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# BioPerl module for Bio::SearchIO::Writer::TextResultWriter |
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# |
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# Please direct questions and support issues to |
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# |
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# Cared for by Jason Stajich |
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# |
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# Copyright Jason Stajich |
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# |
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# You may distribute this module under the same terms as perl itself |
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# POD documentation - main docs before the code |
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=head1 NAME |
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Bio::SearchIO::Writer::TextResultWriter - Object to implement writing |
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a Bio::Search::ResultI in Text. |
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=head1 SYNOPSIS |
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use Bio::SearchIO; |
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use Bio::SearchIO::Writer::TextResultWriter; |
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my $in = Bio::SearchIO->new(-format => 'blast', |
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-file => shift @ARGV); |
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my $writer = Bio::SearchIO::Writer::TextResultWriter->new(); |
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my $out = Bio::SearchIO->new(-writer => $writer); |
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$out->write_result($in->next_result); |
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=head1 DESCRIPTION |
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This object implements the SearchWriterI interface which will produce |
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a set of Text for a specific Bio::Search::Report::ReportI interface. |
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You can also provide the argument -filters =E \%hash to filter the at |
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the hsp, hit, or result level. %hash is an associative array which |
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contains any or all of the keys (HSP, HIT, RESULT). The values |
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pointed to by these keys would be references to a subroutine which |
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expects to be passed an object - one of Bio::Search::HSP::HSPI, |
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Bio::Search::Hit::HitI, and Bio::Search::Result::ResultI respectively. |
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Each function needs to return a boolean value as to whether or not the |
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passed element should be included in the output report - true if it is |
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to be included, false if it to be omitted. |
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For example to filter on sequences in the database which are too short |
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for your criteria you would do the following. |
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Define a hit filter method |
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sub hit_filter { |
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my $hit = shift; |
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return $hit->length E 100; # test if length of the hit sequence |
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# long enough |
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} |
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my $writer = Bio::SearchIO::Writer::TextResultWriter->new( |
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-filters => { 'HIT' =E \&hit_filter } |
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); |
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Another example would be to filter HSPs on percent identity, let's |
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only include HSPs which are 75% identical or better. |
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sub hsp_filter { |
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my $hsp = shift; |
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return $hsp->percent_identity E 75; |
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} |
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my $writer = Bio::SearchIO::Writer::TextResultWriter->new( |
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-filters => { 'HSP' =E \&hsp_filter } |
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); |
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See L for more info on the filter method. |
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This module will use the module Text::Wrap if it is installed to wrap |
