Bio::SearchIO::Writer HTMLResultWriter
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Summary
Bio::SearchIO::Writer::HTMLResultWriter - write a Bio::Search::ResultI in HTML
Package variables
No package variables defined.
Inherit
Bio::Root::Root Bio::SearchIO::SearchWriterI
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.
Methods
BEGIN Code
newDescriptionCode
remote_database_urlDescriptionCode
to_stringDescriptionCode
hit_link_descDescriptionCode
default_hit_link_descDescriptionCode
hit_link_alignDescriptionCode
hit_desc_lineDescriptionCode
default_hit_desc_lineDescriptionCode
start_reportDescriptionCode
default_start_reportDescriptionCode
titleDescriptionCode
default_titleDescriptionCode
introductionDescriptionCode
default_introductionDescriptionCode
end_reportDescriptionCode
id_parserDescriptionCode
default_id_parserDescriptionCode
MAX
No description
Code
footer
No description
Code
algorithm_referenceDescriptionCode
_numwithcommas
No description
Code
no_wublastlinksDescriptionCode
Methods description
newcode    nextTop
 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_urlcodeprevnextTop
 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_stringcodeprevnextTop
 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_desccodeprevnextTop
 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()
default_hit_link_desccodeprevnextTop
 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
hit_link_aligncodeprevnextTop
 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_linecodeprevnextTop
 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: default_hit_link_desc()
default_hit_desc_linecodeprevnextTop
 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 "See Also: hit_link_align, remote_database, id_parser
start_reportcodeprevnextTop
  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_reportcodeprevnextTop
 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
titlecodeprevnextTop
 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_titlecodeprevnextTop
 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
introductioncodeprevnextTop
 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_introductioncodeprevnextTop
 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_reportcodeprevnextTop
 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_parsercodeprevnextTop
  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_parsercodeprevnextTop
  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_referencecodeprevnextTop
 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 : Bio::Search::Result::ResultI to reference
no_wublastlinkscodeprevnextTop
 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)
Methods code
BEGINTop
BEGIN {
    $Revision = '$Id$';
    $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;
    $AlignmentLineWidth = 60;
}
newdescriptionprevnextTop
sub new {
  my($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 $self;
}
remote_database_urldescriptionprevnextTop
sub remote_database_url {
   my ($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};
}
to_stringdescriptionprevnextTop
sub to_string {
    my ($self,$result,$num) = @_; 
    $num ||= 0;
    return unless defined $result;
    my $links = $self->no_wublastlinks;
    my ($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|HMM(PFAM|SEARCH)/i ) { $qtype = $dbtype = ''; $type = $dbseqtype = 'PROTEIN'; } elsif( $alg =~ /(FAST|BLAST)[XY]/i ) { $qtype = 'translated'; $dbtype = 'PROTEIN'; $dbseqtype = $type = 'PROTEIN'; } else { $self->warn("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( $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; if( ! @hsps ) { # no HSPs so no link
$str .= sprintf('<tr><td>%s %s</td><td>%s</td><td>%.2g</td></tr>'."\n", $url_desc, $descsub, ($hit->bits ? $hit->bits : (defined $hsps[0] ? $hsps[0]->bits : ' ')), ( $hit->significance ? $hit->significance : (defined $hsps[0] ? $hsps[0]->evalue : ' ')) ); } else { # 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->bits ? $hit->bits : (defined $hsps[0] ? $hsps[0]->bits : ' ')), $acc, ( $hit->significance ? $hit->significance : (defined $hsps[0] ? $hsps[0]->evalue : ' ')) ); my $dline = &{$self->hit_desc_line}($self, $hit, $result); $hspstr .= "<a name=\"$acc\">\n". sprintf("><b>%s</b> %s</br><dd>Length = %s</dd><p>\n\n", $url_align, $dline , &_numwithcommas($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->score || $hsp->bits, $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, $hframe+1); } } if($links && $hsp->can('links') && defined(my $lnks = $hsp->links) ) { $hspstr .= sprintf("<br>\nLinks = %s\n",$lnks); } $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";
} $str .= "</table><p>\n".$hspstr; my ($pav, $sav) = ($result->available_parameters, $result->available_statistics); if ($pav || $sav) { # make table of search statistics and end the web page
$str .= "<p><p><hr><h2>Search Parameters</h2>"; if ($pav) { $str .= "<table border=1><tr><th>Parameter</th><th>Value</th>\n"; foreach my $param ( sort $result->available_parameters ) { $str .= "<tr><td>$param</td><td>". $result->get_parameter($param) ."</td></tr>\n"; } $str .= "</table>"; } if ($sav) { $str .= "<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>\n"; } $str .= "</tr></table>"; } } $str .= $self->footer() . "<P>\n"; return $str;
}
hit_link_descdescriptionprevnextTop
sub hit_link_desc {
    my( $self, $code ) = @_; 
    if ($code) {
        $self->{'_hit_link_desc'} = $code;
    }
    return $self->{'_hit_link_desc'} ||\& default_hit_link_desc;
}
default_hit_link_descdescriptionprevnextTop
sub default_hit_link_desc {
    my($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 $url;
}
hit_link_aligndescriptionprevnextTop
sub hit_link_align {
    my ($self,$code) = @_;
    if ($code) {
        $self->{'_hit_link_align'} = $code;
    }
    return $self->{'_hit_link_align'} ||\& default_hit_link_desc;
}
hit_desc_linedescriptionprevnextTop
sub hit_desc_line {
    my( $self, $code ) = @_; 
    if ($code) {
        $self->{'_hit_desc_line'} = $code;
    }
    return $self->{'_hit_desc_line'} ||\& default_hit_desc_line;
}
default_hit_desc_linedescriptionprevnextTop
sub default_hit_desc_line {
    my($self, $hit, $result) = @_;
    my $type = ( $result->algorithm =~ /(P|X|Y)$/i ) ? 'PROTEIN' : 'NUCLEOTIDE';
    my @descs = split /\x01/, $hit->description;
    #my $descline = join("</br>",@descs)."</br>";
my $descline = ''; #return $descline;
for my $sec (@descs) { my $url = ''; if ($sec =~ s/((?:gi\|(\d+)\|)? # optional GI
(\w+)\|([A-Z\d\.\_]+) # main
(\|[A-Z\d\_]+)?) # optional secondary ID//xms
) { my ($name, $gi, $db, $acc) = ($1, $2, $3, $4); #$acc ||= ($rest) ? $rest : $gi;
$acc =~ s/^\s+(\S+)/$1/; $acc =~ s/(\S+)\s+$/$1/; $url = length($self->remote_database_url($type)) > 0 ? sprintf('<a href="%s">%s</a> %s', sprintf($self->remote_database_url($type), $gi || $acc || $db), $name, $sec) : $sec; } else { $url = $sec; } $descline .= "$url</br>\n"; } return $descline;
}
start_reportdescriptionprevnextTop
sub start_report {
    my( $self, $code ) = @_; 
    if ($code) {
        $self->{'_start_report'} = $code;
    }
    return $self->{'_start_report'} ||\& default_start_report;
}
default_start_reportdescriptionprevnextTop
sub default_start_report {
    my ($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);
}
titledescriptionprevnextTop
sub title {
    my( $self, $code ) = @_; 
    if ($code) {
        $self->{'_title'} = $code;
    }
    return $self->{'_title'} ||\& default_title;
}
default_titledescriptionprevnextTop
sub default_title {
    my ($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());
}
introductiondescriptionprevnextTop
sub introduction {
    my( $self, $code ) = @_; 
    if ($code) {
        $self->{'_introduction'} = $code;
    }
    return $self->{'_introduction'} ||\& default_introduction;
}
default_introductiondescriptionprevnextTop
sub default_introduction {
    my ($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()),
		   );
}
end_reportdescriptionprevnextTop
sub end_report {
    return "</BODY>\n</HTML>\n";
}

