Bio::SearchIO::Writer::HTMLResultWriter.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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
 
 
  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()>
 
 
  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

  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
 
 
  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)