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the Query description line. If you do not have Text::Wrap installed |
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this module will work fine but you won't have the Query line wrapped. |
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You will see a warning about this when you first instantiate a |
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TextResultWriter - to avoid these warnings from showing up, simply set |
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the verbosity upon initialization to -1 like this: my $writer = new |
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Bio::SearchIO::Writer::TextResultWriter(-verbose =E -1); |
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=head1 FEEDBACK |
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=head2 Mailing Lists |
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User feedback is an integral part of the evolution of this and other |
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Bioperl modules. Send your comments and suggestions preferably to |
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the Bioperl mailing list. Your participation is much appreciated. |
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bioperl-l@bioperl.org - General discussion |
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists |
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=head2 Support |
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Please direct usage questions or support issues to the mailing list: |
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I |
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rather than to the module maintainer directly. Many experienced and |
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reponsive experts will be able look at the problem and quickly |
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address it. Please include a thorough description of the problem |
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with code and data examples if at all possible. |
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=head2 Reporting Bugs |
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Report bugs to the Bioperl bug tracking system to help us keep track |
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of the bugs and their resolution. Bug reports can be submitted via the |
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web: |
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https://github.com/bioperl/bioperl-live/issues |
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=head1 AUTHOR - Jason Stajich |
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Email jason@bioperl.org |
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=head1 APPENDIX |
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The rest of the documentation details each of the object methods. |
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Internal methods are usually preceded with a _ |
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=cut |
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# Let the code begin... |
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package Bio::SearchIO::Writer::TextResultWriter; |
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use vars qw($MaxNameLen $MaxDescLen $AlignmentLineWidth $DescLineLen $TextWrapLoaded); |
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use strict; |
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# Object preamble - inherits from Bio::Root::RootI |
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BEGIN { |
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$MaxDescLen = 65; |
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$AlignmentLineWidth = 60; |
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eval { require Text::Wrap; $TextWrapLoaded = 1;}; |
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if( $@ ) { |
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$TextWrapLoaded = 0; |
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} |
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} |
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use POSIX; |
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use base qw(Bio::Root::Root Bio::SearchIO::SearchWriterI); |
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=head2 new |
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Title : new |
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Usage : my $obj = Bio::SearchIO::Writer::TextResultWriter->new(); |
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Function: Builds a new Bio::SearchIO::Writer::TextResultWriter object |
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Returns : Bio::SearchIO::Writer::TextResultWriter |
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Args : -filters => hashref with any or all of the keys (HSP HIT RESULT) |
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which have values pointing to a subroutine reference |
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which will expect to get a Hit,HSP, Result object respectively |
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-no_wublastlinks => boolean. Do not display WU-BLAST lines even if |
