Raw content of Bio::SearchIO::Writer::HTMLResultWriter # $Id: HTMLResultWriter.pm,v 1.12.2.4 2003/09/15 16:08:55 jason Exp $ # # BioPerl module for Bio::SearchIO::Writer::HTMLResultWriter # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # Changes 2003-07-31 (jason) # Gary has cleaned up the code a lot to produce better looking # HTML # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::Writer::HTMLResultWriter - Object to implement writing a Bio::Search::ResultI in HTML. =head1 SYNOPSIS 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); =head1 DESCRIPTION This object implements the SearchWriterI interface which will produce a set of HTML for a specific Bio::Search::Report::ReportI interface. You can also provide the argument -filters => \%hash to filter the at the hsp, hit, or result level. %hash is an associative array which contains any or all of the keys (HSP, HIT, RESULT). 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. For example to filter on sequences in the database which are too short for your criteria you would do the following. Define a hit filter method sub hit_filter { my $hit = shift; return $hit->length E<gt> 100; # test if length of the hit sequence # long enough } my $writer = new Bio::SearchIO::Writer::TextResultWriter( -filters => { 'HIT' =E<gt> \&hit_filter } ); Another example would be to filter HSPs on percent identity, let's only include HSPs which are 75% identical or better. sub hsp_filter { my $hsp = shift; return $hsp->percent_identity E<gt> 75; } my $writer = new Bio::SearchIO::Writer::TextResultWriter( -filters => { 'HSP' =E<gt> \&hsp_filter } ); See L<Bio::SearchIO::SearchWriterI> for more info on the filter method. =head1 FEEDBACK =head2 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/MailList.shtml - About the mailing lists =head2 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/ =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 CONTRIBUTORS Gary Williams G.Williams@hgmp.mrc.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SearchIO::Writer::HTMLResultWriter; use vars qw(@ISA %RemoteURLDefault $MaxDescLen $DATE $AlignmentLineWidth $Revision); use strict; $Revision = '$Id: HTMLResultWriter.pm,v 1.12.2.4 2003/09/15 16:08:55 jason Exp $'; #' # Object preamble - inherits from Bio::Root::RootI BEGIN { $DATE = localtime(time); %RemoteURLDefault = ( 'PROTEIN' => 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=%s', 'NUCLEOTIDE' => 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=%s' ); $MaxDescLen = 60; $AlignmentLineWidth = 60; } use Bio::Root::Root; use Bio::SearchIO::SearchWriterI; @ISA = qw(Bio::Root::Root Bio::SearchIO::SearchWriterI); =head2 new Title : new Usage : my $obj = new Bio::SearchIO::Writer::HTMLResultWriter(); Function: Builds a new Bio::SearchIO::Writer::HTMLResultWriter object Returns : Bio::SearchIO::Writer::HTMLResultWriter Args : -filters => hashref with any or all of the keys (HSP HIT RESULT) which have values pointing to a subroutine reference which will expect to get a =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($p,$n,$filters) = $self->_rearrange([qw(PROTEIN_URL NUCLEOTIDE_URL FILTERS)],@args); $self->remote_database_url('p',$p || $RemoteURLDefault{'PROTEIN'}); $self->remote_database_url('n',$n || $RemoteURLDefault{'NUCLEOTIDE'}); 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; } =head2 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 $value - new value to set [optional] =cut sub remote_database_url{ my ($self,$type,$value) = @_; if( ! defined $type || $type !