Additional algorithm 85.html

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<!-- #  John Wiley & Sons, Inc.                                                                                                   # -->
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<!-- #  Book:   Algorithms in Bioinformatics: Theory and Implementation                                                           # -->
<!-- #  Author: Dr. Paul A. Gagniuc                                                                                               # -->
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<!-- #  Institution:                                                                                                              # -->
<!-- #    University Politehnica of Bucharest                                                                                     # -->
<!-- #    Faculty of Engineering in Foreign Languages                                                                             # -->
<!-- #    Department of Engineering in Foreign Languages                                                                          # -->
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<!-- #  Area:   European Union                                                                                                    # -->
<!-- #  Date:   04/01/2021                                                                                                        # -->
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<!-- #  Cite this work as:                                                                                                        # -->
<!-- #    Paul A. Gagniuc. Algorithms in Bioinformatics: Theory and Implementation. John Wiley & Sons, 2021, ISBN: 9781119697961. # -->
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<canvas id="bio" height="300" width="1100"></canvas>

<script>

// SCANNER
// THE INFORMATION ENTROPY
// THE INFORMATION CONTENT

var z = "AAAAAACAGGTGAGTAAAAAAAA";

var signal_s = '';
var signal_e = '';

var wl = 12;
var w = '';

var u = z.length - wl + 1;

for(var l=0; l<u; l++) {
    w = z.substr(l, wl);
    signal_s += content(w); 
    signal_e += entropy(w);
    
    if(l<u-1){
        signal_s += ',';
        signal_e += ',';
    }
}

document.write('<hr>Sequence: '+z+'<br>');
document.write('Information CONTENT: '+signal_s+'<br>');
document.write('Information ENTROPY: '+signal_e+'<br>');

Chart(signal_s, '#ff0000', 'y')
Chart(signal_e, '#000000', 'n')

//INFORMATION CONTENT (SELF-SEQUENCE ALIGNMENT)

function content(s)
{
    var t = 0;
    var m = 0;
    var x = [];
    
    x = s.split('');

    for (var u=1; u<=(s.length - 1); u++)
    {
        for (var i=0; i<=(s.length-u); i++)
        {m += f(x[i], x[u+i]);} 
        t += (m / (s.length-u) * 100);
        m = 0;
    }

    return (100 - (t / (s.length - 1))).toFixed(1);
}

function f(x1, x2){
    if (x1 == x2) {return 1;} else {return 0;}
}

//INFORMATION ENTROPY
function entropy(c){

    //ALPHABET DETECTION
    var a = [];
    var t = c.split('');
    var k = t.length;

    for(var i=0; i<=k; i++){
        var q = 1;
        for(var j=0; j<=a.length; j++){
            if (t[i] === a[j]) {q = 0;}
        }
        if (q === 1) {a.push(t[i]);}
    }

    var e = 0;
    var r = '';

    for(var i=0; i<=a.length-1; i++){
        r = c.replace(new RegExp(a[i], 'g'),'').length;
        a[i]=(k-r)/k;
        //e += -(a[i]*Log(2,a[i]));
        e += (a[i]*Log(2,(1/a[i])));
    }

    return e.toFixed(1);
}


function Log(n, v) {
  return Math.log(v) / Math.log(n);
}


function Chart(q,c,e) {
    
    var s = q.split(",");
    var mx = Math.max.apply(null, s);

    var canvas = document.getElementById('bio');

    var w = canvas.width;
    var h = canvas.height;
    
    if (canvas.getContext) {

        var ctx = canvas.getContext('2d');

        if(e=='y'){ctx.clearRect(0, 0, w, h);}
        
        ctx.moveTo(0, 0);
        ctx.beginPath();
        
        for (var i=0; i<=s.length-1; i++)
        {
            var y = h-((h / mx) * s[i]);
            var x = (w / s.length) * i;
            
            ctx.lineTo(x, y+2);
        }
        ctx.lineWidth = 2;
        ctx.strokeStyle = c;
        ctx.stroke();
    }
}

</script>