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they are parsed out |
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Links = (1) |
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=cut |
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sub new { |
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my($class,@args) = @_; |
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my $self = $class->SUPER::new(@args); |
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my ($filters,$nowublastlinks) = $self->_rearrange([qw(FILTERS |
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NO_WUBLASTLINKS)], |
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@args); |
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if( defined $filters ) { |
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if( !ref($filters) =~ /HASH/i ) { |
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$self->warn("Did not provide a hashref for the FILTERS option, ignoring."); |
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} else { |
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while( my ($type,$code) = each %{$filters} ) { |
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$self->filter($type,$code); |
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} |
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} |
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} |
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$self->no_wublastlinks(! $nowublastlinks); |
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unless( $TextWrapLoaded ) { |
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$self->warn("Could not load Text::Wrap - the Query Description will not be line wrapped\n"); |
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} else { |
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$Text::Wrap::columns = $MaxDescLen; |
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} |
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return $self; |
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} |
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=head2 to_string |
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Purpose : Produces data for each Search::Result::ResultI in a string. |
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: This is an abstract method. For some useful implementations, |
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: see ResultTableWriter.pm, HitTableWriter.pm, |
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: and HSPTableWriter.pm. |
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Usage : print $writer->to_string( $result_obj, @args ); |
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Argument : $result_obj = A Bio::Search::Result::ResultI object |
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: @args = any additional arguments used by your implementation. |
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Returns : String containing data for each search Result or any of its |
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: sub-objects (Hits and HSPs). |
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Throws : n/a |
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200
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=cut |
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202
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sub to_string { |
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my ($self,$result,$num) = @_; |
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$num ||= 0; |
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return unless defined $result; |
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my $links = $self->no_wublastlinks; |
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my ($resultfilter,$hitfilter, $hspfilter) = ( $self->filter('RESULT'), |
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$self->filter('HIT'), |
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$self->filter('HSP') ); |
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4
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return '' if( defined $resultfilter && ! &{$resultfilter}($result) ); |
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my ($qtype,$dbtype,$dbseqtype,$type); |
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5
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my $alg = $result->algorithm; |
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my $wublast = ($result->algorithm_version =~ /WashU/) ? 1 : 0; |
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217
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# This is actually wrong for the FASTAs I think |
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0
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|
|
8
|
if( $alg =~ /T(FAST|BLAST)([XY])/i ) { |
|
|
0
|
0
|
|
|
|
|
|
|
0
|
|
|
|
|
|
|
|
0
|
|
|
|
|
|
|
|
0
|
|
|
|
|
|
219
|
1
|
|
|
|
|
2
|
$qtype = $dbtype = 'translated'; |
220
|
1
|
|
|
|
|
2
|
$dbseqtype = $type = 'PROTEIN'; |
221
|
|
|
|
|
|
|
} elsif( $alg =~ /T(FAST|BLAST)N/i ) { |
222
|
0
|
|
|
|
|
0
|
$qtype = ''; |
223
|
0
|
|
|
|
|
0
|
$dbtype = 'translated'; |
224
|
0
|
|
|
|
|
0
|
$type = 'PROTEIN'; |
