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BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SearchIO::Writer::HTMLResultWriter

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
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)