[Biophp-dev] sample

[Nico Stuurman]

Hi Can,

Thanks for contributing!  The code looks fine.  A long time ago we all
promised to adhere to the PEAR coding standards.  They are described
here: http://pear.php.net/manual/en/standards.php
Very short summary: 
- Use 4 spaces instead of tabs
- Curly braces: after function/object definitions on new line, otherwise
at end of line
- spaces in places I would not put them
- Lots of comments (do not use Perl style # comments)
- Use phpdoc style of commenting (http://www.phpdoc.org).  

It would be nice if you could add more comments in the source
(preferably using the phpdoc convention).  For instance, what does this
function do, what do the variables mean, what are the numbers in array
$aminoacids and where do they come from (a reference would be great). 

I hope I don't discourage you, but I do think this will make the code
more useful in the long run.

For 'testcases' we have a directory 'testfiles' where code
demonstrating/testing functions/objects should go (with associated
'testdata' in 'testdata').


Another question is where the code should go.  I plan to 'pearify' the
seq_inc.php file.  Currently there is a bunch of functions in this file,
and two objects (protein and seq if I am not mistaken).  It makes sense
to me to split this out into at least three files: one with functions
(maybe two: one for DNA and the other for protein), and one each for
each object.  As a general strategy of making biophp useful even if you
do not want to use the biophp objects, I think it makes sense to make
every function available outside of the object and to simply make object
member functions that call the appropriate function outside of the
object.  Does this make sense?  I probably should just get started...


Best,

Nico 


On Mon, 2004-03-29 at 22:12, Can Tran wrote:
> Hi,
> Sorry about my late start in biophp development.
> I've been pretty busy with work.
> Just wanted to run a sample function by you guys to see
> if it meets coding standard. I wasn't sure if you had any
> coding conventions.
> Best wishes,
> can
> 
> <?php
> 
> function hydropathy($sequence, $window, &$x, &$y)
> {
> 
> 	$aminoacids = array(
>      "G"=>-0.400, "A"=>1.800, "V"=>4.200, "L"=>3.800,
>      "I"=>4.500, "M"=>1.900, "F"=>2.800, "P"=>-1.600,
>      "S"=>-0.800, "T"=>-0.700, "C"=>2.500, "N"=>-3.500,
>      "Q"=>-3.500, "Y"=>-1.300, "W"=>-0.900, "D"=>-3.500,
>      "E"=>-3.500, "H"=>-3.200, "K"=>-3.900, "R"=>-4.500
>      );
> 
> 	$midpt = ($window + 1) / 2;
> 	$length = strlen($sequence);
> 	for($i = 0; $i < $length - $window; $i++)
> 	{
> 		$total = 0;
> 		for($j = 0; $j < $window; $j++)
> 		{
> 			$total = $total + $aminoacids[$sequence[$i + $j]];
> 		}
> 		$total = $total / $window;
> 
> 		$x[$i] = $i + $midpt;
> 		$y[$i] = $total;
> 
> 		if($total > $max)
> 		{
> 			$max = $total;
> 		}
> 
> 		if($total < $min)
> 		{  
> 			$min = $total;
> 		}
> 	}
> }
> 
> 
> 
> $sequence = 
> "MPPMLSGLLARLVKLLLGRHGSALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRLVAVVVMVAGITSFGLVTAALATWFVGREQERRGHFVRHSEKAAEEAYTRTTRALHERFDRLERMLDDNRR";
> 
> hydropathy($sequence, 19, $array1, $array2);
> echo "<PRE>";
> for($i = 0; $i < count($array1); $i++)
> {
> 	echo "$array1[$i] \t $array2[$i] \n";
> }
> echo "</PRE>";
> ?>