225
|
0
|
|
|
|
|
0
|
$dbseqtype = 'NUCLEOTIDE'; |
226
|
|
|
|
|
|
|
} elsif( $alg =~ /(FAST|BLAST)N/i || |
227
|
|
|
|
|
|
|
$alg =~ /(WABA|EXONERATE)/i ) { |
228
|
0
|
|
|
|
|
0
|
$qtype = $dbtype = ''; |
229
|
0
|
|
|
|
|
0
|
$type = $dbseqtype = 'NUCLEOTIDE'; |
230
|
|
|
|
|
|
|
} elsif( $alg =~ /(FAST|BLAST)P/ || |
231
|
|
|
|
|
|
|
$alg =~ /SSEARCH|(HMM|SEARCH|PFAM)/i ) { |
232
|
0
|
|
|
|
|
0
|
$qtype = $dbtype = ''; |
233
|
0
|
|
|
|
|
0
|
$type = $dbseqtype = 'PROTEIN'; |
234
|
|
|
|
|
|
|
} elsif( $alg =~ /(FAST|BLAST)[XY]/i ) { |
235
|
0
|
|
|
|
|
0
|
$qtype = 'translated'; |
236
|
0
|
|
|
|
|
0
|
$dbtype = 'PROTEIN'; |
237
|
0
|
|
|
|
|
0
|
$dbseqtype = $type = 'PROTEIN'; |
238
|
|
|
|
|
|
|
} else { |
239
|
0
|
|
|
|
|
0
|
print STDERR "algorithm was ", $result->algorithm, " couldn't match\n"; |
240
|
|
|
|
|
|
|
} |
241
|
|
|
|
|
|
|
|
242
|
|
|
|
|
|
|
|
243
|
1
|
50
|
|
|
|
11
|
my %baselens = ( 'Sbjct:' => ( $dbtype eq 'translated' ) ? 3 : 1, |
|
|
50
|
|
|
|
|
|
244
|
|
|
|
|
|
|
'Query:' => ( $qtype eq 'translated' ) ? 3 : 1); |
245
|
|
|
|
|
|
|
|
246
|
1
|
|
|
|
|
2
|
my $str; |
247
|
1
|
50
|
33
|
|
|
5
|
if( ! defined $num || $num <= 1 ) { |
248
|
1
|
|
|
|
|
1
|
$str = &{$self->start_report}($result); |
|
1
|
|
|
|
|
4
|
|
249
|
|
|
|
|
|
|
} |
250
|
|
|
|
|
|
|
|
251
|
1
|
|
|
|
|
2
|
$str .= &{$self->title}($result); |
|
1
|
|
|
|
|
3
|
|
252
|
1
|
|
|
|
|
6
|
$str .= $result->algorithm . " " . $result->algorithm_version . "\n\n\n"; |
253
|
1
|
|
33
|
|
|
6
|
$str .= $result->algorithm_reference || $self->algorithm_reference($result); |
254
|
1
|
|
|
|
|
5
|
$str .= &{$self->introduction}($result); |
|
1
|
|
|
|
|
6
|
|
255
|
|
|
|
|
|
|
|
256
|
|
|
|
|
|
|
|
257
|
1
|
|
|
|
|
3
|
$str .= qq{ |
258
|
|
|
|
|
|
|
Score E |
259
|
|
|
|
|
|
|
Sequences producing significant alignments: (bits) value |
260
|
|
|
|
|
|
|
}; |
261
|
1
|
|
|
|
|
2
|
my $hspstr = ''; |
262
|
1
|
50
|
|
|
|
15
|
if( $result->can('rewind')) { |
263
|
1
|
|
|
|
|
5
|
$result->rewind(); # support stream based parsing routines |
264
|
|
|
|
|
|
|
} |
265
|
1
|
|
|
|
|
4
|
while( my $hit = $result->next_hit ) { |
266
|
20
|
50
|
33
|
|
|
46
|
next if( defined $hitfilter && ! &{$hitfilter}($hit) ); |
|
0
|
|
|
|
|
0
|
|
267
|
20
|
|
|
|
|
46
|
my $nm = $hit->name(); |
268
|
20
|
50
|
|
|
|
36
|
$self->debug( "no $nm for name (".$hit->description(). "\n") |
269
|
|
|
|
|
|
|
unless $nm; |
270
|
20
|
|
|
|
|
28
|
my ($gi,$acc) = &{$self->id_parser}($nm); |
|
20
|
|
|
|
|
43
|
|
271
|
20
|
|
|
|
|
54
|
my $p = "%-$MaxDescLen". "s"; |
272
|
20
|
|
|
|
|
21
|
my $descsub; |
273
|
20
|
|
|
|
|
51
|
my $desc = sprintf("%s %s",$nm,$hit->description); |
274
|
20
|
50
|
|
|
|
52
|
if( length($desc) - 3 > $MaxDescLen) { |
275
|
20
|
|
|
|
|
62
|
$descsub = sprintf($p, |
276
|
|
|
|
|
|
|
substr($desc,0,$MaxDescLen-3) . |
277
|
|
|
|
|
|
|
"..."); |
278
|
|
|
|
|
|
|
} else { |
279
|
0
|
|
|
|
|
0
|
$descsub = sprintf($p,$desc); |
280
|
|
|
|
|
|
|
} |
281
|
20
|
0
|
|
|
|
57
|
$str .= $wublast ? sprintf("%s %-4s %s\n", |
|
|
0
|
|
|
|
|
|
|
|
50
|
|
|
|
|
|
|
|
50
|
|
|
|
|
|
|
|
50
|
|
|
|
|
|
282
|
|
|
|
|
|
|
$descsub, |
283
|
|
|
|
|
|
|
defined $hit->raw_score ? $hit->raw_score : ' ', |
284
|
|
|
|
|
|
|
defined $hit->significance ? $hit->significance : '?') : |
285
|
|
|
|
|
|
|
sprintf("%s %-4s %s\n", |
286
|
|
|
|
|
|
|
$descsub, |
287
|
|
|
|
|
|
|
defined $hit->bits ? $hit->bits: ' ', |
288
|
|
|
|
|
|
|
defined $hit->significance ? $hit->significance : '?'); |
289
|
20
|
|
|
|
|
56
|
my @hsps = $hit->hsps; |
290
|
20
|
50
|
|
|
|
43
|
if( @hsps ) { |
291
|
20
|
50
|
|
|
|
46
|
$hspstr .= sprintf(">%s %s\n%9sLength = %d\n\n", |
292
|
|
|
|
|
|
|
$hit->name, |
293
|
|
|
|
|
|
|
defined $hit->description ? $hit->description : '', |
294
|
|
|
|
|
|
|
'', # empty is for the %9s in the str formatting |
295
|
|
|
|
|
|
|
$hit->length); |
296
|
|
|
|
|
|
|
|
297
|
20
|
|
|
|
|
43
|
foreach my $hsp ( @hsps ) { |
298
|
21
|
50
|
33
|
|
|
38
|
next if( defined $hspfilter && ! &{$hspfilter}($hsp) ); |
|
0
|
|
|
|
|
0
|
|
299
|
21
|
|
|
|
|
48
|
$hspstr .= sprintf(" Score = %4s bits (%s), Expect = %s", |
300
|
|
|
|
|
|
|
$hsp->bits, $hsp->score, $hsp->evalue); |
301
|
21
|
50
|
|
|
|
51
|
if( $hsp->pvalue ) { |
302
|
0
|
|
|
|
|
0
|
$hspstr .= ", P = ".$hsp->pvalue; |
303
|
|
|
|
|
|
|
} |
304
|
21
|
|
|
|
|
65
|
$hspstr .= "\n"; |
305
|
21
|
|
|
|
|
40
|
$hspstr .= sprintf(" Identities = %d/%d (%d%%)", |
306
|
|
|
|
|
|
|
( $hsp->frac_identical('total') * |
307
|
|
|
|
|
|
|
$hsp->length('total')), |
308
|
|
|
|
|
|
|
$hsp->length('total'), |
309
|
|
|
|
|
|
|
POSIX::floor($hsp->frac_identical('total') |
310
|
|
|
|
|
|
|
* 100)); |
311
|
|
|
|
|
|
|
|
312
|
21
|
50
|
|
|
|
55
|
if( $type eq 'PROTEIN' ) { |
313
|
21
|
|
|
|
|
42
|
$hspstr .= sprintf(", Positives = %d/%d (%d%%)", |
314
|
|
|
|
|
|
|
( $hsp->frac_conserved('total') * |
315
|
|
|
|
|
|
|
$hsp->length('total')), |
316
|
|
|
|
|
|
|
$hsp->length('total'), |
317
|
|
|
|
|
|
|
POSIX::floor($hsp->frac_conserved('total') * 100)); |
318
|
|
|
|
|
|
|
|
319
|
|
|
|
|
|
|
} |
320
|
21
|
50
|
|
|
|
49
|
if( $hsp->gaps ) { |
321
|
0
|
|
|
|
|
0
|
$hspstr .= sprintf(", Gaps = %d/%d (%d%%)", |
322
|
|
|
|
|
|
|
$hsp->gaps('total'), |
323
|
|
|
