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index.js
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index.js
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/*
* biojs-vis-blasterjs
* https://github.com/sing-group/blasterjs
*
* Copyright (c) 2018 SING - Sistemas Informaticos de Nueva Generacion
* Licensed under the MIT license.
*
*
* BlasterJS
*
* @class
* @extends Biojs
*
* @author <a href="mailto:aiblanco@uvigo.es">Aitor Blanco Miguez</a>
* @version 1.1.3
* @category 3
*
* @requires Bootstrap 3
* @dependency <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" integrity="sha384-1q8mTJOASx8j1Au+a5WDVnPi2lkFfwwEAa8hDDdjZlpLegxhjVME1fgjWPGmkzs7" crossorigin="anonymous"></link>
*
* @requires <a href='html2canvas.js'>HTML2CANVAS</a>
* @dependency <script type="text/javascript" src="lib/html2canvas.js"></script>
*
*
* @param {Object} options An object with the options for BlasterJS component.
*
* @option {string} input
* Identifier of the INPUT tag where the BLAST output file should be selected.
*
* @option {string} multipleAlignments
* Identifier of the DIV tag where the multiple alignments should be displayed.
*
* @option {string} alignmentsTable
* Identifier of the DIV tag where the alignments table should be displayed.
*
* @option {string} singleAlignment
* Identifier of the DIV tag where the single should be displayed.
*
* @example
* var instance = new Biojs.blasterjs({
* input: "blastinput",
* multipleAlignments: "blast-multiple-alignments",
* alignmentsTable: "blast-alignments-table",
singleAlignment: "blast-single-alignment"
* });
*/
var blasterjs;
var Class = require('js-class');
module.exports = blasterjs = Class(
/** @lends Biojs.blasterjs# */
{
constructor: function (options) {
var self = this;
require('js-extend').extend(this.opt, options);
var css = 'table tbody tr td button:hover{ text-decoration: underline;}';
var style = document.createElement('style');
if (style.styleSheet) {
style.styleSheet.cssText = css;
} else {
style.appendChild(document.createTextNode(css));
}
document.getElementsByTagName('head')[0].appendChild(style);
if (self.opt.string) {
var myBlob = new Blob([self.opt.string], {type : "text/plain"});
var fakeEvent = {
target: { files: [myBlob] }
};
self._displayAlignments(fakeEvent, self);
}else{
document.getElementById(self.opt.input).addEventListener('change', function(evt) { self._displayAlignments(evt, self) }, false);
}
},
/**
* Default values for the options
* @name Biojs.blasterjs-opt
*/
opt : {
input: "blastinput",
multipleAlignments: "blast-multiple-alignments",
alignmentsTable: "blast-alignments-table",
singleAlignment: "blast-single-alignment"
},
/**
* Private: Read and display BLAST alignments.
