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bio::tools::analysis::simpleanalysisbase(3pm) [debian man page]

Bio::Tools::Analysis::SimpleAnalysisBase(3pm)		User Contributed Perl Documentation	     Bio::Tools::Analysis::SimpleAnalysisBase(3pm)

NAME

       Bio::Tools::Analysis::SimpleAnalysisBase - abstract superclass for SimpleAnalysis implementations

SYNOPSIS

       # not to be run directly

DESCRIPTION

       This class is a generic implementation of SimpleAnalysisI and should be used as a base class for specific implementations.

       Modules implementing SimpleAnalysisBase only need to provide specific _init(), _run() and result() methods, plus any get/set methods for
       parameters to the analysis program.

SEE ALSO

       Bio::SimpleAnalysisI, Bio::WebAgent

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:

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

AUTHORS

       Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

APPENDIX

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

   new
	Usage	: $job->new(...)
	Returns : a new analysis object,
	Args	: none (but an implementation may choose
		  to add arguments representing parameters for the analysis
		  program. Each key value of must have a method implemented
		  for it in a subclass. A seq () method is provided here as
		  this will probably be needed by all sequence analysis programs

   seq
	Usage	: $job->seq()
	Returns : a Bio::PrimarySeqI implementing sequence object, or void
	Args	: None, or a Bio::PrimarySeqI implementing object

   analysis_name
	   Usage     : $analysis->analysis_name();
	   Returns   : The analysis name
	   Arguments : none

   analysis_spec
	   Usage    :  $analysis->analysis_spec();
	   Returns  :  a hash reference to  a hash of analysis parameters. See
		       Bio::SimpleAnalysisI for a list of recommended key values.
	   Arguments:  none

   clear
	   Usage     : $analysis->clear();
	   Returns   : true value on success
	   Arguments : none
	   Purpose   : to remove raw results from a previous analysis so that
		       an analysis can be repeated with different parameters.

   input_spec
	   Usage     : $analysis->input_spec();
	   Returns   : a  reference to	an array of  hashes of analysis parameters. See
		       Bio::SimpleAnalysisI for a list of recommended key values.
	   Arguments : none

   result_spec
	   Usage     : $analysis->result_spec();
	   Returns   : a  reference to	a   hashes of resultformats. See
		       Bio::SimpleAnalysisI for a list of recommended key values.
		       The key values can be used as parameters to the result()
		       method, the values provide descriptions.
	   Arguments : none

perl v5.14.2							    2012-03-02			     Bio::Tools::Analysis::SimpleAnalysisBase(3pm)

Check Out this Related Man Page

Bio::Seq::SeqFastaSpeedFactory(3pm)			User Contributed Perl Documentation		       Bio::Seq::SeqFastaSpeedFactory(3pm)

NAME

       Bio::Seq::SeqFastaSpeedFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory

SYNOPSIS

	   use Bio::Seq::SeqFastaSpeedFactory;
	   my $factory = Bio::Seq::SeqFastaSpeedFactory->new();
	   my $seq = $factory->create(-seq => 'WYRAVLC',
				      -id  => 'name');

	   # If you want the factory to create Bio::Seq objects instead
	   # of the default Bio::PrimarySeq objects, use the -type parameter:

	   my $factory = Bio::Seq::SeqFastaSpeedFactory->new(-type => 'Bio::Seq');

DESCRIPTION

       This object will build Bio::Seq objects generically.

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 - Jason Stajich
       Email jason@bioperl.org

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 = Bio::Seq::SeqFastaSpeedFactory->new();
	Function: Builds a new Bio::Seq::SeqFastaSpeedFactory object
	Returns : Bio::Seq::SeqFastaSpeedFactory
	Args	: -type => string, name of a PrimarySeqI derived class
			   This is optional. Default=Bio::PrimarySeq.

   create
	Title	: create
	Usage	: my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name');
	Function: Instantiates a new Bio::Seq object, correctly built but very
		  fast, knowing stuff about Bio::PrimarySeq and Bio::Seq
	Returns : Bio::Seq

	Args	: initialization parameters specific to the type of sequence
		  object we want.  Typically
		  -seq	      => $str,
		  -id	      => $name

perl v5.14.2							    2012-03-02				       Bio::Seq::SeqFastaSpeedFactory(3pm)
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