|
|
|
|
$hsp->length('total'), |
324
|
|
|
|
|
|
|
POSIX::floor(100 * $hsp->gaps('total') / |
325
|
|
|
|
|
|
|
$hsp->length('total'))); |
326
|
|
|
|
|
|
|
} |
327
|
21
|
|
|
|
|
33
|
$hspstr .= "\n"; |
328
|
21
|
|
|
|
|
48
|
my ($hframe,$qframe) = ( $hsp->hit->frame, |
329
|
|
|
|
|
|
|
$hsp->query->frame); |
330
|
21
|
|
|
|
|
48
|
my ($hstrand,$qstrand) = ($hsp->hit->strand,$hsp->query->strand); |
331
|
|
|
|
|
|
|
# so TBLASTX will have Query/Hit frames |
332
|
|
|
|
|
|
|
# BLASTX will have Query frame |
333
|
|
|
|
|
|
|
# TBLASTN will have Hit frame |
334
|
21
|
50
|
33
|
|
|
46
|
if( $hstrand || $qstrand ) { |
335
|
21
|
|
|
|
|
35
|
$hspstr .= " Frame = "; |
336
|
21
|
|
|
|
|
31
|
my ($signq, $signh); |
337
|
21
|
50
|
|
|
|
46
|
unless( $hstrand ) { |
338
|
0
|
|
|
|
|
0
|
$hframe = undef; |
339
|
|
|
|
|
|
|
# if strand is null or 0 then it is protein |
340
|
|
|
|
|
|
|
# and this no frame |
341
|
|
|
|
|
|
|
} else { |
342
|
21
|
100
|
|
|
|
41
|
$signh = $hstrand < 0 ? '-' : '+'; |
343
|
|
|
|
|
|
|
} |
344
|
21
|
50
|
|
|
|
32
|
unless( $qstrand ) { |
345
|
0
|
|
|
|
|
0
|
$qframe = undef; |
346
|
|
|
|
|
|
|
# if strand is null or 0 then it is protein |
347
|
|
|
|
|
|
|
} else { |
348
|
21
|
100
|
|
|
|
31
|
$signq =$qstrand < 0 ? '-' : '+'; |
349
|
|
|
|
|
|
|
} |
350
|
|
|
|
|
|
|
# remember bioperl stores frames as 0,1,2 (GFF way) |
351
|
|
|
|
|
|
|
# BLAST reports reports as 1,2,3 so |
352
|
|
|
|
|
|
|
# we have to add 1 to the frame values |
353
|
21
|
50
|
33
|
|
|
87
|
if( defined $hframe && ! defined $qframe) { |
|
|
50
|
33
|
|
|
|
|
354
|
0
|
|
|
|
|
0
|
$hspstr .= "$signh".($hframe+1); |
355
|
|
|
|
|
|
|
} elsif( defined $qframe && ! defined $hframe) { |
356
|
0
|
|
|
|
|
0
|
$hspstr .= "$signq".($qframe+1); |
357
|
|
|
|
|
|
|
} else { |
358
|
21
|
|
|
|
|
89
|
$hspstr .= sprintf(" %s%d / %s%d", |
359
|
|
|
|
|
|
|
$signq,$qframe+1, |
360
|
|
|
|
|
|
|
$signh, $hframe+1); |
361
|
|
|
|
|
|
|
} |
362
|
|
|
|
|
|
|
} |
363
|
|
|
|
|
|
|
|
364
|
21
|
50
|
33
|
|
|
142
|
if( $links && |
|
|
|
33
|
|
|
|
|
365
|
|
|
|
|
|
|
$hsp->can('links') && defined(my $lnks = $hsp->links) ) { |
366
|
0
|
|
|
|
|
0
|
$hspstr .= sprintf(" Links = %s\n",$lnks); |
367
|
|
|
|
|
|
|
} |
368
|
21
|
|
|
|
|
30
|
$hspstr .= "\n\n"; |
369
|
|
|
|
|
|
|
|
370
|
21
|
100
|
50
|
|
|
42
|
my @hspvals = ( {'name' => 'Query:', |
|
|
100
|
50
|
|
|
|
|
|
|
100
|
|
|
|
|
|
|
|
100
|
|
|
|
|
|
371
|
|
|
|
|
|
|
'seq' => $hsp->query_string, |
372
|
|
|
|
|
|
|
'start' => ( $qstrand >= 0 ? |
373
|
|
|
|
|
|
|
$hsp->query->start : |
374
|
|
|
|
|
|
|
$hsp->query->end), |
375
|
|
|
|
|
|
|
'end' => ($qstrand >= 0 ? |
376
|
|
|
|
|
|
|
$hsp->query->end : |
377
|
|
|
|
|
|
|
$hsp->query->start), |
378
|
|
|
|
|
|
|
'index' => 0, |
379
|
|
|
|
|
|
|
'direction' => $qstrand || 1 |
380
|
|
|
|
|
|
|
}, |
381
|
|
|
|
|
|
|
{ 'name' => ' 'x6, # this might need to adjust for long coordinates?? |
382
|
|
|
|
|
|
|
'seq' => $hsp->homology_string, |
383
|
|
|
|
|
|
|
'start' => undef, |
384
|
|
|
|
|
|
|
'end' => undef, |
385
|
|
|
|
|
|
|
'index' => 0, |
386
|
|
|
|
|
|
|
'direction' => 1 |
387
|
|
|
|
|
|
|
}, |
388
|
|
|
|
|
|
|
{ 'name' => 'Sbjct:', |
389
|
|
|
|
|
|
|
'seq' => $hsp->hit_string, |
390
|
|
|
|
|
|
|
'start' => ($hstrand >= 0 ? |
391
|
|
|
|
|
|
|
$hsp->hit->start : $hsp->hit->end), |
392
|
|
|
|
|
|
|
'end' => ($hstrand >= 0 ? |
393
|
|
|
|
|
|
|
$hsp->hit->end : $hsp->hit->start), |
394
|
|
|
|
|
|
|
'index' => 0, |
395
|
|
|
|
|
|
|
'direction' => $hstrand || 1 |
396
|
|
|
|
|
|
|
} |
397
|
|
|
|
|
|
|
); |
398
|
|
|
|
|
|
|
|
399
|
|
|
|
|
|
|
|
400
|
|
|
|
|
|
|
# let's set the expected length (in chars) of the starting number |
401
|
|
|
|
|
|
|
# in an alignment block so we can have things line up |
402
|
|
|
|
|
|
|
# Just going to try and set to the largest |
403
|
|
|
|
|
|
|
|
404
|
85
|
|
|
|
|
151
|
my ($numwidth) = sort { $b <=> $a }(length($hspvals[0]->{'start'}), |
405
|
|
|
|
|
|
|
length($hspvals[0]->{'end'}), |
406
|
|
|
|
|
|
|
length($hspvals[2]->{'start'}), |
407
|
21
|
|
|
|
|
123
|
length($hspvals[2]->{'end'})); |
408
|
21
|
|
|
|
|
37
|
my $count = 0; |
409
|
21
|
|
|
|
|
51
|
while ( $count <= $hsp->length('total') ) { |
410
|
21
|
|
|
|
|
44
|
foreach my $v ( @hspvals ) { |
411
|
63
|
|
|
|
|
117
|
my $piece = substr($v->{'seq'}, $v->{'index'} +$count, |
412
|
|
|
|
|
|
|
$AlignmentLineWidth); |
413
|
63
|
|
|
|
|
72
|
my $cp = $piece; |
414
|
63
|
|
|
|
|
78
|
my $plen = scalar ( $cp =~ tr/\-//); |
415
|
63
|
|
|
|
|
95
|
my ($start,$end) = ('',''); |
416
|
63
|
100
|
|
|
|
103
|
if( defined $v->{'start'} ) { |
417
|
42
|
|
|
|
|
48
|
$start = $v->{'start'}; |
418
|
|
|
|
|
|
|
# since strand can be + or - use the direction |
419
|
|
|
|
|
|
|
# to signify which whether to add or subtract from end |
420
|
|
|
|
|
|
|
my $d = $v->{'direction'} * ( $AlignmentLineWidth - $plen )* |
421
|
42
|
|
|
|
|
80
|
$baselens{$v->{'name'}}; |
422
|
42
|
50
|
|
|
|
66
|
if( length($piece) < $AlignmentLineWidth ) { |
423
|
|
|
|
|
|
|
$d = (length($piece) - $plen) * $v->{'direction'} * |
424
|
42
|
|
|
|
|
56
|
$baselens{$v->{'name'}}; |
425
|
|
|
|
|
|
|
} |
426
|
42
|
|
|
|
|
52
|
$end = $v->{'start'} + $d - $v->{'direction'}; |
427
|
42
|
|
|
|
|
49
|
$v->{'start'} += $d; |
