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listAll.js
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console.log('loaded listAll.js')
// for debugging run directly as
// VCFmodule(VCF.dir.vcfs[0].div)
// after uncommenting module existance check in vcf.js
VCFmodule=function(div){
//lala = div
console.log('listAll',div);
var divBB = jQuery('#divBodyBody',div)[0];
divBB.textContent='... listing everything ... :-) :-)';
divBB.style.color='green';
divBB.innerHTML=""; // clear
var n = div.dt.body.CHROM.length;
var tb = document.createElement('table');divBB.appendChild(tb);
tb.style.fontSize='x-small'; tb.id = "listVariantCalls";
var tbd = document.createElement('tbody');tb.appendChild(tbd);
var tr,td1,td2,td3;
for (var i=0;i<n;i++){
tr = document.createElement('tr');tbd.appendChild(tr);
td1 = document.createElement('td');tr.appendChild(td1);
td1.textContent=div.dt.body.CHROM[i];
td2 = document.createElement('td');tr.appendChild(td2);
td2.textContent=div.dt.body.POS[i];
td3 = document.createElement('td');tr.appendChild(td3);
if(div.dt.body.ID[i].length>1){ // SNPs
td3.innerHTML='<a href="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs='+div.dt.body.ID[i]+'" target="_blank">'+div.dt.body.ID[i]+'</a>';
} else{
td3.textContent=div.dt.body.ID[i];textContent=div.dt.body.ID[i];
}
}
// table head
var tbh = document.createElement('thead');tb.appendChild(tbh);
tr = document.createElement('tr');tbh.appendChild(tr);
var th1 = document.createElement('th');tr.appendChild(th1);
th1.textContent='CHROM';
var th2 = document.createElement('th');tr.appendChild(th2);
th2.textContent='POS';
var th3 = document.createElement('th');tr.appendChild(th3);
th3.textContent='ID';
// add field selector to header
var run=function(){
console.log(div.dt.fields)
div.fieldSelector=function(){
var i = this.i;
var F = Object.getOwnPropertyNames(this.dt.body); // fields
var tr = jQuery('#listVariantCalls > thead > tr',this)[0];
var th = document.createElement('th');tr.appendChild(th);
var se = document.createElement('select');th.appendChild(se);
se.dt = this.dt.body;
var opt = document.createElement('option');se.appendChild(opt);opt.textContent='Parm:';
for(var j=0;j<F.length;j++){
var opt = document.createElement('option');se.appendChild(opt);opt.textContent=F[j];
}
se.onchange = function(evt){
var F = this.value; // field
var V = this.dt[F]; // values
var trs = this.parentElement.parentElement.parentElement.parentElement.tBodies[0].childNodes;
for(var i=0;i<V.length;i++){
td = document.createElement('td');td.textContent=V[i];trs[i].appendChild(td);
}
this.parentElement.parentElement.parentElement.parentElement.parentElement.parentElement.parentElement.fieldSelector();
this.parentElement.innerHTML=F;
// add delete column option
var thr = listVariantCalls.childNodes[1].childNodes[0]
var n = thr.children.length
var th = thr.children[n-2]
var sp = document.createElement('span')
sp.i=n-2
sp.style.color='red'
sp.textContent=' X'
th.appendChild(sp)
sp.onclick=function(evt){ // remove column
that = this
var i=this.i
console.log('i',i)
var thr = listVariantCalls.childNodes[1].childNodes[0]
for(var j=i+1;j<thr.children.length;j++){
thr.children[j].children[0].i=thr.children[j].children[0].i-1
}
// remove header
var thr = listVariantCalls.childNodes[1].childNodes[0]
thr.removeChild(thr.children[i])
// remove cells
Object.getOwnPropertyNames(listVariantCalls.children[0].children).forEach(function(c,j){
var tr = listVariantCalls.children[0].children[j]
tr.removeChild(tr.children[i])
})
}
}
}
div.fieldSelector()
}
if(VCF.urlParms){
if(VCF.urlParms.features){
$.get(VCF.urlParms.features).then(function(txt){
if(!VCF.dir.features){
VCF.dir.features={}
}
//VCF.dir.features[VCF.urlParms.features]={}
L = txt.split('\n')
Ft={
head:L[0],
posStart:[],
posEnd:[],
txt:[]
}
n=L.length, j=-1, val=[], Li='' // i lines, j features
///*
//div.dt.body.features=div.dt.body.ID.map(function(x,i){
// return '+'
//})
for(var i=1 ; i<n ; i++){
Li=L[i]
if(Li[0]!=='\t'){ // it's a feature position'
j++
val=Li.split(/\t/)
Ft.posStart[j]=parseInt(val[0])
Ft.posEnd[j]=parseInt(val[1])
Ft.txt[j]=val[2]
}else{
//console.log(Li)
Ft.txt[j]=Ft.txt[j]+'; '+Li
}
}
VCF.dir.features=Ft
//*/
// add new features
//div.dt.fields.push('features')
run();
var trs = listVariantCalls.children[0]
var n = trs.childElementCount
var spFun=function(evt){
//console.log(this)
//var i = this.i
//lala=this
if(this.textContent.slice(1)=='+'){
this.textContent=' -'
var pre = document.createElement('pre')
pre.style.fontSize=9
// extract annotation from features
//pre.innerHTML=new Date()
var pos=parseInt(this.parentElement.parentElement.children[1].textContent)
var h = VCF.dir.features.head.slice(0,9)+'<a href="http://www.ncbi.nlm.nih.gov/nuccore/87125858?report=graph&mk='+pos+'|'+pos+'&v='+Math.max(0,pos-10000)+':'+(pos+10000)+'" target="_blank">'+VCF.dir.features.head.slice(9)+pos+'</a>'
VCF.dir.features.posStart.forEach(function(p,i){
if(VCF.dir.features.posStart[i]>=pos){
if(VCF.dir.features.posEnd[i]<=pos){
h+='<br>'+VCF.dir.features.posStart[i]+'-'+VCF.dir.features.posEnd[i]
h+=' '+VCF.dir.features.txt[i].replace(/;/g,'<br>')
}
}
})
pre.innerHTML=h
this.parentNode.appendChild(pre)
}else{
this.parentElement.removeChild(this.parentElement.children[1])
this.textContent=' +'
}
}
for(var i=0 ; i<n ; i++){
var sp = document.createElement('sp')
sp.i=i
sp.textContent=' +'
sp.style.color='blue'
sp.onclick=spFun
trs.children[i].children[2].appendChild(sp)
}
})
}}else{
run();
}
}