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bio::tools::run::genericparameters(3pm) [debian man page]

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

NAME

       Bio::Tools::Run::GenericParameters - An object for the parameters used to run programs

SYNOPSIS

	 my $void   = $obj->set_parameter("parameter_name","parameter_value");
	 my $value  = $obj->get_parameter("parameter_name");

DESCRIPTION

       This is a basic container to hold the parameters used to run a program.	This module may get incorporated into the more generic
       Bio::Tools::Run framework in bioperl-run distribution.

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 the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

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

AUTHOR - Chad Matsalla
       Email bioinformatics1 at dieselwurks dot com

CONTRIBUTORS

       Sendu Bala, bix@sendu.me.uk

APPENDIX

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

   get_parameter
	Title	: get_parameter
	Usage	: $parameter_object->get_parameter($param_name);
	Function: Get the value of a parameter named $param_name
	Returns : A scalar that should be a string
	Args	: A scalar that should be a string

   set_parameter
	Title	: set_parameter
	Usage	: $parameter_object->set_parameter($param_name => $param_value);
	Function: Set the value of a parameter named $param_name to $param_value
	Returns : Void
	Args	: A hash containing name=>value pairs

   available_parameters
	Title	: available_parameters
	Usage	: my @paramnames = $parameter_object->available_parameters
	Function: Returns the names of the available parameters
	Returns : list of available parameter names
	Args	: none

perl v5.14.2							    2012-03-02				   Bio::Tools::Run::GenericParameters(3pm)

Check Out this Related Man Page

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

NAME

       Bio::Tools::Run::BlastPlus - A wrapper for NCBI's blast+ suite

SYNOPSIS

       Give standard usage here

DESCRIPTION

       Blast+ is NCBI's successor to the "blastall" family of programs.

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 the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

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

AUTHOR - Mark A. Jensen
       Email maj -at- fortinbras -dot- us

       Describe contact details here

CONTRIBUTORS

       Additional contributors names and emails here

APPENDIX

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

   new
	Title	: new
	Usage	: my $obj = new Bio::Tools::Run::BlastPlus();
	Function: Builds a new Bio::Tools::Run::BlastPlus object
	Returns : an instance of Bio::Tools::Run::BlastPlus
	Args	:

   program_version()
	Title	: program_version
	Usage	: $version = $bedtools_fac->program_version()
	Function: Returns the program version (if available)
	Returns : string representing location and version of the program
	Note	: this works around the WrapperBase::version() method conflicting with
		  the -version parameter for SABlast (good argument for not having
		  getter/setters for these)

   package_version()
	Title	: package_version
	Usage	: $version = $bedtools_fac->version()
	Function: Returns the BLAST+ package version (if available)
	Returns : string representing BLAST+ package version (may differ from version())

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