* @ignore
*/
_displayAlignments : function(evt, self) {
if (window.File && window.FileReader && window.FileList && window.Blob) {
var f = evt.target.files[0];
if (f) {
var r = new FileReader();
r.onload = function(e) {
try{
var queries = getQueries(e.target.result);
var alignments = getAlignments(queries[0]);
var queryLength = getQueryLength(queries[0]);
if(alignments.length == 0){
createEmptyAlignmentComparison(queries, [] ,0, queryLength, true, true, self);
}else{
var hsps = alignments[0].hsp.length;
createAlignmentComparison(queries, hsps, 0, alignments, queryLength, true, true, self);
createAlignmentTable(alignments, self);
createSingleAlignment(alignments[0], self, hsps, 0);
}
}catch(err){
var divs = ["blast-multiple-alignments", "blast-alignments-table", "blast-single-alignment"];
for(var i=0; i<divs.length; i++){
var div = document.getElementById(divs[i]);
while (div.firstChild) {
div.removeChild(div.firstChild);
}
}
alert('ERROR WHILE UPLOADING DATA: You have uploaded an invalid BLAST output file.');
}
}
r.readAsText(f);
} else {
alert('ERROR WHILE UPLOADING DATA: Failed to load file.');
}
} else {
alert('The File APIs are not fully supported by your browser.');
}
function BlastAlignment (description,
length,
totalScore,
queryCover,
hsp){
this.description = description;
this.length = length;
this.totalScore = totalScore;
this.queryCover = queryCover;
this.hsp = hsp;
}
function HSP (score,
eValue,
identities,
positives,
gaps,
queryStart,
query,
queryEnd,
comparison,
subjectStart,
subject,
subjectEnd ){
this.score = score;
this.eValue = eValue;
this.identities = identities;
this.positives = positives;
this.gaps = gaps;
this.queryStart = queryStart;
this.query = query;
this.queryEnd = queryEnd;
this.comparison = comparison;
this.subjectStart = subjectStart;
this.subject = subject;
this.subjectEnd = subjectEnd;
}
String.prototype.startsWith = function(prefix) {
return this.indexOf(prefix) === 0;
}
function getQueries(content){
var lines = content.split('\n');
if(lines[2].startsWith("<BlastOutput>")){
return getXMLQueries(content);
}else{
return getTextQueries(content);
}
}
function getXMLQueries(content){
var queries = [];
var lines = content.split('\n');
var count = 0;
for (var i = 0; i < lines.length; i++){
if(lines[i].startsWith('<Iteration>')){
count++;
}
}
if(count==1){
queries.push(content);
}else{
var j = 0;
var init = '';
for (var i = 0; i < lines.length; i++){
j=i;
if(lines[i].startsWith('<Iteration>')){
break;
}else{
init=init+lines[i]+'\n';
}
}
for(var x=0; x<count; x++){
var query = init+lines[j]+'\n';
j++;
while(lines[j] !== undefined && !lines[j].startsWith('<Iteration>')){
query=query+lines[j]+'\n';
j++;
}
queries.push(query);
}
}
return queries;
}
function getTextQueries(content){
var queries = [];
var lines = content.split('\n');
var count = 0;
for (var i = 0; i < lines.length; i++){
if(lines[i].startsWith('Query=')){
count++;
}
}
if(count==1){
queries.push(content);
}else{
var j = 0;
var init = '';
for (var i = 0; i < lines.length; i++){
j=i;
if(lines[i].startsWith('Query=')){
break;
}else{
init=init+lines[i]+'\n';
}
}
for(var x=0; x<count; x++){
var query = init+lines[j]+'\n';
j++;
while(lines[j] !== undefined && !lines[j].startsWith('Query=')){
query=query+lines[j]+'\n';
j++;
}
query=query+'\nend\n';
queries.push(query);
}
}
return queries;
}
function getQueryLength(content){
var lines = content.split('\n');
if(lines[2].startsWith("<BlastOutput>")){
return getXMLQueryLength(content);
}else{
return getTextQueryLength(content);
}
}
function getXMLQueryLength(content){
var lines = content.split('\n');