428
|
|
|
|
|
|
|
} |
429
|
|
|
|
|
|
|
$hspstr .= sprintf("%s %-".$numwidth."s %s %s\n", |
430
|
63
|
|
|
|
|
226
|
$v->{'name'}, |
431
|
|
|
|
|
|
|
$start, |
432
|
|
|
|
|
|
|
$piece, |
433
|
|
|
|
|
|
|
$end |
434
|
|
|
|
|
|
|
); |
435
|
|
|
|
|
|
|
} |
436
|
21
|
|
|
|
|
26
|
$count += $AlignmentLineWidth; |
437
|
21
|
|
|
|
|
41
|
$hspstr .= "\n"; |
438
|
|
|
|
|
|
|
} |
439
|
|
|
|
|
|
|
} |
440
|
20
|
|
|
|
|
86
|
$hspstr .= "\n"; |
441
|
|
|
|
|
|
|
} |
442
|
|
|
|
|
|
|
} |
443
|
1
|
|
|
|
|
23
|
$str .= "\n\n".$hspstr; |
444
|
|
|
|
|
|
|
|
445
|
1
|
|
33
|
|
|
6
|
$str .= sprintf(qq{ Database: %s |
|
|
|
50
|
|
|
|
|
446
|
|
|
|
|
|
|
Posted date: %s |
447
|
|
|
|
|
|
|
Number of letters in database: %s |
448
|
|
|
|
|
|
|
Number of sequences in database: %s |
449
|
|
|
|
|
|
|
|
450
|
|
|
|
|
|
|
Matrix: %s |
451
|
|
|
|
|
|
|
}, |
452
|
|
|
|
|
|
|
$result->database_name(), |
453
|
|
|
|
|
|
|
$result->get_statistic('posted_date') || |
454
|
|
|
|
|
|
|
POSIX::strftime("%b %d, %Y %I:%M %p",localtime), |
455
|
|
|
|
|
|
|
&_numwithcommas($result->database_letters()), |
456
|
|
|
|
|
|
|
&_numwithcommas($result->database_entries()), |
457
|
|
|
|
|
|
|
$result->get_parameter('matrix') || ''); |
458
|
|
|
|
|
|
|
|
459
|
1
|
50
|
|
|
|
4
|
if( defined (my $open = $result->get_parameter('gapopen')) ) { |
460
|
0
|
|
0
|
|
|
0
|
$str .= sprintf("Gap Penalties Existence: %d, Extension: %d\n", |
|
|
|
0
|
|
|
|
|
461
|
|
|
|
|
|
|
$open || 0, $result->get_parameter('gapext') || 0); |
462
|
|
|
|
|
|
|
} |
463
|
|
|
|
|
|
|
|
464
|
|
|
|
|
|
|
# skip those params we've already output |
465
|
1
|
|
|
|
|
5
|
foreach my $param ( grep { ! /matrix|gapopen|gapext/i } |
|
3
|
|
|
|
|
11
|
|
466
|
|
|
|
|
|
|
$result->available_parameters ) { |
467
|
2
|
|
|
|
|
8
|
$str .= "$param: ". $result->get_parameter($param) ."\n"; |
468
|
|
|
|
|
|
|
|
469
|
|
|
|
|
|
|
} |
470
|
1
|
|
|
|
|
5
|
$str .= "Search Statistics\n"; |
471
|
|
|
|
|
|
|
# skip posted date, we already output it |
472
|
1
|
|
|
|
|
9
|
foreach my $stat ( sort grep { ! /posted_date/ } |
|
27
|
|
|
|
|
45
|
|
473
|
|
|
|
|
|
|
$result->available_statistics ) { |
474
|
26
|
|
|
|
|
46
|
my $expect = $result->get_parameter('expect'); |
475
|
26
|
|
|
|
|
48
|
my $v = $result->get_statistic($stat); |
476
|
26
|
100
|
|
|
|
75
|
if( $v =~ /^\d+$/ ) { |
477
|
18
|
|
|
|
|
28
|
$v = &_numwithcommas($v); |
478
|
|
|
|
|
|
|
} |
479
|
26
|
100
|
66
|
|
|
65
|
if( defined $expect && |
480
|
|
|
|
|
|
|
$stat eq 'seqs_better_than_cutoff' ) { |
481
|
1
|
|
|
|
|
3
|
$str .= "seqs_better_than_$expect: $v\n"; |
482
|
|
|
|
|
|
|
} else { |
483
|
25
|
|
|
|
|
75
|
my $v = |
484
|
|
|
|
|
|
|
$str .= "$stat: $v\n"; |
485
|
|
|
|
|
|
|
} |
486
|
|
|
|
|
|
|
} |
487
|
1
|
|
|
|
|
3
|
$str .= "\n\n"; |
488
|
1
|
|
|
|
|
15
|
return $str; |
489
|
|
|
|
|
|
|
} |
490
|
|
|
|
|
|
|
|
491
|
|
|
|
|
|
|
|
492
|
|
|
|
|
|
|
=head2 start_report |
493
|
|
|
|
|
|
|
|
494
|
|
|
|
|
|
|
Title : start_report |
495
|
|
|
|
|
|
|
Usage : $index->start_report( CODE ) |
496
|
|
|
|
|
|
|
Function: Stores or returns the code to |
497
|
|
|
|
|
|
|
write the start of the block, the block </td>
</tr>
<tr>
<td class="h" >
<a name="498">498</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> and the start of the <BODY> block of HTML. Useful </td>
</tr>
<tr>
<td class="h" >
<a name="499">499</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> for (for instance) specifying alternative </td>
</tr>
<tr>
<td class="h" >
<a name="500">500</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> HTML if you are embedding the output in </td>
</tr>
<tr>
<td class="h" >
<a name="501">501</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> an HTML page which you have already started. </td>
</tr>
<tr>
<td class="h" >
<a name="502">502</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> (For example a routine returning a null string). </td>
</tr>
<tr>
<td class="h" >
<a name="503">503</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns \&default_start_report (see below) if not </td>
</tr>
<tr>
<td class="h" >
<a name="504">504</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> set. </td>
</tr>
<tr>
<td class="h" >
<a name="505">505</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Example : $index->start_report( \&my_start_report ) </td>
</tr>
<tr>
<td class="h" >
<a name="506">506</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns : ref to CODE if called without arguments </td>
</tr>
<tr>
<td class="h" >
<a name="507">507</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Args : CODE </td>
</tr>
<tr>
<td class="h" >
<a name="508">508</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="509">509</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =cut </td>
</tr>
<tr>
<td class="h" >
<a name="510">510</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="511">511</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub start_report { </td>
</tr>
<tr>
<td class="h" >
<a name="512">512</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#512-1">
1
</a>
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#512-1">
1
</a>
</td>
<td >
2
</td>
<td class="s"> my( $self, $code ) = @_; </td>
</tr>
<tr>
<td class="h" >
