TextResultWriter documentation.

use Bio::SearchIO; use Bio::SearchIO::Writer::TextResultWriter; my $in = new Bio::SearchIO(-format => 'blast', -file => shift @ARGV); my $writer = new Bio::SearchIO::Writer::TextResultWriter(); my $out = new Bio::SearchIO(-writer => $writer); $out->write_result($in->next_result);

This object implements the SearchWriterI interface which will produce
a set of Text 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.
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 $writer = new
Bio::SearchIO::Writer::TextResultWriter(-verbose => -1);

Title : new Usage : my $obj = new Bio::SearchIO::Writer::TextResultWriter(); 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)

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 : 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="POD4" id="POD4"></a>default_start_report</td><td ><a href="#CODE4">code</a></td><td ><a href="#POD3">prev</a></td><td ><a href="#POD5">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="POD5" id="POD5"></a>title</td><td ><a href="#CODE5">code</a></td><td ><a href="#POD4">prev</a></td><td ><a href="#POD6">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="POD6" id="POD6"></a>default_title</td><td ><a href="#CODE6">code</a></td><td ><a href="#POD5">prev</a></td><td ><a href="#POD7">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 output. Returns : empty for text implementation 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_introduction" id="_pod_introduction"></a><a name="POD7" id="POD7"></a>introduction</td><td ><a href="#CODE7">code</a></td><td ><a href="#POD6">prev</a></td><td ><a href="#POD8">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 : 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</pre></td></tr></table> <div id="sep"></div> <table id="methDescTitle" width="100%"><tr><td WIDTH="200"><a name="_pod_default_introduction" id="_pod_default_introduction"></a><a name="POD8" id="POD8"></a>default_introduction</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_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</pre></td></tr></table> <div id="sep"></div> <table id="methDescTitle" width="100%"><tr><td WIDTH="200"><a name="_pod_end_report" id="_pod_end_report"></a><a name="POD9" id="POD9"></a>end_report</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 : 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</pre></td></tr></table> <div id="sep"></div> <table id="methDescTitle" width="100%"><tr><td WIDTH="200"><a name="_pod_id_parser" id="_pod_id_parser"></a><a name="POD10" id="POD10"></a>id_parser</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 : 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</pre></td></tr></table> <div id="sep"></div> <table id="methDescTitle" width="100%"><tr><td WIDTH="200"><a name="_pod_default_id_parser" id="_pod_default_id_parser"></a><a name="POD11" id="POD11"></a>default_id_parser</td><td ><a href="#CODE11">code</a></td><td ><a href="#POD10">prev</a></td><td ><a href="#POD12">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_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 Args : a fasta header line string</pre></td></tr></table> <div id="sep"></div> <table id="methDescTitle" width="100%"><tr><td WIDTH="200"><a name="_pod_algorithm_reference" id="_pod_algorithm_reference"></a><a name="POD12" id="POD12"></a>algorithm_reference</td><td ><a href="#CODE14">code</a></td><td ><a href="#POD11">prev</a></td><td ><a href="#POD13">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 : algorithm_reference Usage : my $reference = $writer->algorithm_reference($result); Function: Returns the appropriate Bibliographic reference for the algorithm format being produced Returns : String Args : <a href="../../Search/Result/ResultI.html" target="urlWin" id="podUrl">Bio::Search::Result::ResultI</a> to reference</pre></td></tr></table> <div id="sep"></div> <table id="methDescTitle" width="100%"><tr><td WIDTH="200"><a name="_pod_no_wublastlinks" id="_pod_no_wublastlinks"></a><a name="POD13" id="POD13"></a>no_wublastlinks</td><td ><a href="#CODE17">code</a></td><td ><a href="#POD12">prev</a></td><td ><a href="#POD14">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 : 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)</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> $MaxDescLen = 65; $AlignmentLineWidth = 60; eval { require Text::Wrap; $TextWrapLoaded = 1;}; if( $@ ) { $TextWrapLoaded = 0;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE1" id="CODE1"></a>new</td><td ><a href="#POD1">description</a></td><td >prev</td><td ><a href="#CODE2">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub new {<pre> my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($filters,$nowublastlinks) = $self->_rearrange([qw(FILTERS NO_WUBLASTLINKS)], @args); 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); } } } $self->no_wublastlinks(! $nowublastlinks); unless( $TextWrapLoaded ) { $self->warn("Could not load Text::Wrap - the Query Description will not be line wrapped\n"); } else { $Text::Wrap::columns = $MaxDescLen; } return $self;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE2" id="CODE2"></a>to_string</td><td ><a href="#POD2">description</a></td><td ><a href="#CODE1">prev</a></td><td ><a href="#CODE3">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub to_string {<pre> my ($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/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 .