// Трансляция нуклеотидной последовательности

translation = new Array("cga","cgc","cgg","cgt","aga","agg","cta","ctc","ctg","ctt","tta","ttg","tca","tcc","tcg","tct","agc","agt","aca","acc","acg","act","cca","ccc","ccg","cct","gca","gcc","gcg","gct","gga","ggc","ggg","ggt","gta","gtc","gtg","gtt","aaa","aag","aac","aat","caa","cag","cac","cat","gaa","gag","gac","gat","tac","tat","tgc","tgt","ttc","ttt","ata","atc","att","atg","tgg","taa","tag","tga","acs","ggs","gcs","gts","cgs","ccs","tcs","acw","atw","ggw","gcw","gtw","cgw","ccw","tcw","tra","aar","agr","acr","gar","ggr","gcr","gtr","car","cgr","ccr","ttr","tar","tcr","yta","ytg","aay","agy","acy","aty","gay","ggy","gcy","gty","cay","cgy","ccy","tty","tay","tgy","tcy","mga","mgg","acm","atm","ggm","gcm","gtm","cgm","ccm","tcm","ack","ggk","gck","gtk","cgk","cck","tck","ach","ath","ggh","gch","gth","cgh","cch","tch","acb","ggb","gcb","gtb","cgb","ccb","tcb","acd","ggd","gcd","gtd","cgd","ccd","tcd","acv","ggv","gcv","gtv","cgv","ccv","tcv","acn","ggn","gcn","gtn","cgn","ccn","tcn","cts","ctw","ctr","cty","ctk","ctd","ctv","cth","ctb","ctn","ctm","ytr","mgr");

treelett = new Array("Arg","Arg","Arg","Arg","Arg","Arg","Leu","Leu","Leu","Leu","Leu","Leu","Ser","Ser","Ser","Ser","Ser","Ser","Thr","Thr","Thr","Thr","Pro","Pro","Pro","Pro","Ala","Ala","Ala","Ala","Gly","Gly","Gly","Gly","Val","Val","Val","Val","Lys","Lys","Asn","Asn","Gln","Gln","His","His","Glu","Glu","Asp","Asp","Tyr","Tyr","Cys","Cys","Phe","Phe","Ile","Ile","Ile","Met","Trp","Oc*","Am*","Op*","Thr","Gly","Ala","Val","Arg","Pro","Ser","Thr","Ile","Gly","Ala","Val","Arg","Pro","Ser","_*_","Lys","Arg","Thr","Glu","Gly","Ala","Val","Gln","Arg","Pro","Leu","_*_","Ser","Leu","Leu","Asn","Ser","Thr","Ile","Asp","Gly","Ala","Val","His","Arg","Pro","Phe","Tyr","Cys","Ser","Arg","Arg","Thr","Ile","Gly","Ala","Val","Arg","Pro","Ser","Thr","Gly","Ala","Val","Arg","Pro","Ser","Thr","Ile","Gly","Ala","Val","Arg","Pro","Ser","Thr","Gly","Ala","Val","Arg","Pro","Ser","Thr","Gly","Ala","Val","Arg","Pro","Ser","Thr","Gly","Ala","Val","Arg","Pro","Ser","Thr","Gly","Ala","Val","Arg","Pro","Ser","Leu","Leu","Leu","Leu","Leu","Leu","Leu","Leu","Leu","Leu","Leu","Leu","Arg");

onelett = new Array(".R.",".R.",".R.",".R.",".R.",".R.",".L.",".L.",".L.",".L.",".L.",".L.",".S.",".S.",".S.",".S.",".S.",".S.",".T.",".T.",".T.",".T.",".P.",".P.",".P.",".P.",".A.",".A.",".A.",".A.",".G.",".G.",".G.",".G.",".V.",".V.",".V.",".V.",".K.",".K.",".N.",".N.",".Q.",".Q.",".H.",".H.",".E.",".E.",".D.",".D.",".Y.",".Y.",".C.",".C.",".F.",".F.",".I.",".I.",".I.",".M.",".W.",".*.",".*.",".*.",".T.",".G.",".A.",".V.",".R.",".P.",".S.",".T.",".I.",".G.",".A.",".V.",".R.",".P.",".S.",".*.",".K.",".R.",".T.",".E.",".G.",".A.",".V.",".Q.",".R.",".P.",".L.",".*.",".S.",".L.",".L.",".N.",".S.",".T.",".I.",".D.",".G.",".A.",".V.",".H.",".R.",".P.",".F.",".Y.",".C.",".S.",".R.",".R.",".T.",".I.",".G.",".A.",".V.",".R.",".P.",".S.",".T.",".G.",".A.",".V.",".R.",".P.",".S.",".T.",".I.",".G.",".A.",".V.",".R.",".P.",".S.",".T.",".G.",".A.",".V.",".R.",".P.",".S.",".T.",".G.",".A.",".V.",".R.",".P.",".S.",".T.",".G.",".A.",".V.",".R.",".P.",".S.",".T.",".G.",".A.",".V.",".R.",".P.",".S.",".L.",".L.",".L.",".L.",".L.",".L.",".L.",".L.",".L.",".L.",".L.",".L.",".R.");

