Bio::AlignIO::Handler::GenericAlignHandler(3pm) 	User Contributed Perl Documentation	   Bio::AlignIO::Handler::GenericAlignHandler(3pm)

NAME

       Bio::AlignIO::Handler::GenericAlignHandler - Bio::HandlerI-based generic data handler class for alignment-based data

SYNOPSIS

	 # MyHandler is a GenericAlignHandler object.
	 # inside a parser (driver) constructor....

	 $self->alignhandler($handler || MyHandler->new(-format => 'stockholm'));

	 # in next_aln() in driver...

	 $hobj = $self->alignhandler();

	 # roll data up into hashref chunks, pass off into Handler for processing...

	 $hobj->data_handler($data);

	 # or retrieve Handler methods and pass data directly to Handler methods...

	 my $hmeth = $hobj->handler_methods;

	 if ($hmeth->{ $data->{NAME} }) {
	     my $mth = $hmeth->{ $data->{NAME} };
	     $hobj->$mth($data);
	 }

DESCRIPTION

       This is an experimental implementation of a alignment-based HandlerBaseI parser and may change over time. It is possible that the way
       handler methods are set up will change over development to allow more flexibility.

       Standard Developer caveats:

       Here thar be dragoons...

       Consider yourself warned!

   NOTES
       As in the SeqIO Handler object (still in development), data is passed in as chunks. The Annotation and SeqFeatures are essentially the same
       as the SeqIO parser; the significant difference is that data hash being passed could pertain to either the alignment or to a specific
       sequence, so an extra tag may be needed to disambiguate between the two in some cases. Here I use the ALIGNMENT tag as a boolean flag: it
       must be present and set to 0 for the data to be tagged for Bio::LocatableSeq or similar (in all other cases it is assumed to be for the
       alignment). In some cases this will not matter (the actual sequence data, for instance) but it is highly recommmended adding this tag in to
       prevent possible ambiguities.

       This is the current Annotation data chunk (via Data::Dumper):

	 $VAR1 = {
		   'NAME' => 'REFERENCE',
		   'DATA' => '1  (bases 1 to 10001)'
		   'AUTHORS' => 'International Human Genome Sequencing Consortium.'
		   'TITLE' => 'The DNA sequence of Homo sapiens'
		   'JOURNAL' => 'Unpublished(2003)'
		   'ALIGNMENT' => 1,
		 };

       In the case of LocatableSeqs, one can pass them in as follows for simplicity (note the block line):

	 $VAR1 = {
		   'NAME' => 'SEQUENCE',
		   'BLOCK_LINE' => 0,
		   'NSE' => 'Q7WNI7_BORBR/113-292',
		   'ALPHABET' => 'protein',
		   'DATA' => 'VALILGVYRRL...CYVNREM..RAG....QW',
		   'ALIGNMENT' => 0
		 };

       This can be done as the parser parses each block instead of parsing all the blocks and then passing them in one at a time; the handler will
       store the sequence data by the block line in an internal hash, concatenating them along the way.  This behaviour is b/c the alignment
       building step requires that the sequence be checked for start/end/strand, possible meta sequence, optional accession, etc.

       Similarly, a Meta sequence line can be passed in as follows:

	 $VAR1 = {
		   'NAME' => 'NAMED_META',
		   'BLOCK_LINE' => 0,
		   'NSE' => 'Q7WNI7_BORBR/113-292',
		   'META_KEY' => 'pAS',
		   'DATA' => '................................',
		   'ALIGNMENT' => 0
		 };

       The meta sequence will be checked against the NSE for the block position and stored based on the meta tag. A meta sequence does not have to
       correspond to a real sequence. At this time, unique meta sequence tags must be used for each sequence or they will be overwritten (this may
       change).