<a name="513">513</a>
</td>
<td class="c3" >
1
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#513-1">
50
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
3
</td>
<td class="s"> if ($code) { </td>
</tr>
<tr>
<td class="h" >
<a name="514">514</a>
</td>
<td class="c0" >
<a href="#554">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> $self->{'_start_report'} = $code; </td>
</tr>
<tr>
<td class="h" >
<a name="515">515</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="516">516</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--condition.html#516-1">
50
</a>
</td>
<td >
</td>
<td >
</td>
<td >
7
</td>
<td class="s"> return $self->{'_start_report'} || \&default_start_report; </td>
</tr>
<tr>
<td class="h" >
<a name="517">517</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="518">518</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="519">519</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =head2 default_start_report </td>
</tr>
<tr>
<td class="h" >
<a name="520">520</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="521">521</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Title : default_start_report </td>
</tr>
<tr>
<td class="h" >
<a name="522">522</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Usage : $self->default_start_report($result) </td>
</tr>
<tr>
<td class="h" >
<a name="523">523</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Function: The default method to call when starting a report. </td>
</tr>
<tr>
<td class="h" >
<a name="524">524</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns : sting </td>
</tr>
<tr>
<td class="h" >
<a name="525">525</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Args : First argument is a Bio::Search::Result::ResultI </td>
</tr>
<tr>
<td class="h" >
<a name="526">526</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="527">527</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =cut </td>
</tr>
<tr>
<td class="h" >
<a name="528">528</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="529">529</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub default_start_report { </td>
</tr>
<tr>
<td class="h" >
<a name="530">530</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#530-1">
1
</a>
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#530-1">
1
</a>
</td>
<td >
3
</td>
<td class="s"> my ($result) = @_; </td>
</tr>
<tr>
<td class="h" >
<a name="531">531</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
3
</td>
<td class="s"> return ""; </td>
</tr>
<tr>
<td class="h" >
<a name="532">532</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="533">533</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="534">534</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =head2 title </td>
</tr>
<tr>
<td class="h" >
<a name="535">535</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="536">536</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Title : title </td>
</tr>
<tr>
<td class="h" >
<a name="537">537</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Usage : $self->title($CODE) </td>
</tr>
<tr>
<td class="h" >
<a name="538">538</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="539">539</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Function: Stores or returns the code to provide HTML for the given </td>
</tr>
<tr>
<td class="h" >
<a name="540">540</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> BLAST report that will appear at the top of the BLAST report </td>
</tr>
<tr>
<td class="h" >
<a name="541">541</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> HTML output. Useful for (for instance) specifying </td>
</tr>
<tr>
<td class="h" >
<a name="542">542</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> alternative routines to write your own titles. </td>
</tr>
<tr>
<td class="h" >
<a name="543">543</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns \&default_title (see below) if not </td>
</tr>
<tr>
<td class="h" >
<a name="544">544</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> set. </td>
</tr>
<tr>
<td class="h" >
<a name="545">545</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Example : $index->title( \&my_title ) </td>
</tr>
<tr>
<td class="h" >
<a name="546">546</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns : ref to CODE if called without arguments </td>
</tr>
<tr>
<td class="h" >
<a name="547">547</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Args : CODE </td>
</tr>
<tr>
<td class="h" >
<a name="548">548</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="549">549</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =cut </td>
</tr>
<tr>
<td class="h" >
<a name="550">550</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="551">551</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub title { </td>
</tr>
<tr>
<td class="h" >
<a name="552">552</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#552-1">
1
</a>
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#552-1">
1
</a>
</td>
<td >
2
</td>
<td class="s"> my( $self, $code ) = @_; </td>
</tr>
<tr>
<td class="h" >
<a name="553">553</a>
</td>
<td class="c3" >
1
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#553-1">
50
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
3
</td>