nucleotides = new Array("a","g","c","t","n","s","w","r","y","m","k","h","b","d","v");

complement = new Array("t","c","g","a","n","s","w","y","r","k","m","d","v","h","b");


var x;
var al;
var name_seq;
aa = new Array()

function aa_tr(sequence,frame)
{
aaseq = "";
i1 = 0;
sequence = sequence.substring(frame-1);
aalength = Math.floor(sequence.length/3);
while(i1<aalength) { 
	i1++; i2 = 0; let = x;
	while(i2<176) {i2++; if(sequence.substring(i1*3-3,i1*3)==translation[i2-1]) {let = aa[i2-1]; break}} aaseq = aaseq + let;
}
aastrings = Math.floor(aalength/al);
i1 = 0;
aaout = "";
while(i1<aastrings+1) {i1++; aaout = aaout + aaseq.substring((i1-1)*al*3, i1*al*3)+"<br>";}
aaout = aaout.replace(/\./g,"");
id.document.write(name_seq + "  -  " + aalength + " codons" + "<br><font color='Gray'>" + aaout + "</font>");
return aaseq;
}

function translat()
{
// забираем значения, заданные в форме
name_seq = document.transl.s_name.value;
str = document.transl.str.value;


if (document.transl.code.selectedIndex == 0) {aa = onelett; x= ".X.";} else {aa = treelett; x= "Xxx";};

var nl = parseFloat(document.transl.nl.value); 
if(isNaN(nl)){alert(alt13_01); document.transl.nl.focus(); return true;};
nl = Math.floor(Math.abs(nl));
document.transl.nl.value = nl;

al = parseFloat(document.transl.al.value); 
if(isNaN(nl)){alert(alt13_02); document.transl.al.focus(); return true;};
al = Math.floor(Math.abs(al));
document.transl.al.value = al;


// приводим "str" к стандартному виду который будет называться "nseq"
nseq = ""
nseq = str.toLowerCase();
nseq = nseq.replace(/u/g,"t");
nseq = nseq.replace(/[^agctswrymkhbdvn]/g,"");
lnseq = nseq.length;
if(lnseq<3){alert(alt13_03); document.transl.str.focus(); return true;};

// проверяем, что какие-то преобразования выбраны
if(!(document.transl.meth0.checked || document.transl.meth1.checked || document.transl.meth2.checked || document.transl.meth2_1.checked || document.transl.meth2_2.checked || document.transl.meth2_3.checked || document.transl.meth2_4.checked || document.transl.meth2_5.checked || document.transl.meth2_6.checked)) {alert(alt13_04); document.transl.meth0.focus(); return true;}

// открываем окно 
id = window.open('','result', config='height=500,width=600,toolbar=yes,menubar=yes,scrollbars=yes,resizable=yes,location=no,status=no');
id.document.write("<title>&nbsp;&nbsp;&nbsp;6 Frame Translation&nbsp;&nbsp;&nbsp;</title><BODY BGCOLOR='white'>");
id.focus();
nstrings = Math.floor(lnseq/nl);

// выводим исходную последовательность
if(document.transl.meth0.checked) {
i1 = 0;
out0_seq = "";
while(i1<nstrings+1) { i1++; out0_seq = out0_seq + nseq.substring(i1*nl-nl, i1*nl)+"<br>";}

id.document.write("<h4>Original sequence:</h4><TT>");
id.document.write("&gt; " + name_seq + "  -  " + lnseq + " nucleotides" + "<br><font color='Gray'>" + out0_seq + "</TT></font>");
}


if(document.transl.meth1.checked || document.transl.meth2.checked|| document.transl.meth2_4.checked|| document.transl.meth2_5.checked|| document.transl.meth2_6.checked) {
i2 = 0;
c_seq = "";
while(i2<lnseq+1) {
i2++; i3 = 0;
	while(i3<15) {i3++; if(nseq.charAt(lnseq - i2 + 1)==nucleotides[i3-1]) {c_seq = c_seq + complement[i3-1]; break};
	}
}
}

// выводим комплементарную последовательность
if(document.transl.meth1.checked) {

i6 = 0;
out2_seq = "";
while(i6<nstrings+1) { i6++; out2_seq = out2_seq + c_seq.substring(i6*nl-nl, i6*nl)+"<br>";}
id.document.write("<h4>Complementary sequence:</h4><TT>" + "&gt; (5' --&gt; 3' complementary sequence) " + name_seq + "  -  " + lnseq + " nucleotides" + "<br><font color='Gray'>" + out2_seq + "</font></TT>");
}


if(document.transl.meth2.checked || document.transl.meth2_1.checked || document.transl.meth2_2.checked || document.transl.meth2_3.checked) {
id.document.write("<h4><font color=Red>Translation in forward direction:</font></h4>");
}

// выводим aa последовательность в +1 рамке считывания
if(document.transl.meth2.checked || document.transl.meth2_1.checked) {
id.document.write("<TT>" + "<font color=Red>frame +1</font><br>&gt; ");
aa1 = aa_tr(nseq,1);
id.document.write("</TT><br>");
}

