bio::searchio::searchwriteri(3pm) [debian man page]

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

NAME

       Bio::SearchIO::SearchWriterI - Interface for outputting parsed Search results

SYNOPSIS

       Bio::SearchIO::SearchWriterI objects cannot be instantiated since this module defines a pure interface.

       Given an object that implements the Bio::SearchIO::SearchWriterI interface, you can do the following things with it:

	   print $writer->to_string( $result_obj, @args );

DESCRIPTION

       This module defines abstract methods that all subclasses must implement to be used for outputting results from Bio::Search::Result::ResultI
       objects.

AUTHOR

       Steve Chervitz <sac-at-bioperl.org>

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

APPENDIX

       The rest of the documentation details each of the object methods.

   to_string
	Purpose   : Produces data for each Search::Result::ResultI in a string.
		  : This is an abstract method. For some useful implementations,
		  : see ResultTableWriter.pm, HitTableWriter.pm,
		  : and HSPTableWriter.pm.
	Usage	  : print $writer->to_string( $result_obj, @args );
	Argument  : $result_obj = A Bio::Search::Result::ResultI object
		  : @args = any additional arguments used by your implementation.
	Returns   : String containing data for each search Result or any of its
		  : sub-objects (Hits and HSPs).
	Throws	  : n/a

   start_report
	Title	: start_report
	Usage	: $self->start_report()
	Function: The method to call when starting a report. You can override it
		  to make a custom header
	Returns : string
	Args	: none

   end_report
	Title	: end_report
	Usage	: $self->end_report()
	Function: The method to call when ending a report, this is
		  mostly for cleanup for formats which require you to
		  have something at the end of the document (</BODY></HTML>)
		  for HTML
	Returns : string
	Args	: none

   filter
	Title	: filter
	Usage	: $writer->filter('hsp', &hsp_filter);
	Function: Filter out either at HSP,Hit,or Result level
	Returns : none
	Args	: string => data type,
		  CODE reference

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

Bio::SearchIO::Writer::HTMLResultWriter(3pm)		User Contributed Perl Documentation	      Bio::SearchIO::Writer::HTMLResultWriter(3pm)

NAME

       Bio::SearchIO::Writer::HTMLResultWriter - write a Bio::Search::ResultI in HTML

SYNOPSIS

	 use Bio::SearchIO;
	 use Bio::SearchIO::Writer::HTMLResultWriter;

	 my $in = Bio::SearchIO->new(-format => 'blast',
				    -file   => shift @ARGV);

	 my $writer = Bio::SearchIO::Writer::HTMLResultWriter->new();
	 my $out = Bio::SearchIO->new(-writer => $writer);
	 $out->write_result($in->next_result);

	 # to filter your output
	 my $MinLength = 100; # need a variable with scope outside the method
	 sub hsp_filter {
	     my $hsp = shift;
	     return 1 if $hsp->length('total') > $MinLength;
	 }
	 sub result_filter {
	     my $result = shift;
	     return $hsp->num_hits > 0;
	 }

	 my $writer = Bio::SearchIO::Writer::HTMLResultWriter->new
			    (-filters => { 'HSP' => &hsp_filter} );
	 my $out = Bio::SearchIO->new(-writer => $writer);
	 $out->write_result($in->next_result);

	 # can also set the filter via the writer object
	 $writer->filter('RESULT', &result_filter);

DESCRIPTION

       This object implements the SearchWriterI interface which will produce a set of HTML for a specific Bio::Search::Report::ReportI interface.

       See Bio::SearchIO::SearchWriterI for more info on the filter method.

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-dot-org

CONTRIBUTORS

       Gary Williams G.Williams@hgmp.mrc.ac.uk

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::Writer::HTMLResultWriter->new();
	Function: Builds a new Bio::SearchIO::Writer::HTMLResultWriter object
	Returns : Bio::SearchIO::Writer::HTMLResultWriter
	Args	: -filters => hashref with any or all of the keys (HSP HIT RESULT)
		  which have values pointing to a subroutine reference
		  which will expect to get a
		  -nucleotide_url => URL sprintf string base for the nt sequences
		  -protein_url => URL sprintf string base for the aa sequences
		  -no_wublastlinks => boolean. Do not display WU-BLAST lines
				      even if they are parsed out.
				      Links = (1)