~ /^(P|N)/i ) { $self->warn("Must provide a type (PROTEIN or NUCLEOTIDE)"); return ''; } $type = uc $1; if( defined $value) { $self->{'remote_database_url'}->{$type} = $value; } return $self->{'remote_database_url'}->{$type}; } =head2 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 : $result_obj = A Bio::Search::Result::ResultI object : @args = any additional arguments used by your implementation. Returns : String containing data for each search Result or any of its : sub-objects (Hits and HSPs). Throws : n/a =cut sub to_string { my ($self,$result,$num) = @_; $num ||= 0; return unless defined $result; my ($resultfilter,$hitfilter, $hspfilter) = ( $self->filter('RESULT'), $self->filter('HIT'), $self->filter('HSP') ); return '' if( defined $resultfilter && ! &{$resultfilter}($result) ); my ($qtype,$dbtype,$dbseqtype,$type); my $alg = $result->algorithm; # This is actually wrong for the FASTAs I think if( $alg =~ /T(FAST|BLAST)([XY])/i ) { $qtype = $dbtype = 'translated'; $dbseqtype = $type = 'PROTEIN'; } elsif( $alg =~ /T(FAST|BLAST)N/i ) { $qtype = ''; $dbtype = 'translated'; $type = 'PROTEIN'; $dbseqtype = 'NUCLEOTIDE'; } elsif( $alg =~ /(FAST|BLAST)N/i || $alg =~ /(WABA|EXONERATE)/i ) { $qtype = $dbtype = ''; $type = $dbseqtype = 'NUCLEOTIDE'; } elsif( $alg =~ /(FAST|BLAST)P/ || $alg =~ /SSEARCH/i ) { $qtype = $dbtype = ''; $type = $dbseqtype = 'PROTEIN'; } elsif( $alg =~ /(FAST|BLAST)[XY]/i ) { $qtype = 'translated'; $dbtype = 'PROTEIN'; $dbseqtype = $type = 'PROTEIN'; } else { print STDERR "algorithm was ", $result->algorithm, " couldn't match\n"; } my %baselens = ( 'Sbjct:' => ( $dbtype eq 'translated' ) ? 3 : 1, 'Query:' => ( $qtype eq 'translated' ) ? 3 : 1); my $str; if( ! defined $num || $num <= 1 ) { $str = &{$self->start_report}($result); } $str .= &{$self->title}($result); $str .= $result->algorithm_reference || $self->algorithm_reference($result); $str .= &{$self->introduction}($result); $str .= "<table border=0> <tr><th>Sequences producing significant alignments:</th> <th>Score<br>(bits)</th><th>E<br>value</th></tr>"; my $hspstr = '<p><p>'; if( $result->can('rewind')) { $result->rewind(); # support stream based parsing routines } while( my $hit = $result->next_hit ) { next if( $hitfilter && ! &{$hitfilter}($hit) ); my $nm = $hit->name(); $self->debug( "no $nm for name (".$hit->description(). "\n") unless $nm; my ($gi,$acc) = &{$self->id_parser}($nm); my $p = "%-$MaxDescLen". "s"; my $descsub; if( length($hit->description) > ($MaxDescLen - 3) ) { $descsub = sprintf($p, substr($hit->description,0,$MaxDescLen-3) . "..."); } else { $descsub = sprintf($p,$hit->description); } my $url_desc = &{$self->hit_link_desc()}($self,$hit, $result); my $url_align = &{$self->hit_link_align()}($self,$hit, $result); my @hsps = $hit->hsps; # failover to first HSP if the data does not contain a # bitscore/significance value for the Hit (NCBI XML data for one) $str .= sprintf('<tr><td>%s %s</td><td>%s</td><td><a href="#%s">%.2g</a></td></tr>'."\n", $url_desc, $descsub, ($hit->raw_score ? $hit->raw_score : (defined $hsps[0] ? $hsps[0]->score : ' ')), $acc, ( $hit->significance ? $hit->significance : (defined $hsps[0] ? $hsps[0]->evalue : ' ')) ); $hspstr .= "<a name=\"$acc\">\n". sprintf("><b>%s</b> %s\n<dd>Length = %s</dd><p>\n\n", $url_align, defined $hit->description ? $hit->description : '', &_numwithcommas($hit->length)); my $ct = 0; foreach my $hsp (@hsps ) { next if( $hspfilter && ! &{$hspfilter}($hsp) ); $hspstr .= sprintf(" Score = %s bits (%s), Expect = %s", $hsp->bits, $hsp->score, $hsp->evalue); if( defined $hsp->pvalue ) { $hspstr .= ", P = ".$hsp->pvalue; } $hspstr .