// выводим aa последовательность в +2 рамке считывания
if(document.transl.meth2.checked || document.transl.meth2_2.checked) {
id.document.write("<TT>" + "<font color=Red>frame +2</font><br>&gt; ");
aa2 = aa_tr(nseq,2);
id.document.write("</TT><br>");
}

// выводим aa последовательность в +3 рамке считывания
if(document.transl.meth2.checked || document.transl.meth2_3.checked) {
id.document.write("<TT>" + "<font color=Red>frame +3</font><br>&gt; ");
aa3 = aa_tr(nseq,3);
id.document.write("</TT><br>");
}


if(document.transl.meth2.checked || document.transl.meth2_4.checked || document.transl.meth2_5.checked || document.transl.meth2_6.checked) {
id.document.write("<h4><font color=Blue>Translation in reverse direction:</font></h4>");
}

// выводим aa последовательность в -1 рамке считывания
if(document.transl.meth2.checked || document.transl.meth2_4.checked) {
id.document.write("<TT>" + "<font color=Blue>frame -1</font><br>&gt; ");
aa4 = aa_tr(c_seq,1);
id.document.write("</TT><br>");
}

// выводим aa последовательность в -2 рамке считывания
if(document.transl.meth2.checked || document.transl.meth2_5.checked) {
id.document.write("<TT>" + "<font color=Blue>frame -2</font><br>&gt; ");
aa5 = aa_tr(c_seq,2);
id.document.write("</TT><br>");
}

// выводим aa последовательность в -3 рамке считывания
if(document.transl.meth2.checked || document.transl.meth2_6.checked) {
id.document.write("<TT>" + "<font color=Blue>frame -3</font><br>&gt; ");
aa6 = aa_tr(c_seq,3);
id.document.write("</TT><br>");
}

// выводим всё вместе
if(document.transl.meth3.checked) 
{

alignstrings = Math.floor(lnseq/3/al);
if(document.transl.meth2.checked || document.transl.meth2_1.checked || document.transl.meth2_2.checked || document.transl.meth2_3.checked) 
{
	id.document.write("<h4>Sequences alignment:</h4><TT>");
	id.document.write("&gt; " + name_seq + "  -  " + lnseq + " nucleotides" + "<br><font color=Red>Translation in forward direction:</font><br><tt><font color='Gray'>");
	k1 = 0;
	while(k1<alignstrings+1) {
	k1++; 
	id.document.write("<br><font color=Red>DNA:</font>&nbsp;&nbsp;" + nseq.substring(k1*al*3-al*3, k1*al*3));
	if(document.transl.meth2.checked || document.transl.meth2_1.checked) {id.document.write("<br><font color=Red>+1fr:</font>&nbsp;" + aa1.substring((k1-1)*al*3, k1*al*3).replace(/\./g,"&middot;"))};
	if(document.transl.meth2.checked || document.transl.meth2_2.checked) {id.document.write("<br><font color=Red>+2fr:</font>&nbsp;&nbsp;" + aa2.substring((k1-1)*al*3, k1*al*3).replace(/\./g,"&middot;"))};
	if(document.transl.meth2.checked || document.transl.meth2_3.checked) {id.document.write("<br><font color=Red>+3fr:</font>&nbsp;&nbsp;&nbsp;" + aa3.substring((k1-1)*al*3, k1*al*3).replace(/\./g,"&middot;"))};
id.document.write("<br><br>");
	}
}

if(document.transl.meth2.checked || document.transl.meth2_4.checked || document.transl.meth2_5.checked || document.transl.meth2_6.checked) {
	id.document.write("</font></tt>&gt; " + name_seq + "  -  " + lnseq + " nucleotides" + "<br><font color=Blue>Translation in reverse direction:</font><br><tt><font color='Gray'>");
	k1 = 0;
	while(k1<alignstrings+1) {
	k1++; 
	id.document.write("<br><font color=Blue>DNA:</font>&nbsp;&nbsp;" + c_seq.substring((k1-1)*al*3, k1*al*3));
	if(document.transl.meth2.checked || document.transl.meth2_4.checked) {id.document.write("<br><font color=Blue>-1fr:</font>&nbsp;" + aa4.substring((k1-1)*al*3, k1*al*3).replace(/\./g,"&middot;"))};
	if(document.transl.meth2.checked || document.transl.meth2_5.checked) {id.document.write("<br><font color=Blue>-2fr:</font>&nbsp;&nbsp;" + aa5.substring((k1-1)*al*3, k1*al*3).replace(/\./g,"&middot;"))};
	if(document.transl.meth2.checked || document.transl.meth2_6.checked) {id.document.write("<br><font color=Blue>-3fr:</font>&nbsp;&nbsp;&nbsp;" + aa6.substring((k1-1)*al*3, k1*al*3).replace(/\./g,"&middot;"))};
id.document.write("<br><br>");
	}
}
}



// закрываем окно 
id.document.write("</font></tt></body></html>");
id.document.close();
}