# copied from Bio::Index::Fasta
# useful here as well
}
id_parserdescriptionprevnextTop
sub id_parser {
    my( $self, $code ) = @_;
    
    if ($code) {
        $self->{'_id_parser'} = $code;
    }
    return $self->{'_id_parser'} ||\& default_id_parser;
}
default_id_parserdescriptionprevnextTop
sub default_id_parser {
        my ($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);
}
MAXdescriptionprevnextTop
sub MAX {
 $a <=> $b ? $b : $a;
}
footerdescriptionprevnextTop
sub footer {
     my ($self) = @_;
    return "<hr><h5>Produced by Bioperl module ".ref($self)." on $DATE<br>Revision: $Revision</h5>\n"
}
algorithm_referencedescriptionprevnextTop
sub algorithm_reference {
   my ($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
}
_numwithcommasdescriptionprevnextTop
sub _numwithcommas {
    my $num = reverse( $_[0] );
    $num =~ s/(\d{3})(?=\d)(?!\d*\.)/$1,/g;
    return scalar reverse $num;
}
no_wublastlinksdescriptionprevnextTop
sub no_wublastlinks {
    my $self = shift;

    return $self->{'no_wublastlinks'} = shift if @_;
    return $self->{'no_wublastlinks'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 StajichTop
Email jason-at-bioperl-dot-org
CONTRIBUTORSTop
Gary Williams G.Williams@hgmp.mrc.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Methods Bio::SearchIO::SearchWriterITop
Bio::SearchIO::SearchWriterI inherited methods.
filterTop
 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