       An alignment consensus string:

	 $VAR1 = {
		   'NAME' => 'CONSENSUS',
		   'DATA' => 'VALILGVYRRL...CYVNREM..RAG....QW',
		   'ALIGNMENT' => 1
		 };

       A consensus meta sequence:

	 $VAR1 = {
		   'NAME' => 'CONSENSUS_META',
		   'META_KEY' => 'pAS',
		   'DATA' => '................................',
		   'ALIGNMENT' => 1
		 };

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/

AUTHOR - Chris Fields
       Email cjfields at bioperl dot org

APPENDIX

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

   new
	Title	:  new
	Usage	:
	Function:
	Returns :
	Args	:  -format    Sequence format to be mapped for handler methods
		   -builder   Bio::Seq::SeqBuilder object (normally defined in
			      SequenceStreamI object implementation constructor)
	Throws	:  On undefined '-format' sequence format parameter
	Note	:  Still under heavy development

Bio::HandlerBaseI implementing methods
   handler_methods
	Title	:  handler_methods
	Usage	:  $handler->handler_methods('GenBank')
		   %handlers = $handler->handler_methods();
	Function:  Retrieve the handler methods used for the current format() in
		   the handler.  This assumes the handler methods are already
		   described in the HandlerI-implementing class.
	Returns :  a hash reference with the data type handled and the code ref
		   associated with it.
	Args	:  [optional] String representing the sequence format.	If set here
		   this will also set sequence_format()
	Throws	:  On unimplemented sequence format in %HANDLERS

   data_handler
	Title	:  data_handler
	Usage	:  $handler->data_handler($data)
	Function:  Centralized method which accepts all data chunks, then distributes
		   to the appropriate methods for processing based on the chunk name
		   from within the HandlerBaseI object.

		   One can also use
	Returns :  None
	Args	:  an hash ref containing a data chunk.

   reset_parameters
	Title	:  reset_parameters
	Usage	:  $handler->reset_parameters()
	Function:  Resets the internal cache of data (normally object parameters for
		   a builder or factory)
	Returns :  None
	Args	:  None

   format
	Title	:  format
	Usage	:  $handler->format('GenBank')
	Function:  Get/Set the format for the report/record being parsed. This can be
		   used to set handlers in classes which are capable of processing
		   similar data chunks from multiple driver modules.
	Returns :  String with the sequence format
	Args	:  [optional] String with the sequence format
	Note	:  The format may be used to set the handlers (as in the
		   current GenericRichSeqHandler implementation)

   get_params
	Title	:  get_params
	Usage	:  $handler->get_params('-species')
	Function:  Convenience method used to retrieve the specified
		   parameters from the internal parameter cache
	Returns :  Hash ref containing parameters requested and data as
		   key-value pairs.  Note that some parameter values may be
		   objects, arrays, etc.
	Args	:  List (array) representing the parameters requested

   set_params
	Title	:  set_params
	Usage	:  $handler->set_param({'-seqs' => $seqs})
	Function:  Convenience method used to set specific parameters
	Returns :  None
	Args	:  Hash ref containing the data to be passed as key-value pairs

Methods unique to this implementation
   build_alignment
	Title	:  build_alignment
	Usage	:
	Function:
	Returns :  a Bio::SimpleAlign
	Args	:
	Throws	:
	Note	:  This may be replaced by a Builder object at some point

   annotation_collection
	Title	:  annotation_collection
	Usage	:
	Function:
	Returns :
	Args	:
	Throws	:
	Note	:

   seq_annotation_collection
	Title	:  seq_annotation_collection
	Usage	:
	Function:
	Returns :
	Args	:
	Throws	:
	Note	:

   process_seqs
	Title	:  process_seqs
	Usage	:  $handler->process_seqs;
	Function:  checks internal sequences to ensure they are converted over
		   to the proper Bio::AlignI-compatible sequence class
	Returns :  1 if successful
	Args	:  none

perl v5.14.2							    2012-03-02			   Bio::AlignIO::Handler::GenericAlignHandler(3pm)