= qq{ Score E Sequences producing significant alignments: (bits) value }; my $hspstr = ''; if( $result->can('rewind')) { $result->rewind(); # support stream based parsing routines } while( my $hit = $result->next_hit ) { next if( defined $hitfilter && ! &{$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; my $desc = sprintf("%s %s",$nm,$hit->description); if( length($desc) - 3 > $MaxDescLen) { $descsub = sprintf($p, substr($desc,0,$MaxDescLen-3) . "..."); } else { $descsub = sprintf($p,$desc); } $str .= sprintf("%s %-4s %s\n", $descsub, defined $hit->raw_score ? $hit->raw_score : ' ', defined $hit->significance ? $hit->significance : '?'); my @hsps = $hit->hsps; if( @hsps ) { $hspstr .= sprintf(">%s %s\n%9sLength = %d\n\n", $hit->name, defined $hit->description ? $hit->description : '', '', # empty is for the %9s in the str formatting $hit->length); foreach my $hsp ( @hsps ) { next if( defined $hspfilter && ! &{$hspfilter}($hsp) ); $hspstr .= sprintf(" Score = %4s bits (%s), Expect = %s", $hsp->bits, $hsp->score, $hsp->evalue); if( $hsp->pvalue ) { $hspstr .= ", P = ".$hsp->pvalue; } $hspstr .= "\n"; $hspstr .= sprintf(" Identities = %d/%d (%d%%)", ( $hsp->frac_identical('total') * $hsp->length('total')), $hsp->length('total'), POSIX::floor($hsp->frac_identical('total') * 100)); if( $type eq 'PROTEIN' ) { $hspstr .= sprintf(", Positives = %d/%d (%d%%)", ( $hsp->frac_conserved('total') * $hsp->length('total')), $hsp->length('total'), POSIX::floor($hsp->frac_conserved('total') * 100)); } if( $hsp->gaps ) { $hspstr .= sprintf(", Gaps = %d/%d (%d%%)", $hsp->gaps('total'), $hsp->length('total'), POSIX::floor(100 * $hsp->gaps('total') / $hsp->length('total'))); } $hspstr .= "\n"; my ($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) ) { $hspstr .= sprintf(" Links = %s\n",$lnks); } $hspstr .= "\n\n"; my @hspvals = ( {'name' => 'Query:', 'seq' => $hsp->query_string, 'start' => ( $hstrand >= 0 ? $hsp->query->start : $hsp->query->end), 'end' => ($qstrand >= 0 ? $hsp->query->end : $hsp->query->start), 'index' => 0, 'direction' => $qstrand || 1 }, { 'name' => ' 'x6, # this might need to adjust for long coordinates?? '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"; } } $hspstr .= "\n"; } } $str .= "\n\n".$hspstr; $str .= sprintf(qq{ Database: %s Posted date: %s Number of letters in database: %s Number of sequences in database: %s Matrix: %s }, $result->database_name(), $result->get_statistic('posted_date') || POSIX::strftime("%b %d, %Y %I:%M %p",localtime), &_numwithcommas($result->database_entries()), &_numwithcommas($result->database_letters()), $result->get_parameter('matrix') || ''); if( defined (my $open = $result->get_parameter('gapopen')) ) { $str .= sprintf("Gap Penalties Existence: %d, Extension: %d\n", $open || 0, $result->get_parameter('gapext') || 0); } # skip those params we've already output foreach my $param ( grep { ! /matrix|gapopen|gapext/i } $result->available_parameters ) { $str .= "$param: ". $result->get_parameter($param) ."\n"; } $str .= "Search Statistics\n"; # skip posted date, we already output it foreach my $stat ( sort grep { ! /posted_date/ } $result->available_statistics ) { my $expect = $result->get_parameter('expect'); my $v = $result->get_statistic($stat); if( $v =~ /^\d+$/ ) { $v = &_numwithcommas($v); } if( defined $expect && $stat eq 'seqs_better_than_cutoff' ) { $str .= "seqs_better_than_$expect: $v\n"; } else { my $v = $str .= "$stat: $v\n"; } } $str .= "\n\n"; return $str;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE3" id="CODE3"></a>start_report</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 start_report {<pre> my( $self, $code ) = @_; if ($code) { $self->{'_start_report'} = $code; } return $self->{'_start_report'} ||\& default_start_report;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE4" id="CODE4"></a>default_start_report</td><td ><a href="#POD4">description</a></td><td ><a href="#CODE3">prev</a></td><td ><a href="#CODE5">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub default_start_report {<pre> my ($result) = @_; return "";</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE5" id="CODE5"></a>title</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 title {<pre> my( $self, $code ) = @_; if ($code) { $self->{'_title'} = $code; } return $self->{'_title'} ||\& default_title;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE6" id="CODE6"></a>default_title</td><td ><a href="#POD6">description</a></td><td ><a href="#CODE5">prev</a></td><td ><a href="#CODE7">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub default_title {<pre> my ($result) = @_; return ""; # The HTML implementation # 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()); </pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE7" id="CODE7"></a>introduction</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 introduction {<pre> my( $self, $code ) = @_; if ($code) { $self->{'_introduction'} = $code; } return $self->{'_introduction'} ||\& default_introduction;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE8" id="CODE8"></a>default_introduction</td><td ><a href="#POD8">description</a></td><td ><a href="#CODE7">prev</a></td><td ><a href="#CODE9">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub default_introduction {<pre> my ($result) = @_; return sprintf( qq{ Query= %s (%s letters) Database: %s %s sequences; %s total letters }, &_linewrap($result->query_name . " " . $result->query_description), &_numwithcommas($result->query_length), $result->database_name(), &_numwithcommas($result->database_entries()), &_numwithcommas($result->database_letters()), );</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE9" id="CODE9"></a>end_report</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 end_report {<pre> return "";</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE10" id="CODE10"></a>id_parser</td><td ><a href="#POD10">description</a></td><td ><a href="#CODE9">prev</a></td><td ><a href="#CODE11">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub id_parser {<pre> my( $self, $code ) = @_; if ($code) { $self->{'_id_parser'} = $code; } return $self->{'_id_parser'} ||\& default_id_parser;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE11" id="CODE11"></a>default_id_parser</td><td ><a href="#POD11">description</a></td><td ><a href="#CODE10">prev</a></td><td ><a href="#CODE12">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub default_id_parser {<pre> my ($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);</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE12" id="CODE12"></a>MIN</td><td >description</td><td ><a href="#CODE11">prev</a></td><td ><a href="#CODE13">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub MIN {<pre> $a <=> $b ? $a : $b;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE13" id="CODE13"></a>MAX</td><td >description</td><td ><a href="#CODE12">prev</a></td><td ><a href="#CODE14">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub MAX {<pre> $a <=> $b ? $b : $a;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE14" id="CODE14"></a>algorithm_reference</td><td ><a href="#POD12">description</a></td><td ><a href="#CODE13">prev</a></td><td ><a href="#CODE15">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub algorithm_reference {<pre> my ($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. "\n"; if( $result->algorithm_version =~ /WashU/i ) { return $res .qq{ Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA. All Rights Reserved. Reference: Gish, W. (1996-2000) http://blast.wustl.edu }; } else { return $res . qq{ 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 . "\n". "\nReference: Pearson et al, Genomics (1997) 46:24-36\n"; } else { return ''; }</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE15" id="CODE15"></a>_numwithcommas</td><td >description</td><td ><a href="#CODE14">prev</a></td><td ><a href="#CODE16">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub _numwithcommas {<pre> my $num = reverse( $_[0] ); $num =~ s/(\d{3})(?=\d)(?!\d*\.)/$1,/g; return scalar reverse $num;</pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE16" id="CODE16"></a>_linewrap</td><td >description</td><td ><a href="#CODE15">prev</a></td><td ><a href="#CODE17">next</a></td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub _linewrap {<pre> my ($str) = @_; if($TextWrapLoaded) { return Text::Wrap::wrap("","",$str); # use Text::Wrap } else { return $str; } # cannot wrap </pre>}</td></div> <div id="sep"></div> <table id="methCodeTitle" width="100%"><tr><td width="200"><a name="CODE17" id="CODE17"></a>no_wublastlinks</td><td ><a href="#POD13">description</a></td><td ><a href="#CODE16">prev</a></td><td >next</td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="methCodeArea"><td >sub no_wublastlinks {<pre> my $self = shift; return $self->{'no_wublastlinks'} = shift if @_; return $self->{'no_wublastlinks'};</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 <a href="mailto:jason@bioperl.org" id="podEmail">jason@bioperl.org</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> <table id="genInfoTitle" width="100%"><tr><td><a name="_pod_Methods Bio::SearchIO::SearchWriterI" id="_pod_Methods Bio::SearchIO::SearchWriterI"></a>Methods Bio::SearchIO::SearchWriterI</td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="genInfoArea"><a href="../SearchWriterI.html" target="urlWin" id="podUrl">Bio::SearchIO::SearchWriterI</a> inherited methods.</div> <div id="sep"></div> <table id="genInfoTitle" width="100%"><tr><td><a name="_pod_filter" id="_pod_filter"></a>filter</td><td align="right"><a href="#TOP">Top</a></td></tr></table> <div id="genInfoArea"><pre id="podParagraph"> 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</pre></div> <div id="sep"></div> </body> </html>

BEGIN		Code
new	Description	Code
to_string	Description	Code
start_report	Description	Code
default_start_report	Description	Code
title	Description	Code
default_title	Description	Code
introduction	Description	Code
default_introduction	Description	Code
end_report	Description	Code
id_parser	Description	Code
default_id_parser	Description	Code
MIN	No description	Code
MAX	No description	Code
algorithm_reference	Description	Code
_numwithcommas	No description	Code
_linewrap	No description	Code
no_wublastlinks	Description	Code