   remote_database_url
	Title	: remote_database_url
	Usage	: $obj->remote_database_url($type,$newval)
	Function: This should return or set a string that contains a %s which can be
		  filled in with sprintf.
	Returns : value of remote_database_url
	Args	: $type - 'PROTEIN' or 'P' for protein URLS
			  'NUCLEOTIDE' or 'N' for nucleotide URLS
		  $value - new value to set [optional]

   to_string
	Purpose   : Produces data for each Search::Result::ResultI in a string.
		  : This is an abstract method. For some useful implementations,
		  : see ResultTableWriter.pm, HitTableWriter.pm,
		  : and HSPTableWriter.pm.
	Usage	  : print $writer->to_string( $result_obj, @args );
	Argument  : $result_obj = A Bio::Search::Result::ResultI object
		  : @args = any additional arguments used by your implementation.
	Returns   : String containing data for each search Result or any of its
		  : sub-objects (Hits and HSPs).
	Throws	  : n/a

   hit_link_desc
	Title	: hit_link_desc
	Usage	: $self->hit_link_desc(&link_function);
	Function: Get/Set the function which provides an HTML
		  link(s) for the given hit to be used
		  within the description section at the top of the BLAST report.
		  This allows a person reading the report within
		  a web browser to go to one or more database entries for
		  the given hit from the description section.
	Returns : Function reference
	Args	: Function reference
	See Also: L<default_hit_link_desc()>

   default_hit_link_desc
	Title	: default_hit_link_desc
	Usage	: $self->default_hit_link_desc($hit, $result)
	Function: Provides an HTML link(s) for the given hit to be used
		  within the description section at the top of the BLAST report.
		  This allows a person reading the report within
		  a web browser to go to one or more database entries for
		  the given hit from the description section.
	Returns : string containing HTML markup "<a href...")

		  The default implementation returns an HTML link to the
		  URL supplied by the remote_database_url() method
		  and using the identifier supplied by the id_parser() method.
		  It will use the NCBI GI if present, and the accession if not.

	Args	: First argument is a Bio::Search::Hit::HitI
		  Second argument is a Bio::Search::Result::ResultI

       See Also: hit_link_align, remote_database, id_parser

   hit_link_align
	Title	: hit_link_align
	Usage	: $self->hit_link_align(&link_function);
	Function: Get/Set the function which provides an HTML link(s)
		  for the given hit to be used
		  within the HSP alignment section of the BLAST report.
		  This allows a person reading the report within
		  a web browser to go to one or more database entries for
		  the given hit from the alignment section.
	Returns : string containing HTML markup "<a href...")

		  The default implementation delegates to hit_link_desc().

	Args	: First argument is a Bio::Search::Hit::HitI
		  Second argument is a Bio::Search::Result::ResultI

       See Also: hit_link_desc, remote_database, id_parser

   hit_desc_line
	Title	: hit_desc_line
	Usage	: $self->hit_desc_line(&link_function);
	Function: Get/Set the function which provides HTML for the description
		  information from a hit. This allows one to parse
		  the rest of the description and split up lines, add links, etc.
	Returns : Function reference
	Args	: Function reference
	See Also: L<default_hit_link_desc()>

   default_hit_desc_line
	Title	: default_hit_desc_line
	Usage	: $self->default_hit_desc_line($hit, $result)
	Function: Parses the description line information, splits based on the
		  hidden x01 between independent descriptions, checks the lines for
		  possible web links, and adds HTML link(s) for the given hit to be
		  used.

	Returns : string containing HTML markup "<a href...")
		  The default implementation returns an HTML link to the
		  URL supplied by the remote_database_url() method
		  and using the identifier supplied by the id_parser() method.
		  It will use the NCBI GI if present, and the accession if not.

