bio::seqio::tinyseq::tinyseqhandler(3pm) [debian man page]

Bio::SeqIO::tinyseq::tinyseqHandler(3pm)		User Contributed Perl Documentation		  Bio::SeqIO::tinyseq::tinyseqHandler(3pm)

NAME

       Bio::SeqIO::tinyseq::tinyseqHandler - XML event handlers to support NCBI TinySeq XML parsing

SYNOPSIS

       Do not use this module directly; use the SeqIO handler system:

	 $stream = Bio::SeqIO->new( -file => $filename, -format => 'tinyseq' );

	 while ( my $seq = $stream->next_seq ) {
	   ....
	 }

DESCRIPTION

       This object provides event handler methods for parsing sequence files in the NCBI TinySeq XML format.  A TinySeq is a lightweight XML file
       of sequence information on one or more sequences, analgous to FASTA format.

       See <http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.mod.dtd> for the DTD.

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/

SEE ALSO

       Bio::SeqIO, Bio::Seq.

AUTHOR

       Donald Jackson, <donald.jackson@bms.com>

APPENDIX

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

   new
	 Title	       : new
	 Usage	       : $handler = Bio::SeqIO::tinyseq::tinyseqHandler->new()
	 Function      : instantiates a tinyseqHandler for use by
			 XML::Parser::PerlSAX
	 Returns       : Bio::SeqIO::tinyseq::tinyseqHandler object
	 Args	       : NONE

   start_document
	 Title	       : start_document
	 Usage	       : NONE
	 Function      : start_document handler for use by XML::Parser::PerlSAX
	 Returns       : NONE
	 Args	       : NONE

   end_document
	 Title	       : end_document
	 Usage	       : NONE
	 Function      : end_document handler for use by XML::Parser::PerlSAX
	 Returns       : NONE
	 Args	       : NONE

   start_element
	 Title	       : start_element
	 Usage	       : NONE
	 Function      : start_element handler for use by XML::Parser::PerlSAX
	 Returns       : NONE
	 Args	       : NONE

   end_element
	 Title	       : end_element
	 Usage	       : NONE
	 Function      : end_element handler for use by XML::Parser::PerlSAX
	 Returns       : NONE
	 Args	       : NONE

   characters
	 Title	       : characters
	 Usage	       : NONE
	 Function      : characters handler for use by XML::Parser::PerlSAX
	 Returns       : NONE
	 Args	       : NONE

   TSeq
	 Title	       : TSeq
	 Usage	       : NONE
	 Function      : event handler for END of a TSeq element
	 Returns       : loh of parsed sequence atts for Bio::SeqIO::tinyseq
	 Args	       : NONE

   _current_element
	 Title	       : _current_element
	 Usage	       : Internal method
	 Function      : Utility method to return current element info
	 Returns       : XML::Parser::PerlSAX hash for current element
	 Args	       : NONE

perl v5.14.2							    2012-03-02				  Bio::SeqIO::tinyseq::tinyseqHandler(3pm)