Question

i am trying to learn php as i Study genetics and this would be useful for bioinformatics. I am having trouble with my code and im sure its something very stupid but i cant see a solution.

this is my code:

    $query="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC";

$seq=chunk_split($query,40,"<br />");

$truecol="<div style=\"color: hsl(0,100%,50%);\">";


function colorSequence ($seq,$position,$truecol,$TFBSlength){
    $nucleotides = str_split($seq);
    foreach ($nucleotides as $index => $nucl){
        if ($index == $position){
            echo $truecol;
        }
        if ($index == $position + $TFBSlength){
            echo "</div>";
        }

           echo $nucl;
    }
    echo "\n";
}
colorSequence($seq,5,$truecol,3);

The output gives:

AAAAAAAAAA
(this is coloured)AAAAA(end of colour)
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

The first row has 10 letters the second has 5 coloured letters and the 3rd row has 45 letters. All rows should have 60 letters. Can anyone help?

Answer 1

You might want to use the <span> HTML tag instead of <div>.

Because each <div> is normally displayed by browsers with a line-break above and below.

Alternatively you can define how <div> should look like with CSS, but I think that’s too much for the moment:

div {display: inline;}

Example with the <span> HTML element and using substr (I might be off by one or so, I assume you can fix that):

$truecol = 'hsl(0,100%,50%)';
colorSequence($seq, 5, $truecol, 3);

function colorSequence ($seq, $position, $truecol, $TFBSlength)
{
    $before = substr($seq, 0, $position);
    $color  = substr($seq, $position, $TFBSlength);
    $after  = substr($seq, $position + $TFBSLength);
    printf("%s<span style=\"color: %s;\">%s</span>%s\n",
           $before, $truecol, $color, $after);
}