= "<br>\n"; $hspstr .= sprintf(" Identities = %d/%d (%d%%)", ( $hsp->frac_identical('total') * $hsp->length('total')), $hsp->length('total'), $hsp->frac_identical('total') * 100); if( $type eq 'PROTEIN' ) { $hspstr .= sprintf(", Positives = %d/%d (%d%%)", ( $hsp->frac_conserved('total') * $hsp->length('total')), $hsp->length('total'), $hsp->frac_conserved('total') * 100); } if( $hsp->gaps ) { $hspstr .= sprintf(", Gaps = %d/%d (%d%%)", $hsp->gaps('total'), $hsp->length('total'), (100 * $hsp->gaps('total') / $hsp->length('total'))); } my ($hframe,$qframe) = ( $hsp->hit->frame, $hsp->query->frame); my ($hstrand,$qstrand) = ($hsp->hit->strand,$hsp->query->strand); # so TBLASTX will have Query/Hit frames # BLASTX will have Query frame # TBLASTN will have Hit frame if( $hstrand || $qstrand ) { $hspstr .= ", Frame = "; my ($signq, $signh); unless( $hstrand ) { $hframe = undef; # if strand is null or 0 then it is protein # and this no frame } else { $signh = $hstrand < 0 ? '-' : '+'; } unless( $qstrand ) { $qframe = undef; # if strand is null or 0 then it is protein } else { $signq =$qstrand < 0 ? '-' : '+'; } # remember bioperl stores frames as 0,1,2 (GFF way) # BLAST reports reports as 1,2,3 so # we have to add 1 to the frame values if( defined $hframe && ! defined $qframe) { $hspstr .= "$signh".($hframe+1); } elsif( defined $qframe && ! defined $hframe) { $hspstr .= "$signq".($qframe+1); } else { $hspstr .= sprintf(" %s%d / %s%d", $signq,$qframe+1, $signh, $hframe+1); } } # $hspstr .= "</pre></a><p>\n<pre>"; $hspstr .= "</a><p>\n<pre>"; my @hspvals = ( {'name' => 'Query:', 'seq' => $hsp->query_string, 'start' => ($qstrand >= 0 ? $hsp->query->start : $hsp->query->end), 'end' => ($qstrand >= 0 ? $hsp->query->end : $hsp->query->start), 'index' => 0, 'direction' => $qstrand || 1 }, { 'name' => ' 'x6, 'seq' => $hsp->homology_string, 'start' => undef, 'end' => undef, 'index' => 0, 'direction' => 1 }, { 'name' => 'Sbjct:', 'seq' => $hsp->hit_string, 'start' => ($hstrand >= 0 ? $hsp->hit->start : $hsp->hit->end), 'end' => ($hstrand >= 0 ? $hsp->hit->end : $hsp->hit->start), 'index' => 0, 'direction' => $hstrand || 1 } ); # let's set the expected length (in chars) of the starting number # in an alignment block so we can have things line up # Just going to try and set to the largest my ($numwidth) = sort { $b <=> $a }(length($hspvals[0]->{'start'}), length($hspvals[0]->{'end'}), length($hspvals[2]->{'start'}), length($hspvals[2]->{'end'})); my $count = 0; while ( $count <= $hsp->length('total') ) { foreach my $v ( @hspvals ) { my $piece = substr($v->{'seq'}, $v->{'index'} + $count, $AlignmentLineWidth); my $cp = $piece; my $plen = scalar ( $cp =~ tr/\-//); my ($start,$end) = ('',''); if( defined $v->{'start'} ) { $start = $v->{'start'}; # since strand can be + or - use the direction # to signify which whether to add or substract from end my $d = $v->{'direction'} * ( $AlignmentLineWidth - $plen )* $baselens{$v->{'name'}}; if( length($piece) < $AlignmentLineWidth ) { $d = (length($piece) - $plen) * $v->{'direction'} * $baselens{$v->{'name'}}; } $end = $v->{'start'} + $d - $v->{'direction'}; $v->{'start'} += $d; } $hspstr .= sprintf("%s %-".$numwidth."s %s %s\n", $v->{'name'}, $start, $piece, $end ); } $count += $AlignmentLineWidth; $hspstr .= "\n\n"; } $hspstr .= "</pre>\n"; } # $hspstr .= "</pre>\n"; } # make table of search statistics and end the web page $str .= "</table><p>\n".$hspstr."<p><p><hr><h2>Search Parameters</h2><table border=1><tr><th>Parameter</th><th>Value</th>\n"; foreach my $param ( $result->available_parameters ) { $str .