How to wordwrap with different length / string modification? - php

Question

I have a problem with my code that i dont understand.
can anyone help please ?
$query="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC";
$seq=chunk_split($query,50,"<br />");
$truecol = "<span style=\"color: hsl(0,100%,25%);\">";
function colorSequence ($seq,$position,$truecol,$TFBSlength){
$nucleotides = str_split($seq);
foreach ($nucleotides as $index => $nucl){
if ($index == $position){
echo $truecol;
}
if ($index == $position + $TFBSlength){
echo "</span>";
}
echo $nucl;
}
echo "\n";
}
colorSequence($seq,49,$truecol,1);
?>
This is my code. Basically I wan the output code to look like this:
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA(red)A(/red)
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
and it does when i run the function colorSequence($seq,49,$truecol,1);
however if i run colorSequence($seq,49,$truecol,3); i get this:
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA< span="">r />AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC<>(all letters from letter 49 are red, even tho i only want 3 letters form 49 to 51 to be red).
can anyone fix this please ?

Answer 1

$query="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC";
$seq=chunk_split($query,50,'');
$truecol = "<span style=\"color: hsl(0,100%,25%);\">";
function colorSequence ($seq,$position,$truecol,$TFBSlength){
$nucleotides = str_split($seq);
foreach ($nucleotides as $index => $nucl){
if ($index == $position){
echo $truecol;
}
if ($index == $position + $TFBSlength){
echo "</span>";
}
if(($index%50)==0){
echo '<br>';
}
echo $nucl;
}
echo "\n";
}
colorSequence($seq,49,$truecol,1);
echo '<hr>';
colorSequence($seq,49,$truecol,3)

Answer 2

if you print_r($nucleotides), you will see that
Array
(
......
[49] => A
[50] => <
[51] => b
[52] => r
[53] =>
......
)
so you are inserting the <span> into <br /> which destroys the following html...

Answer 3

The span tag added by your function breaks the HTML created by chunk_split.

