bio::treeio::treeeventbuilder(3pm) [debian 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)

Bio::SearchIO::waba(3pm)				User Contributed Perl Documentation				  Bio::SearchIO::waba(3pm)

NAME

       Bio::SearchIO::waba - SearchIO parser for Jim Kent WABA program alignment output

SYNOPSIS

	   # do not use this object directly, rather through Bio::SearchIO

	   use Bio::SearchIO;
	   my $in = Bio::SearchIO->new(-format => 'waba',
				      -file   => 'output.wab');
	   while( my $result = $in->next_result ) {
	       while( my $hit = $result->next_hit ) {
		   while( my $hsp = $result->next_hsp ) {

		   }
	       }
	   }

DESCRIPTION

       This parser will process the waba output (NOT the human readable format).

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::SearchIO::waba->new();
	Function: Builds a new Bio::SearchIO::waba object
	Returns : Bio::SearchIO::waba
	Args	: see Bio::SearchIO

   next_result
	Title	: next_result
	Usage	: my $hit = $searchio->next_result;
	Function: Returns the next Result from a search
	Returns : Bio::Search::Result::ResultI object
	Args	: none

   start_element
	Title	: start_element
	Usage	: $eventgenerator->start_element
	Function: Handles a start element event
	Returns : none
	Args	: hashref with at least 2 keys 'Data' and 'Name'

   end_element
	Title	: start_element
	Usage	: $eventgenerator->end_element
	Function: Handles an end element event
	Returns : none
	Args	: hashref with at least 2 keys 'Data' and 'Name'

   element
	Title	: element
	Usage	: $eventhandler->element({'Name' => $name, 'Data' => $str});
	Function: Convience method that calls start_element, characters, end_element
	Returns : none
	Args	: Hash ref with the keys 'Name' and 'Data'

   characters
	Title	: characters
	Usage	: $eventgenerator->characters($str)
	Function: Send a character events
	Returns : none
	Args	: string

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

   within_element
	Title	: within_element
	Usage	: if( $eventgenerator->within_element($element) ) {}
	Function: Test if we are within a particular element
		  This is different than 'in' because within can be tested
		  for a whole block.
	Returns : boolean
	Args	: string element name

   in_element
	Title	: in_element
	Usage	: if( $eventgenerator->in_element($element) ) {}
	Function: Test if we are in a particular element
		  This is different than 'in' because within can be tested
		  for a whole block.
	Returns : boolean
	Args	: string element name

   start_document
	Title	: start_document
	Usage	: $eventgenerator->start_document
	Function: Handles a start document event
	Returns : none
	Args	: none

   end_document
	Title	: end_document
	Usage	: $eventgenerator->end_document
	Function: Handles an end document event
	Returns : Bio::Search::Result::ResultI object
	Args	: none

   result_count
	Title	: result_count
	Usage	: my $count = $searchio->result_count
	Function: Returns the number of results we have processed
	Returns : integer
	Args	: none

perl v5.14.2							    2012-03-02						  Bio::SearchIO::waba(3pm)