bio::tools::run::phylo::phylip::base(3pm) [debian man page]

Bio::Tools::Run::Phylo::Phylip::Base(3pm)		User Contributed Perl Documentation		 Bio::Tools::Run::Phylo::Phylip::Base(3pm)

NAME

       Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules

SYNOPSIS

       # Do not use directly # This module is for setting basic data sets for the Phylip wrapper # modules

DESCRIPTION

       This module is just a base object for Bioperl Phylip wrappers.

       IMPORTANT PHYLIP VERSION ISSUES By default we assume you have Phylip 3.6 installed, if you have installed Phylip 3.5 you need to set the
       environment variable PHYLIPVERSION

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 - Jason Stajich
       Email jason-at-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::Tools::Run::Phylo::Phylip::Base->new();
	Function: Builds a new Bio::Tools::Run::Phylo::Phylip::Base object
	Returns : an instance of Bio::Tools::Run::Phylo::Phylip::Base
	Args	:

   outfile
	Title	: outfile
	Usage	: $obj->outfile($newval)
	Function: Get/Set default PHYLIP outfile name ('outfile' usually)
		  Changing this is only necessary when you have compiled
		  PHYLIP to use a different filename for the default 'outfile'
		  This will not change the default output filename by
		  PHYLIP
	Returns : value of outfile
	Args	: newvalue (optional)

   treefile
	Title	: treefile
	Usage	: $obj->treefile($newval)
	Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
	Returns : value of treefile
	Args	: newvalue (optional)

   fontfile
	Title	: fontfile
	Usage	: $obj->fontfile($newval)
	Function: Get/Set the fontfile
	Returns : value of fontfile (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   plotfile
	Title	: plotfile
	Usage	: $obj->plotfile($newval)
	Function: Get/Set the plotfile
	Returns : value of plotfile (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   version
	Title	: version
	Usage	: $obj->version($newval)
	Function: Get/Set the version
	Returns : value of version (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

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

Check Out this Related Man Page

Bio::TreeIO::TreeEventBuilder(3pm)			User Contributed Perl Documentation			Bio::TreeIO::TreeEventBuilder(3pm)

NAME

       Bio::TreeIO::TreeEventBuilder - Build Bio::Tree::Tree's and
	 Bio::Tree::Node's from Events

SYNOPSIS

       # internal use only

DESCRIPTION

       This object will take events and build a Bio::Tree::TreeI compliant object makde up of Bio::Tree::NodeI objects.

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-at-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::TreeIO::TreeEventBuilder->new();
	Function: Builds a new Bio::TreeIO::TreeEventBuilder object
	Returns : Bio::TreeIO::TreeEventBuilder
	Args	:

   treetype
	Title	: treetype
	Usage	: $obj->treetype($newval)
	Function:
	Returns : value of treetype
	Args	: newvalue (optional)

   nodetype
	Title	: nodetype
	Usage	: $obj->nodetype($newval)
	Function:
	Returns : value of nodetype
	Args	: newvalue (optional)

   SAX methods
   start_document
	Title	: start_document
	Usage	: $handler->start_document
	Function: Begins a Tree event cycle
	Returns : none
	Args	: none

   end_document
	Title	: end_document
	Usage	: my @trees = $parser->end_document
	Function: Finishes a Phylogeny cycle
	Returns : An array  Bio::Tree::TreeI
	Args	: none

   start_element
	Title	: start_element
	Usage	:
	Function:
	Example :
	Returns :
	Args	: $data => hashref with key 'Name'

   end_element
	Title	: end_element
	Usage	:
	Function:
	Returns : none
	Args	: $data => hashref with key 'Name'

   in_element
	Title	: in_element
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   within_element
	Title	: within_element
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   characters
	Title	: characters
	Usage	: $handler->characters($text);
	Function: Processes characters
	Returns : none
	Args	: text string

perl v5.14.2							    2012-03-02					Bio::TreeIO::TreeEventBuilder(3pm)

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bio::tools::run::phylo::phylip::base(3pm) [debian man page]

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