var length = 0;
for (var i = 0; i < lines.length; i++){
if(lines[i].includes('<Iteration_query-len>')){
length = lines[i].split('>')[1].split('</')[0];
break;
}
}
return length;
}
function getTextQueryLength(content){
var lines = content.split('\n');
var length = 0;
for (var i = 0; i < lines.length; i++){
if(lines[i].startsWith('Length=')){
length = lines[i].split('=')[1];
break;
}
}
return length;
}
function getAlignments(content){
var lines = content.split('\n');
if(lines[2].startsWith("<BlastOutput>")){
return parseBlastXML(content);
}else{
return parseBlastText(content);
}
}
function parseBlastXML(content){
var lines = content.split('\n');
var alignments = [];
for (var i = 0; i < lines.length; i++){
if(lines[i].startsWith('<Hit>')){
var hit = '';
for(var c = i; c < lines.length; c++){
hit += lines[c];
if(lines[c].includes("</Hit>")){
break;
}
}
var id = hit.split("<Hit_id>")[1].split("</")[0];
var def = hit.split("<Hit_def>")[1].split("</")[0];
var description = id.concat(' ').concat(def);
var length = hit.split("<Hit_len>")[1].split("</")[0];
var hsps_a = [];
var multiple = false;
var hsps_s = hit.split('<Hit_hsps>')[1].split('</Hit_hsps>')[0];
var hsps = hsps_s.split("</Hsp>");
for(var h=0; h<hsps.length-1; h++){
var score = hsps[h].split("<Hsp_bit-score>")[1].split("</")[0];
var eValue = hsps[h].split("<Hsp_evalue>")[1].split("</")[0];
var idnt = hsps[h].split("<Hsp_identity>")[1].split("</")[0];
var a_length = hsps[h].split("<Hsp_align-len>")[1].split("</")[0];
var identities = idnt/a_length*100;
if(lines[3].includes('<BlastOutput_program>blastn</BlastOutput_program>')){
var positives = 'N/A';
var gps = hsps[h].split("<Hsp_gaps>")[1].split("</")[0];
var gaps = gps/a_length*100;
}else{
var pstves = hsps[h].split("<Hsp_positive>")[1].split("</")[0];
var positives = parseFloat(pstves/a_length*100).toFixed(0);
var gps = hsps[h].split("<Hsp_gaps>")[1].split("</")[0];
var gaps = gps/a_length*100;
}
var queryStart = hsps[h].split("<Hsp_query-from>")[1].split("</")[0];
var query = hsps[h].split("<Hsp_qseq>")[1].split("</")[0];
var queryEnd = hsps[h].split("<Hsp_query-to>")[1].split("</")[0];
var comparison = hsps[h].split("<Hsp_midline>")[1].split("</")[0];
var sbjctStart = hsps[h].split("<Hsp_hit-from>")[1].split("</")[0];
var sbjct = hsps[h].split("<Hsp_hseq>")[1].split("</")[0];
var sbjctEnd = hsps[h].split("<Hsp_hit-to>")[1].split("</")[0];
var hsp = new HSP(score, eValue, parseFloat(identities).toFixed(0), positives, parseFloat(gaps).toFixed(0), queryStart, query, queryEnd, comparison, sbjctStart, sbjct, sbjctEnd);
hsps_a.push(hsp);
}
var totalScore = parseFloat(hsps_a[0].score);
for(var x = 1; x< hsps_a.length; x++){
totalScore = totalScore + parseFloat(hsps_a[x].score);
}
var alignment = new BlastAlignment( description, length, totalScore.toFixed(1), getQueryCover(hsps_a, getQueryLength(content)), hsps_a);
alignments.push(alignment);
}
}
return alignments;
}
function parseBlastText(content){
var lines = content.split('\n');
var alignments = [];
for (var i = 0; i < lines.length; i++){
if(lines[i].startsWith('>')){
var line1 = lines[i].split('>')[1];
var line2 = "";
var currentLine = i;
while (line2 == ""){
currentLine = currentLine +1;
if(lines[currentLine].startsWith('Length=')){
line2 = lines[currentLine];
}else{
line1 += lines[currentLine];
}
}
var description = line1;
var length = line2.split('=')[1];
var hsps = [];
var multiple = false;
do{
if(multiple){
currentLine = currentLine-1;
}
if(lines[currentLine+2].startsWith(' Features in this part of subject sequence:')){
currentLine = currentLine+3;