	Args	: First argument is a Bio::Search::Hit::HitI
		  Second argument is a Bio::Search::Result::ResultI

       See Also: hit_link_align, remote_database, id_parser

   start_report
	 Title	 : start_report
	 Usage	 : $index->start_report( CODE )
	 Function: Stores or returns the code to
		   write the start of the <HTML> block, the <TITLE> block
		   and the start of the <BODY> block of HTML.	Useful
		   for (for instance) specifying alternative
		   HTML if you are embedding the output in
		   an HTML page which you have already started.
		   (For example a routine returning a null string).
		   Returns &default_start_report (see below) if not
		   set.
	 Example : $index->start_report( &my_start_report )
	 Returns : ref to CODE if called without arguments
	 Args	 : CODE

   default_start_report
	Title	: default_start_report
	Usage	: $self->default_start_report($result)
	Function: The default method to call when starting a report.
	Returns : sting
	Args	: First argument is a Bio::Search::Result::ResultI

   title
	Title	: title
	Usage	: $self->title($CODE)

	 Function: Stores or returns the code to provide HTML for the given
		   BLAST report that will appear at the top of the BLAST report
		   HTML output.  Useful for (for instance) specifying
		   alternative routines to write your own titles.
		   Returns &default_title (see below) if not
		   set.
	 Example : $index->title( &my_title )
	 Returns : ref to CODE if called without arguments
	 Args	 : CODE

   default_title
	Title	: default_title
	Usage	: $self->default_title($result)
	Function: Provides HTML for the given BLAST report that will appear
		  at the top of the BLAST report HTML output.
	Returns : string containing HTML markup
		  The default implementation returns <CENTER> <H1> HTML
		  containing text such as:
		  "Bioperl Reformatted HTML of BLASTP Search Report
			    for gi|1786183|gb|AAC73113.1|"
	Args	: First argument is a Bio::Search::Result::ResultI

   introduction
	Title	: introduction
	Usage	: $self->introduction($CODE)

	 Function: Stores or returns the code to provide HTML for the given
		   BLAST report detailing the query and the
		   database information.
		   Useful for (for instance) specifying
		   routines returning alternative introductions.
		   Returns &default_introduction (see below) if not
		   set.
	 Example : $index->introduction( &my_introduction )
	 Returns : ref to CODE if called without arguments
	 Args	 : CODE

   default_introduction
	Title	: default_introduction
	Usage	: $self->default_introduction($result)
	Function: Outputs HTML to provide the query
		  and the database information
	Returns : string containing HTML
	Args	: First argument is a Bio::Search::Result::ResultI
		  Second argument is string holding literature citation

   end_report
	Title	: end_report
	Usage	: $self->end_report()
	Function: The method to call when ending a report, this is
		  mostly for cleanup for formats which require you to
		  have something at the end of the document (</BODY></HTML>)
		  for HTML
	Returns : string
	Args	: none

   id_parser
	 Title	 : id_parser
	 Usage	 : $index->id_parser( CODE )
	 Function: Stores or returns the code used by record_id to
		   parse the ID for record from a string.  Useful
		   for (for instance) specifying a different
		   parser for different flavours of FASTA file.
		   Returns &default_id_parser (see below) if not
		   set. If you supply your own id_parser
		   subroutine, then it should expect a fasta
		   description line.  An entry will be added to
		   the index for each string in the list returned.
	 Example : $index->id_parser( &my_id_parser )
	 Returns : ref to CODE if called without arguments
	 Args	 : CODE

   default_id_parser
	 Title	 : default_id_parser
	 Usage	 : $id = default_id_parser( $header )
	 Function: The default Fasta ID parser for Fasta.pm
		   Returns $1 from applying the regexp /^>s*(S+)/
		   to $header.
	 Returns : ID string
		   The default implementation checks for NCBI-style
		   identifiers in the given string ('gi|12345|AA54321').
		   For these IDs, it extracts the GI and accession and
		   returns a two-element list of strings (GI, acc).
	 Args	 : a fasta header line string

   algorithm_reference
	Title	: algorithm_reference
	Usage	: my $reference = $writer->algorithm_reference($result);
	Function: Returns the appropriate Bibliographic reference for the
		  algorithm format being produced
	Returns : String
	Args	: L<Bio::Search::Result::ResultI> to reference

   Methods Bio::SearchIO::SearchWriterI
       Bio::SearchIO::SearchWriterI inherited methods.

   filter
	Title	: filter
	Usage	: $writer->filter('hsp', &hsp_filter);
	Function: Filter out either at HSP,Hit,or Result level
	Returns : none
	Args	: string => data type,
		  CODE reference

   no_wublastlinks
	Title	: no_wublastlinks
	Usage	: $obj->no_wublastlinks($newval)
	Function: Get/Set boolean value regarding whether or not to display
		  Link = (1)
		  type output in the report output (WU-BLAST only)
	Returns : boolean
	Args	: on set, new boolean value (a scalar or undef, optional)

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