HTMLResultWriter documentation.

  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.
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 > 100; # test if length of the hit sequence
                                     # long enough    
  }
  my $writer = new Bio::SearchIO::Writer::TextResultWriter(
       -filters => { 'HIT' => \&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 > 75;
   }
   my $writer = new Bio::SearchIO::Writer::TextResultWriter(
       -filters => { 'HSP' => \&hsp_filter }  
      );

See Bio::SearchIO::SearchWriterI for more info on the filter method.

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

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]

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: 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 "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 "See Also: hit_link_desc, remote_database, id_parser

Title : start_report Usage : $index->start_report( CODE ) Function: Stores or returns the code to write the start of the block, the 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</pre></td></tr></table> <div id="sep"></div> <table id="methDescTitle" width="100%"><tr><td WIDTH="200"><a name="_pod_default_start_report" id="_pod_default_start_report"></a><a name="POD8" id="POD8"></a>default_start_report</td><td ><a href="#CODE8">code</a></td><td ><a href="#POD7">prev</a></td><td ><a href="#POD9">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <table id="methDescArea" width="100%"><tr><td><pre id="podParagraph"> 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</pre></td></tr></table> <div id="sep"></div> <table id="methDescTitle" width="100%"><tr><td WIDTH="200"><a name="_pod_title" id="_pod_title"></a><a name="POD9" id="POD9"></a>title</td><td ><a href="#CODE9">code</a></td><td ><a href="#POD8">prev</a></td><td ><a href="#POD10">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <table id="methDescArea" width="100%"><tr><td><pre id="podParagraph"> 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</pre></td></tr></table> <div id="sep"></div> <table id="methDescTitle" width="100%"><tr><td WIDTH="200"><a name="_pod_default_title" id="_pod_default_title"></a><a name="POD10" id="POD10"></a>default_title</td><td ><a href="#CODE10">code</a></td><td ><a href="#POD9">prev</a></td><td ><a href="#POD11">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <table id="methDescArea" width="100%"><tr><td><pre id="podParagraph"> 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</pre></td></tr></table> <div id="sep"></div> <a name="MethCode" id="MethCode"></a> <div id="mainTitle">Methods code</div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="BEGIN1" id="BEGIN1"></a>BEGIN</td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >BEGIN {<pre> $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; $AlignmentLineWidth = 60;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE1" id="CODE1"></a>new</td><td ><a href="#POD1">description</a></td><td >prev</td><td ><a href="#CODE2">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub new {<pre> my($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 $self;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE2" id="CODE2"></a>remote_database_url</td><td ><a href="#POD2">description</a></td><td ><a href="#CODE1">prev</a></td><td ><a href="#CODE3">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub remote_database_url {<pre> my ($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};</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE3" id="CODE3"></a>to_string</td><td ><a href="#POD3">description</a></td><td ><a href="#CODE2">prev</a></td><td ><a href="#CODE4">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub to_string {<pre> 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 (bits)</th><th>E value</th></tr>"; my $hspstr = ''; 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(">%s %s\n<dd>Length = %s</dd>\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 .= " \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>\n<pre>"; $hspstr .= "</a>\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 $str .= "</table>\n".$hspstr."<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><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"; } $str .= "</table>".$self->footer() . "\n"; return $str;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE4" id="CODE4"></a>hit_link_desc</td><td ><a href="#POD4">description</a></td><td ><a href="#CODE3">prev</a></td><td ><a href="#CODE5">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub hit_link_desc {<pre> my( $self, $code ) = @_; if ($code) { $self->{'_hit_link_desc'} = $code; } return $self->{'_hit_link_desc'} ||\& default_hit_link_desc;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE5" id="CODE5"></a>default_hit_link_desc</td><td ><a href="#POD5">description</a></td><td ><a href="#CODE4">prev</a></td><td ><a href="#CODE6">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub default_hit_link_desc {<pre> my($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 $url;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE6" id="CODE6"></a>hit_link_align</td><td ><a href="#POD6">description</a></td><td ><a href="#CODE5">prev</a></td><td ><a href="#CODE7">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub hit_link_align {<pre> my ($self,$code) = @_; if ($code) { $self->{'_hit_link_align'} = $code; } return $self->{'_hit_link_align'} ||\& default_hit_link_desc;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE7" id="CODE7"></a>start_report</td><td ><a href="#POD7">description</a></td><td ><a href="#CODE6">prev</a></td><td ><a href="#CODE8">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub start_report {<pre> my( $self, $code ) = @_; if ($code) { $self->{'_start_report'} = $code; } return $self->{'_start_report'} ||\& default_start_report;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE8" id="CODE8"></a>default_start_report</td><td ><a href="#POD8">description</a></td><td ><a href="#CODE7">prev</a></td><td ><a href="#CODE9">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub default_start_report {<pre> my ($result) = @_; return sprintf( qq{<HTML> <HEAD> <CENTER><TITLE>Bioperl Reformatted HTML of %s output with Bioperl Bio::SearchIO system</TITLE></CENTER></HEAD>      <BODY BGCOLOR="WHITE"> },$result->algorithm,$Revision);</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE9" id="CODE9"></a>title</td><td ><a href="#POD9">description</a></td><td ><a href="#CODE8">prev</a></td><td ><a href="#CODE10">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub title {<pre> my( $self, $code ) = @_; if ($code) { $self->{'_title'} = $code; } return $self->{'_title'} ||\& default_title;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE10" id="CODE10"></a>default_title</td><td ><a href="#POD10">description</a></td><td ><a href="#CODE9">prev</a></td><td >next</td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub default_title {<pre> my ($result) = @_; return sprintf( qq{<CENTER><H1><a href="http://bioperl.org">Bioperl</a> Reformatted HTML of %s Search Report 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 <a href="../../Search/Result/ResultI.html">Bio::Search::Result::ResultI</a> Second argument is string holding literature citation =cut sub default_introduction { my ($result) = @_; return sprintf( qq{ Query= %s %s <dd>(%s letters)</dd> Database: %s <dd>%s sequences; %s total letters</dd> }, $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 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 . ""; if( $result->algorithm_version =~ /WashU/i ) { return $res . "Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA. All Rights Reserved. Reference: Gish, W. (1996-2000) <a href=\"http://blast.wustl.edu\">http://blast.wustl.edu</a>"; } else { return $res . "Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), \" Gapped BLAST and PSI-BLAST: a new generation of protein database search programs\", Nucleic Acids Res. 25:3389-3402."; } } elsif( $result->algorithm =~ /FAST/i ) { return $result->algorithm . " " . $result->algorithm_version . " " . "\nReference: Pearson et al, Genomics (1997) 46:24-36"; } 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 <a href="../SearchWriterI.html">Bio::SearchIO::SearchWriterI</a> 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;</pre>}</td></div> <div id="sep"></div> <a name="General" id="General"></a> <div id="mainTitle">General documentation</div> <div id="sep"></div> <table id="genInfoTitle" width="100%"><tr><td><a name="_pod_FEEDBACK" id="_pod_FEEDBACK"></a>FEEDBACK</td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="genInfoArea"></div> <div id="sep"></div> <table id="genInfoTitle" width="100%"><tr><td><a name="_pod_Mailing Lists" id="_pod_Mailing Lists"></a>Mailing Lists</td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="genInfoArea">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. <pre id="podParagraph"> bioperl-l@bioperl.org - General discussion <a href="http://bioperl.org/MailList.shtml" target="urlWin" id="podUrl">http://bioperl.org/MailList.shtml</a> - About the mailing lists</pre></div> <div id="sep"></div> <table id="genInfoTitle" width="100%"><tr><td><a name="_pod_Reporting Bugs" id="_pod_Reporting Bugs"></a>Reporting Bugs</td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="genInfoArea">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: <pre id="podParagraph"> bioperl-bugs@bioperl.org <a href="http://bugzilla.bioperl.org" target="urlWin" id="podUrl">http://bugzilla.bioperl.org</a>/</pre></div> <div id="sep"></div> <table id="genInfoTitle" width="100%"><tr><td><a name="_pod_AUTHOR - Jason Stajich" id="_pod_AUTHOR - Jason Stajich"></a>AUTHOR - Jason Stajich</td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="genInfoArea">Email jason-at-bioperl-dot-org</div> <div id="sep"></div> <table id="genInfoTitle" width="100%"><tr><td><a name="_pod_CONTRIBUTORS" id="_pod_CONTRIBUTORS"></a>CONTRIBUTORS</td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="genInfoArea">Gary Williams <a href="mailto:G.Williams@hgmp.mrc.ac.uk" id="podEmail">G.Williams@hgmp.mrc.ac.uk</a></div> <div id="sep"></div> <table id="genInfoTitle" width="100%"><tr><td><a name="_pod_APPENDIX" id="_pod_APPENDIX"></a>APPENDIX</td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="genInfoArea">The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _</div> <div id="sep"></div> </body> </html>

BEGIN		Code
new	Description	Code
remote_database_url	Description	Code
to_string	Description	Code
hit_link_desc	Description	Code
default_hit_link_desc	Description	Code
hit_link_align	Description	Code
start_report	Description	Code
default_start_report	Description	Code
title	Description	Code
default_title	Description	Code