while(!lines[currentLine+2].startsWith(" Score =")){
currentLine++;
}
}
var score = lines[currentLine+2].split(',')[0].replace(/\s\s+/g, ' ').split(' ')[3];
var eValue = lines[currentLine+2].split(',')[1].split(' ')[4];
var identities = lines[currentLine+3].split(',')[0].split('(')[1].substr(0, lines[currentLine+3].split(',')[0].split('(')[1].length-2);
if(lines[0].startsWith('BLASTN')){
var positives = 'N/A';
var gaps = lines[currentLine+3].split(',')[1].split('(')[1].substr(0, lines[currentLine+3].split(',')[1].split('(')[1].length-2);
}else{
var positives = lines[currentLine+3].split(',')[1].split('(')[1].substr(0, lines[currentLine+3].split(',')[1].split('(')[1].length-2);
var gaps = lines[currentLine+3].split(',')[2].split('(')[1].substr(0, lines[currentLine+3].split(',')[2].split('(')[1].length-2);
}
if(lines[currentLine+4].split(',')[0].split(' ')[1] == 'Frame' || lines[currentLine+4].startsWith(' Strand')){
currentLine = currentLine+1;
}
var queryStart = lines[currentLine+5].substring(5).replace(/^\s+/g, '').split(' ')[0];
var query = lines[currentLine+5].substring(5).replace(/\s+/g, '').replace(/[0-9]/g, '');
var queryEnd = lines[currentLine+5].substring(5).replace(/^\s+/g, '').split(' ')[lines[currentLine+5].substring(5).replace(/^\s+/g, '').split(' ').length-1];
var comparison = lines[currentLine+6].replace(/^\s+/g, '');
var sbjctStart = lines[currentLine+7].substring(5).replace(/^\s+/g, '').split(' ')[0];
var sbjct = lines[currentLine+7].substring(5).replace(/\s+/g, '').replace(/[0-9]/g, '');
var sbjctEnd = lines[currentLine+7].substring(5).replace(/^\s+/g, '').split(' ')[lines[currentLine+7].substring(5).replace(/^\s+/g, '').split(' ').length-1];
currentLine = currentLine+9;
while (lines[currentLine].startsWith('Query')){
var nextQuery = lines[currentLine].substring(5).replace(/\s+/g, '').replace(/[0-9]/g, '');
query += nextQuery;
queryEnd = lines[currentLine].substring(5).replace(/^\s+/g, '').split(' ')[lines[currentLine].substring(5).replace(/^\s+/g, '').split(' ').length-1];
sbjct += lines[currentLine+2].substring(5).replace(/\s+/g, '').replace(/[0-9]/g, '');
sbjctEnd = lines[currentLine+2].substring(5).replace(/^\s+/g, '').split(' ')[lines[currentLine+2].substring(5).replace(/^\s+/g, '').split(' ').length-1];
var nextComparison = lines[currentLine+1].replace(/^\s+/g, '');
if(nextQuery.length > nextComparison.length){
var diference = nextQuery.length-nextComparison.length;
for(var j = 0; j < diference; j++){
nextComparison = ' '+nextComparison;
}
}
comparison += nextComparison;
currentLine = currentLine+4;
}
var hsp = new HSP(score, eValue, identities, positives, gaps, queryStart, query, queryEnd, comparison, sbjctStart, sbjct, sbjctEnd);
hsps.push(hsp);
multiple = true;
}while(lines[currentLine+1].startsWith(' Score'));
var totalScore = parseFloat(hsps[0].score);
for(var x = 1; x< hsps.length; x++){
totalScore = totalScore + parseFloat(hsps[x].score);
}
var alignment = new BlastAlignment( description, length, totalScore.toFixed(1), getQueryCover(hsps, getQueryLength(content)), hsps);
alignments.push(alignment);
}
}
return alignments;
}
function getQueryCover(hsps, length){
var cover = 0;
var noOver = getHSPWithoutOverlapping(hsps);
for(var i=0; i<noOver.length; i++){
cover = cover + parseInt(100 * (noOver[i].end - noOver[i].start +1) / length);
}
return cover;
}
function getHSPWithoutOverlapping(hsps){
var hspNoOver=[];
for(var i=0; i<hsps.length; i++){
if(parseInt(hsps[i].queryStart)>parseInt(hsps[i].queryEnd)){
hspNoOver.push({start:parseInt(hsps[i].queryEnd),end:parseInt(hsps[i].queryStart)});
}else{
