bio::searchio::xml::psiblasthandler(3pm) [debian man page]
Bio::SearchIO::XML::PsiBlastHandler(3pm) User Contributed Perl Documentation Bio::SearchIO::XML::PsiBlastHandler(3pm) NAME
Bio::SearchIO::XML::PsiBlastHandler - XML Handler for NCBI Blast PSIBLAST XML parsing. SYNOPSIS
# This is not to be used directly. DESCRIPTION
This is the XML handler for BLAST PSIBLAST XML parsing. Currently it passes elements off to the event handler, which is ultimately responsible for Bio::Search object generation. This was recently split off from the original code for Bio::SearchIO::blastxml primarily for maintenance purposes. DEPENDENCIES
In addition to parts of the Bio:: hierarchy, this module uses: XML::SAX::Base which comes with the XML::SAX 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 - Jason Stajich, Chris Fields Email jason-at-bioperl.org Email cjfields-at-uiuc dot edu APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ SAX methods start_document Title : start_document Usage : $parser->start_document; Function: SAX method to indicate starting to parse a new document Returns : none Args : none end_document Title : end_document Usage : $parser->end_document; Function: SAX method to indicate finishing parsing a new document Returns : Bio::Search::Result::ResultI object Args : none start_element Title : start_element Usage : $parser->start_element($data) Function: SAX method to indicate starting a new element Returns : none Args : hash ref for data end_element Title : end_element Usage : $parser->end_element($data) Function: Signals finishing an element Returns : Bio::Search object dpending on what type of element Args : hash ref for data characters Title : characters Usage : $parser->characters($data) Function: Signals new characters to be processed Returns : characters read Args : hash ref with the key 'Data' perl v5.14.2 2012-03-02 Bio::SearchIO::XML::PsiBlastHandler(3pm)
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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)