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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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NAME

Bio::EnsEMBL::Utils::Argument - Utility functions for argument handling

SYNOPSIS

  use Bio::EnsEMBL::Utils::Argument qw(rearrange)

  package Feature;

  sub new {
    my $class = shift;
    my ( $start, $end, $strand ) =
      rearrange( [ 'START', 'END', 'STRAND' ], @_ );

    return
      bless( { 'start' => $start, 'end' => $end, 'strand' => $strand },
      $class );
  }

DESCRIPTION

This is derived from the Bio::Root module in BioPerl. The _rearrange object method taken from BioPerl has been renamed rearrange and is now a static class method. This method was originally written by Lincoln Stein, and has since been refactored several times by various people (as described below).

It is recommended that this package be used instead of inheriting unnecessarily from the Bio::EnsEMBL::Root or Bio::Root object.

METHODS

rearrange_pp

 Usage     : rearrange( array_ref, list_of_arguments)
 Purpose   : Rearranges named parameters to requested order.
 Example   : use Bio::EnsEMBL::Utils::Argument qw(rearrange);
           : rearrange([qw(SEQUENCE ID DESC)],@param);
           : Where @param = (-sequence => $s, 
                 :                 -id       => $i, 
                 :                     -desc     => $d);
 Returns   : @params - an array of parameters in the requested order.
           : The above example would return ($s, $i, $d)
 Argument  : $order : a reference to an array which describes the desired
           :          order of the named parameters.
           : @param : an array of parameters, either as a list (in
           :          which case the function simply returns the list),
           :          or as an associative array with hyphenated tags
           :          (in which case the function sorts the values 
           :          according to @{$order} and returns that new array.)
           :          The tags can be upper, lower, or mixed case
           :          but they must start with a hyphen (at least the
           :          first one should be hyphenated.)
 Source    : This function was taken from CGI.pm, written by Dr. Lincoln
           : Stein, and adapted for use in Bio::Seq by Richard Resnick and
           : then adapted for use in Bio::Root::Object.pm by Steve A. Chervitz.
           : This has since been adapted as an exported static method in this 
             class Bio::EnsEMBL::Utils::Argument 
 Comments  : (SAC)
           : This method may not be appropriate for method calls that are
           : within in an inner loop if efficiency is a concern.
           :
           : Parameters can be specified using any of these formats:
           :  @param = (-name=>'me', -color=>'blue');
           :  @param = (-NAME=>'me', -COLOR=>'blue');
           :  @param = (-Name=>'me', -Color=>'blue');
           : A leading hyphenated argument is used by this function to 
           : indicate that named parameters are being used.
           : Therefore, a ('me', 'blue') list will be returned as-is.
           :
           : Note that Perl will confuse unquoted, hyphenated tags as 
           : function calls if there is a function of the same name 
           : in the current namespace:
           :    -name => 'foo' is interpreted as -&name => 'foo'
           :
           : For ultimate safety, put single quotes around the tag:
                 :    ('-name'=>'me', '-color' =>'blue');
           : This can be a bit cumbersome and I find not as readable
           : as using all uppercase, which is also fairly safe:
           :    (-NAME=>'me', -COLOR =>'blue');
                 :
           : Personal note (SAC): I have found all uppercase tags to
           : be more managable: it involves less single-quoting,
           : the code is more readable, and there are no method naming 
           : conlicts.
           : Regardless of the style, it greatly helps to line
                 : the parameters up vertically for long/complex lists.