= "<tr><td>$param</td><td>". $result->get_parameter($param) ."</td></tr>\n"; } $str .= "</table><p><h2>Search Statistics</h2><table border=1><tr><th>Statistic</th><th>Value</th></tr>\n"; foreach my $stat ( sort $result->available_statistics ) { $str .= "<tr><td>$stat</td><td>". $result->get_statistic($stat). "</td></th>\n"; } $str .= "</table><P>".$self->footer() . "<P>\n"; return $str; } =head2 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()> =cut sub hit_link_desc{ my( $self, $code ) = @_; if ($code) { $self->{'_hit_link_desc'} = $code; } return $self->{'_hit_link_desc'} || \&default_hit_link_desc; } =head2 default_hit_link_desc Title : defaulthit_link_desc Usage : $self->default_hit_link_desc($hit, $result) Function: Provides an HTML link(s) for the given hit to be used within the description section at the top of the BLAST report. This allows a person reading the report within a web browser to go to one or more database entries for the given hit from the description section. Returns : string containing HTML markup "<a href...") The default implementation returns an HTML link to the URL supplied by the remote_database_url() method and using the identifier supplied by the id_parser() method. It will use the NCBI GI if present, and the accession if not. Args : First argument is a Bio::Search::Hit::HitI Second argument is a Bio::Search::Result::ResultI See Also: L<hit_link_align>, L<remote_database>, L<id_parser> =cut sub default_hit_link_desc { my($self, $hit, $result) = @_; my $type = ( $result->algorithm =~ /(P|X|Y)$/i ) ? 'PROTEIN' : 'NUCLEOTIDE'; my ($gi,$acc) = &{$self->id_parser}($hit->name); my $url = length($self->remote_database_url($type)) > 0 ? sprintf('<a href="%s">%s</a>', sprintf($self->remote_database_url($type),$gi || $acc), $hit->name()) : $hit->name(); return $url; } =head2 hit_link_align Title : hit_link_align Usage : $self->hit_link_align(\&link_function); Function: Get/Set the function which provides an HTML link(s) for the given hit to be used within the HSP alignment section of the BLAST report. This allows a person reading the report within a web browser to go to one or more database entries for the given hit from the alignment section. Returns : string containing HTML markup "<a href...") The default implementation delegates to hit_link_desc(). Args : First argument is a Bio::Search::Hit::HitI Second argument is a Bio::Search::Result::ResultI See Also: L<hit_link_desc>, L<remote_database>, L<id_parser> =cut sub hit_link_align { my ($self,$code) = @_; if ($code) { $self->{'_hit_link_align'} = $code; } return $self->{'_hit_link_align'} || \&default_hit_link_desc; } =head2 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 =cut sub start_report { my( $self, $code ) = @_; if ($code) { $self->{'_start_report'} = $code; } return $self->{'_start_report'} || \&default_start_report; } =head2 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 =cut sub default_start_report { my ($result) = @_; return sprintf( qq{<HTML> <HEAD> <CENTER><TITLE>Bioperl Reformatted HTML of %s output with Bioperl Bio::SearchIO system</TITLE></CENTER></HEAD> <!-------------------------------------------------------------------> <!-- Generated by Bio::SearchIO::Writer::HTMLResultWriter --> <!-- %s --> <!-- http://bioperl.org --> <!