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.\" ========================================================================
.\"
.IX Title "Bio::SearchIO::Writer::TextResultWriter 3pm"
.TH Bio::SearchIO::Writer::TextResultWriter 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::SearchIO::Writer::TextResultWriter \- Object to implement writing
a Bio::Search::ResultI in Text.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  use Bio::SearchIO;
\&  use Bio::SearchIO::Writer::TextResultWriter;
\&
\&  my $in = Bio::SearchIO\->new(\-format => \*(Aqblast\*(Aq,
\&                             \-file   => shift @ARGV);
\&
\&  my $writer = Bio::SearchIO::Writer::TextResultWriter\->new();
\&  my $out = Bio::SearchIO\->new(\-writer => $writer);
\&  $out\->write_result($in\->next_result);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object implements the SearchWriterI interface which will produce
a set of Text for a specific Bio::Search::Report::ReportI interface.
.PP
You can also provide the argument \-filters => \e%hash to filter the at
the hsp, hit, or result level.  \f(CW%hash\fR is an associative array which
contains any or all of the keys (\s-1HSP, HIT, RESULT\s0).  The values
pointed to by these keys would be references to a subroutine which
expects to be passed an object \- one of Bio::Search::HSP::HSPI,
Bio::Search::Hit::HitI, and Bio::Search::Result::ResultI respectively.
Each function needs to return a boolean value as to whether or not the
passed element should be included in the output report \- true if it is
to be included, false if it to be omitted.
.PP
For example to filter on sequences in the database which are too short
for your criteria you would do the following.
.PP
Define a hit filter method
.PP
.Vb 8
\&  sub hit_filter { 
\&      my $hit = shift;
\&      return $hit\->length E<gt> 100; # test if length of the hit sequence
\&                                     # long enough    
\&  }
\&  my $writer = Bio::SearchIO::Writer::TextResultWriter\->new(
\&       \-filters => { \*(AqHIT\*(Aq =E<gt> \e&hit_filter }  
\&      );
.Ve
.PP
Another example would be to filter HSPs on percent identity, let's
only include HSPs which are 75% identical or better.
.PP
.Vb 7
\&   sub hsp_filter {
\&       my $hsp = shift;
\&       return $hsp\->percent_identity E<gt> 75;
\&   }
\&   my $writer = Bio::SearchIO::Writer::TextResultWriter\->new(
\&       \-filters => { \*(AqHSP\*(Aq =E<gt> \e&hsp_filter }  
\&      );
.Ve
.PP
See Bio::SearchIO::SearchWriterI for more info on the filter method.
.PP
This module will use the module Text::Wrap if it is installed to wrap
the Query description line.  If you do not have Text::Wrap installed
this module will work fine but you won't have the Query line wrapped.
You will see a warning about this when you first instantiate a
TextResultWriter \- to avoid these warnings from showing up, simply set
the verbosity upon initialization to \-1 like this: my \f(CW$writer\fR = new
Bio::SearchIO::Writer::TextResultWriter(\-verbose => \-1);
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason@bioperl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 10
\& Title   : new
\& Usage   : my $obj = Bio::SearchIO::Writer::TextResultWriter\->new();
\& Function: Builds a new Bio::SearchIO::Writer::TextResultWriter object 
\& Returns : Bio::SearchIO::Writer::TextResultWriter
\& 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 Hit,HSP, Result object respectively
\&           \-no_wublastlinks => boolean. Do not display WU\-BLAST lines even if 
\&                               they are parsed out
\&                               Links = (1)
.Ve
.SS "to_string"
.IX Subsection "to_string"
.Vb 10
\& 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
.Ve
.SS "start_report"
.IX Subsection "start_report"
.Vb 10
\&  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 \e&default_start_report (see below) if not
\&            set. 
\&  Example : $index\->start_report( \e&my_start_report )
\&  Returns : ref to CODE if called without arguments
\&  Args    : CODE
.Ve
.SS "default_start_report"
.IX Subsection "default_start_report"
.Vb 5
\& 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
.Ve
.SS "title"
.IX Subsection "title"
.Vb 2
\& 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 \e&default_title (see below) if not
\&            set. 
\&  Example : $index\->title( \e&my_title )
\&  Returns : ref to CODE if called without arguments
\&  Args    : CODE
.Ve
.SS "default_title"
.IX Subsection "default_title"
.Vb 6
\& 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 output.
\& Returns : empty for text implementation
\& Args    : First argument is a Bio::Search::Result::ResultI
.Ve
.SS "introduction"
.IX Subsection "introduction"
.Vb 2
\& 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 \e&default_introduction (see below) if not
\&            set. 
\&  Example : $index\->introduction( \e&my_introduction )
\&  Returns : ref to CODE if called without arguments
\&  Args    : CODE
.Ve
.SS "default_introduction"
.IX Subsection "default_introduction"
.Vb 7
\& 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
.Ve
.SS "end_report"
.IX Subsection "end_report"
.Vb 8
\& 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
.Ve
.SS "id_parser"
.IX Subsection "id_parser"
.Vb 10
\&  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 \e&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( \e&my_id_parser )
\&  Returns : ref to CODE if called without arguments
\&  Args    : CODE
.Ve
.SS "default_id_parser"
.IX Subsection "default_id_parser"
.Vb 7
\&  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 /^>\es*(\eS+)/
\&            to $header.
\&  Returns : ID string
\&  Args    : a fasta header line string
.Ve
.SS "algorithm_reference"
.IX Subsection "algorithm_reference"
.Vb 6
\& 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
.Ve
.SS "Methods Bio::SearchIO::SearchWriterI"
.IX Subsection "Methods Bio::SearchIO::SearchWriterI"
Bio::SearchIO::SearchWriterI inherited methods.
.SS "filter"
.IX Subsection "filter"
.Vb 6
\& Title   : filter
\& Usage   : $writer\->filter(\*(Aqhsp\*(Aq, \e&hsp_filter);
\& Function: Filter out either at HSP,Hit,or Result level
\& Returns : none
\& Args    : string => data type,
\&           CODE reference
.Ve
.SS "no_wublastlinks"
.IX Subsection "no_wublastlinks"
.Vb 7
\& 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)
.Ve