hspNoOver.push({start:parseInt(hsps[i].queryStart),end:parseInt(hsps[i].queryEnd)});
}
}
return getNoOverlappingArray(partitionIntoOverlappingRanges(hspNoOver));
}
function partitionIntoOverlappingRanges(array) {
array.sort(function (a,b) {
if (a.start < b.start)
return -1;
if (a.start > b.start)
return 1;
return 0;
});
var getMaxEnd = function(array) {
if (array.length==0) return false;
array.sort(function (a,b) {
if (a.end < b.end)
return 1;
if (a.end > b.end)
return -1;
return 0;
});
return array[0].end;
};
var rarray=[];
var g=0;
rarray[g]=[array[0]];
for (var i=1,l=array.length;i<l;i++) {
if ( (array[i].start>=array[i-1].start)
&&
(array[i].start<getMaxEnd(rarray[g]))
) {
rarray[g].push(array[i]);
} else {
g++;
rarray[g]=[array[i]];
}
}
return rarray;
}
function getNoOverlappingArray(array){
var result = [];
for(var i=0; i<array.length; i++){
var start=array[i][0].start;
var end= array[i][0].end;
for(var j=0; j<array[i].length; j++){
if(array[i][j].start<start)
start = array[i][j].start;
if(array[i][j].end>end)
end = array[i][j].end;
}
result.push({start:start,end:end});
}
return result;
}
function getColor(colored, scoring, score, evalue){
var colorNb;
if(!scoring){
if (evalue>100){
colorNb=1;
}else if (evalue<=100 && evalue>1){
colorNb=2;
}else if (evalue<=1 && evalue>0.01){
colorNb=3;
}else if (evalue<=0.01 && evalue>0.00001){
colorNb=4
}else {
colorNb=5;
}
}else{
if (score<40){
colorNb=1;
}else if (score>=40 && score<50){
colorNb=2;
}else if (score>=50 && score<80){
colorNb=3;
}else if (score>=80 && score<200){
colorNb=4
}else {
colorNb=5;
}
}
return getDivColor(colored, colorNb);
}
function getDivColorText(scoring,div){
if(!scoring){
switch(div) {
case 1:
return '>100';
break;
case 2:
return '100-1';
break;
case 3:
return '1-1e<sup>-2</sup>';
break;
case 4:
return '1e<sup>-2</sup>-1e<sup>-5</sup>';
break;
case 5:
return '<1e<sup>-5</sup>';
break;
default:
return '0';
}
}else{
switch(div) {
case 1:
return '<40';
break;
case 2:
return '40-50';
break;
case 3:
return '50-80';
break;
case 4:
return '80-200';
break;
case 5:
return '>=200';
break;
default:
return '0';
}
}
}
function getDivColor(colored, div){
if(colored){
switch(div) {
case 1:
return '#5C6D7E';
break;
case 2:
return '#9B59B6';
break;
case 3:
return '#5CACE2';
break;
case 4:
return '#57D68D';
break;
case 5:
return '#C0392B';
break;
default:
return '#FFF';
}
}else{
switch(div) {
case 1:
return '#BCBCBC';
break;
case 2:
return '#989898';
break;
case 3:
return '#747474';
break;
case 4:
return '#565656';
break;
case 5:
return '#343434';
break;
default:
return '#FFF';
}
}
}
function selectAlignment(alignment){
var item = document.getElementById(alignment).parentElement.parentElement;
var items = document.getElementsByClassName('alignment-table-description');
var i;
for (i = 0; i < items.length; i++) {
items[i].style.fontWeight = 'normal';
items[i].parentElement.parentElement.style.fontWeight = 'normal';
}
item.style.fontWeight = 'bold';
document.getElementById(alignment).style.fontWeight = 'bold';
}
function createColorsDiv(colored,scoring){
var container = document.createElement('div');
var divSpace = document.createElement('div');
var divClear = document.createElement('div');
container.style.color = '#EEE';
divSpace.style.minWidth = '50px';
divSpace.style.minHeight = '10px';
divSpace.style.float = 'left';
container.appendChild(divSpace);
for(var i = 1; i <= 5; i++){
var div = document.createElement('div');
div.style.minWidth = '100px';
div.style.textAlign = 'center';
div.style.float = 'left';
div.innerHTML = getDivColorText(scoring, i).bold();
div.style.backgroundColor = getDivColor(colored, i);