Answer 4

When you modify the DNS string $query you need to differ between the position of the nucleotides and general string offsets.
While at first both are identical, the more you add to the string, the more this differs.
If you encapsulate the string into an object of it's own that take care of the HTML tags and don't count them (including surrounding whitespace around the tags), things become easy again:
$query = "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC";
// wrap line: 11 lines à 50 nucleotids
$seq = chunk_split($query, 50, "<br />\n");
// get help from sequence object
$sequence = new AmendSequence($seq);
// some HTML comments for demonstration purposes
$sequence->insertAt(0, "<!-- first line -->\n");
$sequence->insertAt(50, "<!-- second line -->\n", TRUE); # TRUE: Place after <br />
$sequence->insertAt(75, "<!-- inside second line -->");
$sequence->insertAt(550, "<!-- at end -->", TRUE); # TRUE: Place after <br />
// colorize
$color = '<span style="color: hsl(0,100%,25%);">';
$sequence->insertAt(49, $color);
$sequence->insertAt(50, '</span>');
printf("Sequence with %d nucleotids:\n", count($sequence)); # count gives length w/o amends
echo $sequence, "\n"; # that prints your sequence with all amends
Which creates the following output:
Sequence with 550 nucleotids:
<!-- first line -->
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA<span style="color: hsl(0,100%,25%);">A</span><br />
<!-- second line -->
AAAAAAAAAAAAAAAAAAAAAAAAA<!-- inside second line -->AAAAAAAAAAAAAAAAAAAAAAAAA<br />
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA<br />
AAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB<br />
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB<br />
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB<br />
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBCCCCCC<br />
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC<br />
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC<br />
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC<br />
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC<br />
<!-- at end -->
So the actual magic here is the insertAt method which accepts the offset position of the nucledotide and calculates the string offset for it. It's all encapsulated into a class of it's own which probably is a bit too much for the beginning, however the real action is dividing the string that contains the DNA and the HTML into segements of DNS only and getting their actual string offset. The full source code:
<?php
/**
* #link http://stackoverflow.com/questions/10446162/how-to-wordwrap-with-different-length-string-modification
*/
/**
* Treat text with "tags" as text without tags when insertAt() is called.
*/
class AmendSequence implements IteratorAggregate, Countable
{
/**
* regex pattern for a tag
*/
const TAG = '\s*<[^>]*>\s*';
/**
* #var string
*/
private $query;
/**
* #param string $query
*/
public function __construct($query = '')
{
$this->setQuery($query);
}
/**
* #param int $offset
* #param string $string
* #param bool $after (optional) prefer after next tag instead before
*/
public function insertAt($offset, $string, $after = FALSE)
{
$offset = $this->translate($offset, $after);
$this->query = substr_replace($this->query, $string, $offset, 0);
}
/**
* Translate virtual offset to string offset
* #param int $virtualOffset
* #return int
* #throws InvalidArgumentException
*/
public function translate($virtualOffset, $after)
{
if ($virtualOffset < 0) throw new InvalidArgumentException(sprintf('Offset can not be lower than 0, is %d.', $virtualOffset));
$virtualCurrent = 0;
foreach ($this as $segment) {
list(, $current, $length) = $segment;
$delta = ($virtualOffset - $virtualCurrent) - $length;
if ($delta < 0 || ($delta === 0 && !$after)) {
return $current + $length + $delta;
}
$virtualCurrent += $length;
}
if ($virtualCurrent === $virtualOffset && $after) {
return strlen($this->query);
}
throw new InvalidArgumentException(sprintf('Offset can not be larger than %d, is %d.', $virtualCurrent, $virtualOffset));
}
/**
* #return array
*/
public function getSegments()
{
$segments = preg_split('/' . self::TAG . '/', $this->query, 0, PREG_SPLIT_OFFSET_CAPTURE | PREG_SPLIT_NO_EMPTY);
foreach ($segments as &$segment) {
$segment[2] = strlen($segment[0]);
}
return $segments;
}
public function getSequence()
{
$buffer = '';
foreach ($this as $segment) {
$buffer .= $segment[0];
}
return $buffer;
}
/**
* #return string
*/
public function getQuery()
{
return $this->query;
}
/**
* #param string $query
*/
public function setQuery($query)
{
$this->query = (string)$query;
}
/**
* Retrieve an external iterator
* #link http://php.net/manual/en/iteratoraggregate.getiterator.php
* #return Traversable An instance of an object implementing <b>Iterator</b> or <b>Traversable</b>
*/
public function getIterator()
{
return new ArrayIterator($this->getSegments());
}
/**
* #link http://php.net/manual/en/countable.count.php
* #return int The custom count as an integer.
*/
public function count()
{
$length = 0;
foreach ($this as $segment) {
$length += $segment[2];
}
return $length;
}
/**
* #return string
*/
public function __toString()
{
return $this->query;
}
}
$query = "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC";
// wrap line: 11 lines à 50 nucleotids
$seq = chunk_split($query, 50, "<br />\n");
// get help from sequence object
$sequence = new AmendSequence($seq);
// some HTML comments for demonstration purposes
$sequence->insertAt(0, "<!-- first line -->\n");
$sequence->insertAt(50, "<!-- second line -->\n", TRUE); # TRUE: Place after <br />
$sequence->insertAt(75, "<!-- inside second line -->");
$sequence->insertAt(550, "<!-- at end -->", TRUE); # TRUE: Place after <br />
// colorize
$color = '<span style="color: hsl(0,100%,25%);">';
$sequence->insertAt(49, $color);
$sequence->insertAt(50, '</span>');
printf("Sequence with %d nucleotids:\n", count($sequence)); # count gives length w/o amends
echo $sequence, "\n"; # that prints your sequence with all amends
echo $sequence->getSequence(); # without the amends
Feel free now to colorize as many parts as you like - with or without other HTML already inside the sequence.