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/*
Functions for the multiple sequence alignment results page.
*/
function toggleClustalColors() {
var d = document.getElementById('alignment');
var l = document.getElementById('msa_show_hide_button');
if (d.className == 'msa') {
d.className = 'msa-nocolour';
if (l.value != null) {
l.value = 'show colours';
} else {
l.innerHTML = 'show colours';
}
}
else {
d.className = 'msa';
l.innerHTML = 'hide colours';
}
}
function toggleClustalWrap() {
var w = document.getElementById('wrapped');
var u = document.getElementById('unwrapped');
var l = document.getElementById('msa_wrap_button');
if (w.style.display == 'none') {
w.style.display = '';
u.style.display = 'none';
l.innerHTML = 'show unwrapped';
}
else {
w.style.display = 'none';
u.style.display = '';
l.innerHTML = 'show wrapped';
}
}
function submitAlignJob() {
var form = document.getElementById('alignForm');
jQuery.post("ajax/align/submit", { input: form.input.value },
function(result, status) {
jQuery('#waiting').hide();
if (status == "success") {
if (result.error != null && result.error.length > 0) {
alert("Retrieving align results failed:\n" + result.error);
}
if (result.alignment != null && result.alignment.length > 0) {
displayAlignResults(result.alignment);
}
} else {
alert('Error receiving alignment results');
}
}, "json");
// let the user know we're working
jQuery('#waiting').show();
jQuery('#result').hide();
}
function displayAlignResults(s) {
var d = document.getElementById('result');
d.style.display = '';
var r = new Array();
var r2 = new Array();
s = unescape(s);
var re = />(.+)\n/m;
var a = s.split(/(?=>)/);
for (i in a) {
var m = re.exec(a[i]);
if (m == null) {
continue;
}
var seq = a[i].substr(m[0].length).replace(/\n/g, '');
seq = seq.replace(/([DE]+)/g, "<span class='c1'>$1</span>");
seq = seq.replace(/([KR]+)/g, "<span class='c2'>$1</span>");
seq = seq.replace(/([H]+)/g, "<span class='c3'>$1</span>");
seq = seq.replace(/([NQ]+)/g, "<span class='c4'>$1</span>");
seq = seq.replace(/([CM]+)/g, "<span class='c5'>$1</span>");
seq = seq.replace(/([GP]+)/g, "<span class='c6'>$1</span>");
seq = seq.replace(/([AVLIWF]+)/g, "<span class='c7'>$1</span>");
seq = seq.replace(/([YST]+)/g, "<span class='c8'>$1</span>");
var id = m[1].substr(0, 15);
id += ' '.substr(id.length);
var al = { id: id, a: seq };
r.push(al);
// for wrapped version
var aa = new Array();
seq = a[i].substr(m[0].length).replace(/\n/g, '');
for (var j = 0; j < seq.length; j += 60) {
var s2 = seq.substr(j, 60);
s2 = s2.replace(/([DE]+)/g, "<span class='c1'>$1</span>");
s2 = s2.replace(/([KR]+)/g, "<span class='c2'>$1</span>");
s2 = s2.replace(/([H]+)/g, "<span class='c3'>$1</span>");
s2 = s2.replace(/([NQ]+)/g, "<span class='c4'>$1</span>");
s2 = s2.replace(/([CM]+)/g, "<span class='c5'>$1</span>");
s2 = s2.replace(/([GP]+)/g, "<span class='c6'>$1</span>");
s2 = s2.replace(/([AVLIWF]+)/g, "<span class='c7'>$1</span>");
s2 = s2.replace(/([YST]+)/g, "<span class='c8'>$1</span>");
aa.push(s2);
}
r2.push(aa);
}
s = '';
for (i in r) {
s += r[i].id;
s += r[i].a;
s += '\n';
}
document.getElementById('unwrapped').innerHTML = s;
s = '';
for (var j = 0; j < r2[0].length; ++j) {
for (i in r) {
s += r[i].id;
s += r2[i][j];
s += '\n';
}
s += '\n';
}
document.getElementById('wrapped').innerHTML = s;
}
function initAlignPage() {
var form = document.getElementById('alignForm');
var fasta = form.input.value;
if (fasta.length > 0) {
submitAlignJob();
}
}
addLoadEvent(initAlignPage);
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