container.appendChild(div);
}
divClear.style.clear = 'both';
container.appendChild(divClear);
return container;
}
function createQueryDiv(colored){
var container = document.createElement('div');
var divSpace = document.createElement('div');
var divQuery = document.createElement('div');
var divClear = document.createElement('div');
container.style.marginTop = '3px';
container.style.color = '#5C6D7E';
container.style.fontSize = '10px';
divSpace.style.width = '50px';
divSpace.innerHTML = 'QUERY'.bold();
divSpace.style.float = 'left';
divQuery.style.width = '500px';
divQuery.style.height = '10px';
divQuery.style.float = 'left';
divQuery.style.marginTop = '2px';
divClear.style.clear = 'both';
if(colored){
divQuery.style.backgroundColor = '#C0392B';
} else{
divQuery.style.backgroundColor = '#343434';
}
container.appendChild(divSpace);
container.appendChild(divQuery);
container.appendChild(divClear);
return container;
}
function createNumbersDiv(lenght){
var container = document.createElement('div');
var divSpace = document.createElement('div');
var divNumbers = document.createElement('div');
var divClear = document.createElement('div');
container.style.marginBottom = '5px';
container.style.fontSize = '11px';
divSpace.style.minWidth = '50px';
divSpace.style.minHeight = '10px';
divSpace.style.float = 'left';
divNumbers.style.float = 'left';
divClear.style.clear = 'both';
divNumbers = divideDivNumbers(divNumbers, lenght);
container.appendChild(divSpace);
container.appendChild(divNumbers);
container.appendChild(divClear);
return container;
}
function divideDivNumbers(container, lenght){
var divClear = document.createElement('div');
if(lenght > 4){
if(lenght % 5 == 0){
container = createDivisionsDivNumbers(container, 5, lenght/5, 100);
}else{
var pixels = 500/(5+((lenght%5)/5));
container = createDivisionsDivNumbers(container, 5, parseInt(lenght/5), parseInt(pixels));
//We can do this or not
var pxrest = parseInt(500-(pixels*5));
var div = document.createElement('div');
div.style.float = 'left';
div.style.width = pxrest+'px';
div.style.textAlign = 'right';
div.innerHTML = lenght;
container.appendChild(div);
}
}else{
container = createDivisionsDivNumbers(container, lenght, 1, parseInt(500/lenght));
}
divClear.style.clear = 'both';
container.appendChild(divClear);
return container;
}
function createDivisionsDivNumbers(container, divisions, size, pixels){
for(var i = 0; i<divisions; i++){
if(i == 0){
var px2 = pixels/2;
var div1 = document.createElement('div');
var div2 = document.createElement('div');
div1.style.float = 'left';
div1.style.width = px2+'px';
div1.style.textAlign = 'left';
div1.innerHTML = '0';
div2.style.float = 'left';
div2.style.width = px2+'px';
div2.style.textAlign = 'right';
div2.innerHTML = size*(i+1);
container.appendChild(div1);
container.appendChild(div2);
}else{
var div = document.createElement('div');
div.style.float = 'left';
div.style.width = pixels+'px';
div.style.textAlign = 'right';
div.innerHTML = size*(i+1);
container.appendChild(div);
}
}
return container;
}
function createHeader(container, colored, scoring, lenght){
var text = document.createElement('div');
var colors = createColorsDiv(colored, scoring);
var query = createQueryDiv(colored);
var numbers = createNumbersDiv(lenght);
text.style.color = '#5C6D7E';
text.style.textAlign = 'center';
text.style.paddingBottom = '5px';
text.innerHTML = 'COLOR KEY FOR ALIGNMENT SCORES'.bold();
container.appendChild(text);
container.appendChild(colors);
container.appendChild(query);
container.appendChild(numbers);
return container;
}