-------------------------------------------------------------------> <BODY BGCOLOR="WHITE"> },$result->algorithm,$Revision); } =head2 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 =cut sub title { my( $self, $code ) = @_; if ($code) { $self->{'_title'} = $code; } return $self->{'_title'} || \&default_title; } =head2 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 =cut sub default_title { my ($result) = @_; return sprintf( qq{<CENTER><H1><a href="http://bioperl.org">Bioperl</a> Reformatted HTML of %s Search Report<br> for %s</H1></CENTER>}, $result->algorithm, $result->query_name()); } =head2 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 =cut sub introduction { my( $self, $code ) = @_; if ($code) { $self->{'_introduction'} = $code; } return $self->{'_introduction'} || \&default_introduction; } =head2 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 =cut sub default_introduction { my ($result) = @_; return sprintf( qq{ <b>Query=</b> %s %s<br><dd>(%s letters)</dd> <p> <b>Database:</b> %s<br><dd>%s sequences; %s total letters<p></dd> <p> }, $result->query_name, $result->query_description, &_numwithcommas($result->query_length), $result->database_name(), &_numwithcommas($result->database_entries()), &_numwithcommas($result->database_letters()), ); } =head2 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 =cut sub end_report { return "</BODY>\n</HTML>\n"; } # copied from Bio::Index::Fasta # useful here as well =head2 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 =cut sub id_parser { my( $self, $code ) = @_; if ($code) { $self->{'_id_parser'} = $code; } return $self->{'_id_parser'} || \&default_id_parser; } =head2 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 $header. Returns : ID string The default implementation checks for NCBI-style identifiers in the given string ('gi|12345|AA54321'). For these IDs, it extracts the GI and accession and returns a two-element list of strings (GI, acc). Args : a fasta header line string =cut sub default_id_parser { my ($string) = @_; my ($gi,$acc); if( $string =~ s/gi\|(\d+)\|?// ) { $gi = $1; $acc = $1;} if( $string =~ /(\w+)\|([A-Z\d\.\_]+)(\|[A-Z\d\_]+)?/ ) { $acc = defined $2 ? $2 : $1; } else { $acc = $string; $acc =~ s/^\s+(\S+)/$1/; $acc =~ s/(\S+)\s+$/$1/; } return ($gi,$acc); } sub MIN { $a <=> $b ? $a : $b; } sub MAX { $a <=> $b ? $b : $a; } sub footer { my ($self) = @_; return "<hr><h5>Produced by Bioperl module ".ref($self)." on $DATE<br>Revision: $Revision</h5>\n" } =head2 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 =cut sub algorithm_reference { my ($self,$result) = @_; return '' if( ! defined $result || !ref($result) || ! $result->isa('Bio::Search::Result::ResultI')) ; if( $result->algorithm =~ /BLAST/i ) { my $res = $result->algorithm . ' ' . $result->algorithm_version . "<p>"; if( $result->algorithm_version =~ /WashU/i ) { return $res . "Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA.<br> All Rights Reserved.<p> <b>Reference:</b> Gish, W. (1996-2000) <a href=\"http://blast.wustl.edu\">http://blast.wustl.edu</a><p>"; } else { return $res . "<b>Reference:</b> Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,<br> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),<br> \"Gapped BLAST and PSI-BLAST: a new generation of protein database search<br> programs\", Nucleic Acids Res. 25:3389-3402.<p>"; } } elsif( $result->algorithm =~ /FAST/i ) { return $result->algorithm . " " . $result->algorithm_version . "<br>" . "\n<b>Reference:</b> Pearson et al, Genomics (1997) 46:24-36<p>"; } else { return ''; } } # from Perl Cookbook 2.17 sub _numwithcommas { my $num = reverse( $_[0] ); $num =~ s/(\d{3})(?=\d)(?!\d*\.)/$1,/g; return scalar reverse $num; } =head2 Methods Bio::SearchIO::SearchWriterI L<Bio::SearchIO::SearchWriterI> inherited methods. =head2 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 =cut 1;