2b:null 2c:["$","title",null,{"children":"plotorf | Coornaert David | Observable"}] 31:T468,myda={ var orfbox=[] var unfinished=[] var ends=[] var starts=[] var start=0 var started=true var fra=parseInt(frame) function isstop(i) { if (stop.has(seq.slice(i,i+3))) {return true} return false} function isstart(i) {return seq.slice(i,i+3)=="atg"} function risstop(i) { if (rstop.has(seq.slice(i,i+3))) {return true} return false} function risstart(i) {return seq.slice(i,i+3)=="cat"} if (fra<=2) { var starts=[0] for (var i=fra;id>s)) if(r>=ls) {unfinished.push([s,ls-s])} else { orfbox.push([s,r-s])}} } if (fra>=3) { var starts=[ls] for (var i=fra-3;idp[0]*width/ls)\n .attr(\"y\",35)\n .attr(\"width\",p=>p[1]*width/ls)\n .attr(\"height\",30)\n svg.append(\"g\")\n .attr(\"fill\",\"green\")\n .selectAll(\"rect\")\n .data(myda[1])\n .join(\"rect\")\n .attr(\"x\",p=>p[0]*width/ls)\n .attr(\"y\",35)\n .attr(\"width\",p=>p[1]*width/ls)\n .attr(\"height\",30)\n svg.append(\"g\")\n .attr(\"fill\",\"red\")\n .selectAll(\"rect\")\n .data(myda[2])\n .join(\"rect\")\n .attr(\"x\",p=>p*width/ls)\n .attr(\"y\",33)\n .attr(\"width\",1)\n .attr(\"height\",32)\n svg.append(\"g\")\n .attr(\"fill\",\"black\")\n .selectAll(\"rect\")\n .data(myda[3])\n .join(\"rect\")\n .attr(\"x\",p=>p*width/ls)\n .attr(\"y\",35)\n .attr(\"width\",1)\n .attr(\"height\",32)\n return svg.node();\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":108,"value":"viewof frame = radio({\n title: 'Frame ?',\n description: 'Please select the frame you want to see',\n options: [\n { label: '+1', value: 0 },\n { label: '+2', value: 1 },\n { label: '+3', value: 2 },\n { label: '-1', value: 3 },\n { label: '-2', value: 4 },\n { label: '-3', value: 5 },\n ],\n value: 0\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":439,"value":"md`**Blue bars**: possible proteins extents\n**Green bars**: unfinished/unstarted possible proteins\n**Red Ticks**: Methionine residues (start codons)\n**Black ticks**: Stop Codons`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":279,"value":"chart = {\n const svg = d3.create(\"svg\")\n .attr(\"viewBox\", [0, 0, ls, 250]);\n svg.append(\"g\")\n .attr(\"fill\", \"steelblue\")\n .selectAll(\"rect\")\n .data(myda[0])\n .join(\"rect\")\n .attr(\"x\", p=>p[0])\n .attr(\"y\", 90)\n .attr(\"height\", 80)\n .attr(\"width\", p=>p[1]);\n svg.append(\"g\")\n .attr(\"fill\", \"green\")\n .selectAll(\"rect\")\n .data(myda[1])\n .join(\"rect\")\n .attr(\"x\", p=>p[0])\n .attr(\"y\", 90)\n .attr(\"height\", 80)\n .attr(\"width\", p=>p[1]);\nsvg.append(\"g\")\n .attr(\"fill\", \"red\")\n .selectAll(\"rect\")\n .data(myda[2])\n .join(\"rect\")\n .attr(\"x\", p=>p)\n .attr(\"y\", 0)\n .attr(\"height\", 80)\n .attr(\"width\", 3);\n svg.append(\"g\")\n .attr(\"fill\", \"black\")\n .selectAll(\"rect\")\n .data(myda[3])\n .join(\"rect\")\n .attr(\"x\", p=>p)\n .attr(\"y\", 180)\n .attr(\"height\", 80)\n .attr(\"width\", 3);\n //svg.append(\"g\")\n //.call(xAxis);\n\n //svg.append(\"g\")\n // .call(yAxis);\n\n return svg.node();\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":281,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":247,"value":"md `# Or all 6 frames at once Stop codons`\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":118,"value":"md `+1${sparkline(z[0])}
\n+2${sparkline(z[1])}
\n+3${sparkline(z[2])}
\n-1${sparkline(z[3])}
\n-2${sparkline(z[4])}
\n-3${sparkline(z[5])}
`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":52,"value":"md `stop codons using sparkline\n${sparkline(z[frame])}`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":58,"value":"function sparkline(values, width = 900, height = 24) {\n const x = d3.scaleLinear().domain([0, values.length - 1]).range([0.5, width - 0.5]);\n const y = d3.scaleLinear().domain(d3.extent(values)).range([height - 0.5, 0.5]);\n const context = DOM.context2d(width, height);\n const line = d3.line().x((d, i) => x(i)).y(y).context(context);\n context.beginPath(), line(values), context.stroke();\n return context.canvas;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":466,"value":"nchart = {\n const svg = d3.create(\"svg\")\n // .attr(\"viewBox\", [0, 0, width, 200]);\n\n // svg.append(\"g\")\n // .call(xAxis);\n\n // svg.append(\"g\")\n // .call(yAxis);\n\n svg.append(\"g\")\n .attr(\"fill\", \"steelblue\")\n .attr(\"stroke-width\", 10)\n .attr(\"pointer-events\", \"all\")\n .selectAll(\"rect\")\n .data(z)\n .join(\"rect\")\n .attr(\"x\", d => 25)\n .attr(\"y\", d => 90)\n .attr(\"width\", 1.5)\n // .attr(\"height\", y.bandwidth())\n .append(\"title\")\n .text(d => `${d.name}\n${(d.value * 100).toFixed(1)}% ${d.age}`);\n\n return svg.node();\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":485,"value":"nz","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":473,"value":"nz={\n const svg = d3.create(\"svg\")\n svg.append(\"g\")\n .attr(\"fill\", \"steelblue\")\n .attr(\"stroke-width\", 10)\n \n var z=[]\n for (var t=0;t<6;t++){z.push([])}\n for (var i=0;id!=\"\")\n .join('').toLowerCase()\n })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":193,"value":"setter = {\n mutable seq = nseq;\n }","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":214,"value":"mutable seq = bla.split(/\\r*\\n/).slice(1).filter(d=>d!=\"\").join(\"\").toLowerCase()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":208,"value":"bla=FileAttachment(\"35n\").text()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W32","stdlib":"1","titling":"auto"}} 30:"$2f:body"