function createBody(alignments, queryLength, container, colored, scoring){
var alignmentContainer = document.createElement('div');
alignmentContainer.style.paddingBottom = '10px';
for(var i = 0; i < alignments.length; i++){
var alignment = createAlignmentDiv(getColor(colored, scoring, alignments[i].hsp[0].score, alignments[i].hsp[0].eValue), alignments[i], queryLength);
alignment.style.marginBottom = '4px';
alignmentContainer.appendChild(alignment);
}
container.appendChild(alignmentContainer);
return container;
}
function createAlignmentDiv(color, alignment, queryLength){
var noOver = getHSPWithoutOverlapping(alignment.hsp);
var container = document.createElement('div');
var divClear = document.createElement('div');
container.style.minHeight = '12px';
for(var i =0; i<noOver.length; i++){
var white = document.createElement('div');
var colored = document.createElement('div');
var link = document.createElement('a');
if(i==0){
if(noOver[0].start == 1)
var init = parseInt(50+((500*(noOver[0].start-1))/queryLength));
else
var init = parseInt(50+((500*(noOver[0].start))/queryLength));
var offset = parseInt(550-init-(500*(queryLength-noOver[0].end)/queryLength));
}else{
var init = parseInt((500*(noOver[i].start-noOver[i-1].end)/queryLength));
var offset = parseInt((500*(noOver[i].end-noOver[i].start)/queryLength));
}
white.style.width = init+'px';
white.style.minHeight = '4px';
white.style.float = 'left';
colored.style.width = offset+'px';
colored.style.minHeight = '12px';
colored.style.float = 'left';
colored.style.backgroundColor = color;
colored.onmouseout = function(){document.getElementById('defline').value=' Mouse over to show defline and scores, click to show alignments';};
colored.onmouseover = function(){document.getElementById('defline').value=' '+alignment.description+'. S='+alignment.hsp[0].score+' E='+alignment.hsp[0].eValue;};
link.href = '#'+alignment.description.split(' ')[0];
link.onclick=function(){ selectAlignment(alignment.description.split(' ')[0]); };
link.appendChild(colored);
container.appendChild(white);
container.appendChild(link);
}
divClear.style.clear = 'both';
container.appendChild(divClear);
return container;
}
function createChangeScoringButton(queries, hsps, position, alignments, lenght, colored, scoring, self){
var button = document.createElement('button');
button.id = 'changeScore';
button.className = 'btn';
button.style.marginRight = '10px';
button.style.marginTop = '5px';
if(scoring == true){
var text = document.createTextNode('Change scoring to E value');
}else{
var text = document.createTextNode('Change scoring to Max score');
}
button.appendChild(text);
button.onclick=function(){ changeScoring(queries, hsps, position, alignments, lenght, button, colored, scoring, self); };
return button;
}
function createChangeColorButton(queries, hsps, position, alignments, lenght, colored, scoring, self){
var button = document.createElement('button');
button.id = 'changeColors';
button.className = 'btn';
button.style.marginRight = '10px';
button.style.marginTop = '5px';
if(colored == true){
var text = document.createTextNode('Change colours to grayscale');
}else{
var text = document.createTextNode('Change colours to full colored');
}
button.appendChild(text);
button.onclick=function(){ changeColors(queries, hsps, position, alignments, lenght, button, colored, scoring, self); };
return button;
}
function createDownloadButton(type){
var button = document.createElement('button');
button.id = 'downloadAlignments'+type;
button.className = 'btn';
button.style.marginRight = '10px';
button.style.marginTop = '5px';
