go::utils(3pm) [debian man page]

GO::Utils(3pm)						User Contributed Perl Documentation					    GO::Utils(3pm)

NAME

       GO::Utils - utilities for GO modules

   rearrange()
	Usage	 : n/a
	Function : Rearranges named parameters to requested order.
	Returns  : @params - an array of parameters in the requested order.
	Argument : $order : a reference to an array which describes the desired
			    order of the named parameters.
		   @param : an array of parameters, either as a list (in
			    which case the function simply returns the list),
			    or as an associative array (in which case the
			    function sorts the values according to @{$order}
			    and returns that new array.

	Exceptions : carps if a non-recognised parameter is sent

   get_param()
       Usage	: get_param('name',(-att1=>'ben',-name=>'the_name')) Function : Fetches a  named parameter.  Returns  : The value of the requested
       parameter.  Argument : $name : The name of the the parameter desired
		  @param : an array of parameters, as an associative array Exceptions : carps if a non-recognised parameter is sent

       Based on rearrange(), which is originally from CGI.pm by Lincoln Stein and BioPerl by Richard Resnick.  See rearrange() for details.

   remove_duplicates
       remove duplicate items from an array

	usage: remove_duplicates(@arr)

       affects the array passed in, and returns the modified array

merge_hashes
       joins two hashes together

	usage: merge_hashes(\%h1, \%h2);

       %h1 will now contain the key/val pairs of %h2 as well. if there are key conflicts, %h2 values will take precedence.

get_method_ref
	returns a pointer to a particular objects method
	e.g.   my $length_f = get_method_ref($seq, 'length');
	       $len = &$length_f();

   pset2hash
	 Usage	 - my $h = pset2hash([{name=>"id", value=>"56"}, {name=>"name", value=>"jim"}]);
	 Returns - hashref
	 Args	 - arrayref of name/value keyed hashrefs

   spell_greek
       takes a word as a parameter and spells out any greek symbols encoded within (eg s/&agr;/alpha/g)

   check_obj_graph
	 Usage	 -
	 Returns - true if cycle detected
	 Args	 - any object

perl v5.14.2							    2013-02-07							    GO::Utils(3pm)

Bio::Tools::Run::Prints(3pm)				User Contributed Perl Documentation			      Bio::Tools::Run::Prints(3pm)

NAME

       Bio::Tools::Run::Prints

SYNOPSIS

	 Build a Prints factory

	 my @params = ('DB',$dbfile);
	 my $factory = Bio::Tools::Run::Prints->new($params);

	 # Pass the factory a Bio::Seq object
	 # @feats is an array of Bio::SeqFeature::Generic objects
	 my @feats = $factory->run($seq);

DESCRIPTION

	 FingerPRINTScan II is a PRINTS fingerprint identification algorithm.
	 Copyright (C) 1998,1999  Phil Scordis

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Bala
	Email savikalpa@fugu-sg.org

APPENDIX

	The rest of the documentation details each of the object
	methods. Internal methods are usually preceded with a _

   program_name
	Title	: program_name
	Usage	: $factory>program_name()
	Function: holds the program name
	Returns:  string
	Args	: None

   program_dir
	Title	: program_dir
	Usage	: $factory->program_dir(@params)
	Function: returns the program directory, obtained from ENV variable.
	Returns:  string
	Args	:

   new
	Title	: new
	Usage	: $prints->new(@params)
	Function: creates a new Prints factory
	Returns:  Bio::Tools::Run::Prints
	Args	:

   predict_protein_features
	Title	:   predict_protein_features()
	Usage	:   DEPRECATED. Use $obj->run($seqFile) instead.
	Function:   Runs Prints and creates an array of featrues
	Returns :   An array of Bio::SeqFeature::Generic objects
	Args	:   A Bio::PrimarySeqI

   run
	Title	:   run
	Usage	:   $obj->run($seq)
	Function:   Runs Prints
	Returns :   An array of Bio::SeqFeature::Generic objects
	Args	:   A Bio::PrimarySeqI, or a Fasta file name

   _input
	Title	:   _input
	Usage	:   obj->_input($seqFile)
	Function:   Internal(not to be used directly)
	Returns :
	Args	:

   _run
	Title	:   _run
	Usage	:   $obj->_run()
	Function:   Internal(not to be used directly)
	Returns :   An array of Bio::SeqFeature::Generic objects
	Args	:

   _writeSeqFile
	Title	:   _writeSeqFile
	Usage	:   obj->_writeSeqFile($seq)
	Function:   Internal(not to be used directly)
	Returns :
	Args	:

perl v5.12.3							    2011-06-18					      Bio::Tools::Run::Prints(3pm)