Bio::SearchIO::Writer::HTMLResultWriter - Object to implement writing a Bio::Search::ResultI in HTML. use Bio::SearchIO; use Bio::SearchIO::Writer::HTMLResultWriter; my $in = new Bio::SearchIO(-format => 'blast', -file => shift @ARGV); my $writer = new Bio::SearchIO::Writer::HTMLResultWriter(); my $out = new Bio::SearchIO(-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 = new Bio::SearchIO::Writer::HTMLResultWriter (-filters => { 'HSP' => \&hsp_filter} ); my $out = new Bio::SearchIO(-writer => $writer); $out->write_result($in->next_result); # can also set the filter via the writer object $writer->filter('RESULT', \&result_filter); 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.

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email jason-at-bioperl-dot-org Gary Williams G.Williams@hgmp.mrc.ac.uk The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::SearchIO::Writer::HTMLResultWriter(); Function: Builds a new Bio::SearchIO::Writer::HTMLResultWriter object Returns : Bio::SearchIO::Writer::HTMLResultWriter Args : -filters => hashref with any or all of the keys (HSP HIT RESULT) which have values pointing to a subroutine reference which will expect to get a -nucleotide_url => URL sprintf string base for the nt sequences -protein_url => URL sprintf string base for the aa sequences -no_wublastlinks => boolean. Do not display WU-BLAST lines even if they are parsed out. Links = (1) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($p,$n,$filters, $nowublastlinks) = $self->_rearrange([qw(PROTEIN_URL NUCLEOTIDE_URL FILTERS NO_WUBLASTLINKS)],@args); $self->remote_database_url('p',$p || $RemoteURLDefault{'PROTEIN'}); $self->remote_database_url('n',$n || $RemoteURLDefault{'NUCLEOTIDE'}); $self->no_wublastlinks(! $nowublastlinks); if( defined $filters ) { if( !ref($filters) =~ /HASH/i ) { $self->warn("Did not provide a hashref for the FILTERS option, ignoring."); } else { while( my ($type,$code) = each %{$filters} ) { $self->filter($type,$code); } } } return $self; }

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 : defaulthit_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

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)