var text = document.createTextNode('Download as '+type);
button.appendChild(text);
button.addEventListener("click", function(){
downloadAlignmentsImg(type);
}, false);
return button;
}
function changeColors(queries, hsps, position, alignments, lenght, button, colored, scoring, self){
if(colored == true){
colored = false;
}else{
colored = true;
}
button.removeChild(button.childNodes[0]);
var blastDiv = document.getElementById(self.opt.multipleAlignments);
while (blastDiv.firstChild) {
blastDiv.removeChild(blastDiv.firstChild);
}
createAlignmentComparison(queries, hsps, position, alignments, lenght, colored, scoring, self);
}
function changeScoring(queries, hsps, position, alignments, lenght, button, colored, scoring, self){
if(scoring == true){
scoring = false;
}else{
scoring = true;
}
button.removeChild(button.childNodes[0]);
var blastDiv = document.getElementById(self.opt.multipleAlignments);
while (blastDiv.firstChild) {
blastDiv.removeChild(blastDiv.firstChild);
}
createAlignmentComparison(queries, hsps, position, alignments, lenght, colored, scoring, self);
}
function downloadAlignmentsImg(type){
var buttons = document.getElementById('blast-multiple-alignments-buttons');
var input = document.getElementById('defline');
var container = document.getElementById('alignments-container');
container.removeChild(buttons);
container.removeChild(input);
html2canvas(container, {
onrendered: function(canvas) {
document.body.appendChild(canvas);
var a = document.createElement('a');
document.body.appendChild(a);
if(type=='JPEG'){
a.href = canvas.toDataURL('image/jpeg');
}else{
a.href = canvas.toDataURL('img/png');
}
a.download = 'alignments.'+type.toLowerCase();
a.click();
document.body.removeChild(canvas);
document.body.removeChild(a);
container.appendChild(input);
container.appendChild(buttons);
a = document.createElement('a');
document.body.appendChild(a);
a.href = '#blast-multiple-alignments'
a.click();
document.body.removeChild(a);
}
});
}
function getQueryText(content){
var lines = content.split('\n');
if(lines[2].startsWith("<BlastOutput>")){
return getXMLQueryText(content);
}else{
return getTextQueryText(content);
}
}
function getXMLQueryText(content){
var lines = content.split('\n');
for (var i = 0; i < lines.length; i++){
if(lines[i].includes('<Iteration_query-def>')){
return lines[i].split('>')[1].split('</')[0];
}
}
}
function getTextQueryText(content){
var lines = content.split('\n');
var text = '';
for (var i = 0; i < lines.length; i++){
if(lines[i].startsWith('Query=')){
text = lines[i].split('=')[1];
i++;
while(!lines[i].startsWith('Length=')){
text=text+' '+lines[i];
i++;
}
break;
}
}
return text;
}
function goToQuery(queries, hsps, position, queryLength, colored, scoring, self){
var alignments = getAlignments(queries[position]);
var queryLength = getQueryLength(queries[position]);
if(alignments.length == 0){
var divs = ["blast-alignments-table", "blast-single-alignment"];
for(var i=0; i<divs.length; i++){
var div = document.getElementById(divs[i]);
while (div.firstChild) {
div.removeChild(div.firstChild);
}
}
createEmptyAlignmentComparison(queries, [] ,position, queryLength, true, true, self);
}else{
createAlignmentComparison(queries, hsps, position, alignments, queryLength, colored, scoring, self);
createAlignmentTable(alignments, self);
var hsps = alignments[0].hsp.length;
createSingleAlignment(alignments[0], self, hsps, 0);
}
}
function createSelectQueries(queries, hsps, position, queryLength, colored, scoring, self){
var selectQuery = document.createElement('select');
selectQuery.style.width = '430px';
selectQuery.style.marginBottom = '20px';