}
-function createJSONRestriction(targetSites){
-	json = {
-      "children": [],
-      "data": {
-        "$type": "none",
-      },
-      "id": "Source",
-      "name": "Restriction 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 = 1000
-	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": {
-        "$type": "none",
-      },
-      "id": "Source",
-      "name": "Memory Plasmid"
-    };
-	json.children[0] = {}
-	json.children[0].data = {}
-	json.children[0].data.description = memoryPlasmid.features[1].description
-	json.children[0].data.$color = '#B2ABF4'
-	json.children[0].data.length = memoryPlasmid.features[1].end - memoryPlasmid.features[1].start
-	json.children[0].data.$angularWidth = 1000
-	json.children[0].data.type = memoryPlasmid.features[1].type
-	json.children[0].data.dna = memoryPlasmid.dna
-	json.children[0].children = []
-	json.children[0].name = memoryPlasmid.features[1].description
-	json.children[0].id = memoryPlasmid.features[1].description
-     i = 1
-    for (memoryObject in memoryPlasmid.memoryObjects){
-		for (item in memoryPlasmid.memoryObjects[memoryObject]){
-			json.children[i] = {}
-			json.children[i].children = []
-			json.children[i].data = {}
-			json.children[i].data.description = memoryPlasmid.memoryObjects[memoryObject][item].description
-			type = memoryPlasmid.memoryObjects[memoryObject][item].type
 			if (type == 'Sensor'){
 				color = '#00FFFF'
@@ Line 951: / Line 776: @@
 				color = '#B2ABF4'
 			}
-			json.children[i].data.$color = color
+			json.children[1].children[i].data.$color = color
-			json.children[i].data.length = memoryPlasmid.memoryObjects[memoryObject][item].end - memoryPlasmid.memoryObjects[memoryObject][item].start
+			json.children[1].children[i].data.length = memoryPlasmid.memoryObjects[memoryObject][feature].end - memoryPlasmid.memoryObjects[memoryObject][feature].start
-			json.children[i].data.$angularWidth = 1000
+			json.children[1].children[i].data.$angularWidth = 1000
-			json.children[i].data.type = type
+			json.children[1].children[i].data.type = type
-			json.children[i].data.dna = memoryPlasmid.memoryObjects[memoryObject][item].sequence
+			json.children[1].children[i].id = i
-			json.children[i].id = i
+			json.children[1].children[i].name = memoryPlasmid.memoryObjects[memoryObject][feature].description
-			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
+   return json
      //end
 }
@@ Line 975: / Line 794: @@
 <div id="main-content">
 {{Team:Amsterdam/toolForm}}
+<div id="infovis"></div>
 </div>
 {{Team:Amsterdam/Foot}}