<td class="s"> if ($code) { </td>
</tr>
<tr>
<td class="h" >
<a name="554">554</a>
</td>
<td class="c0" >
<a href="#602">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> $self->{'_title'} = $code; </td>
</tr>
<tr>
<td class="h" >
<a name="555">555</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="556">556</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--condition.html#556-1">
50
</a>
</td>
<td >
</td>
<td >
</td>
<td >
6
</td>
<td class="s"> return $self->{'_title'} || \&default_title; </td>
</tr>
<tr>
<td class="h" >
<a name="557">557</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="558">558</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="559">559</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =head2 default_title </td>
</tr>
<tr>
<td class="h" >
<a name="560">560</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="561">561</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Title : default_title </td>
</tr>
<tr>
<td class="h" >
<a name="562">562</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Usage : $self->default_title($result) </td>
</tr>
<tr>
<td class="h" >
<a name="563">563</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Function: Provides HTML for the given BLAST report that will appear </td>
</tr>
<tr>
<td class="h" >
<a name="564">564</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> at the top of the BLAST report output. </td>
</tr>
<tr>
<td class="h" >
<a name="565">565</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns : empty for text implementation </td>
</tr>
<tr>
<td class="h" >
<a name="566">566</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Args : First argument is a Bio::Search::Result::ResultI </td>
</tr>
<tr>
<td class="h" >
<a name="567">567</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="568">568</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =cut </td>
</tr>
<tr>
<td class="h" >
<a name="569">569</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="570">570</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub default_title { </td>
</tr>
<tr>
<td class="h" >
<a name="571">571</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#571-1">
1
</a>
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#571-1">
1
</a>
</td>
<td >
3
</td>
<td class="s"> my ($result) = @_; </td>
</tr>
<tr>
<td class="h" >
<a name="572">572</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
2
</td>
<td class="s"> return ""; </td>
</tr>
<tr>
<td class="h" >
<a name="573">573</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> # The HTML implementation </td>
</tr>
<tr>
<td class="h" >
<a name="574">574</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> # return sprintf( </td>
</tr>
<tr>
<td class="h" >
<a name="575">575</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> # qq{<CENTER><H1><a href="http://bioperl.org">Bioperl</a> Reformatted HTML of %s Search Report<br> for %s</H1></CENTER>}, </td>
</tr>
<tr>
<td class="h" >
<a name="576">576</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> # $result->algorithm, </td>
</tr>
<tr>
<td class="h" >
<a name="577">577</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> # $result->query_name()); </td>
</tr>
<tr>
<td class="h" >
<a name="578">578</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="579">579</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="580">580</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="581">581</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =head2 introduction </td>
</tr>
<tr>
<td class="h" >
<a name="582">582</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="583">583</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Title : introduction </td>
</tr>
<tr>
<td class="h" >
<a name="584">584</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Usage : $self->introduction($CODE) </td>
</tr>
<tr>
<td class="h" >
<a name="585">585</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="586">586</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Function: Stores or returns the code to provide HTML for the given </td>
</tr>
<tr>
<td class="h" >
<a name="587">587</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> BLAST report detailing the query and the </td>
</tr>
<tr>
<td class="h" >
<a name="588">588</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> database information. </td>
</tr>
<tr>
<td class="h" >
<a name="589">589</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Useful for (for instance) specifying </td>
</tr>
<tr>
<td class="h" >
<a name="590">590</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> routines returning alternative introductions. </td>
</tr>
<tr>
<td class="h" >
<a name="591">591</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns \&default_introduction (see below) if not </td>
</tr>
<tr>
<td class="h" >
<a name="592">592</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> set. </td>
</tr>
<tr>
<td class="h" >
<a name="593">593</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Example : $index->introduction( \&my_introduction ) </td>
</tr>
<tr>
<td class="h" >
<a name="594">594</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns : ref to CODE if called without arguments </td>
</tr>
<tr>
<td class="h" >
<a name="595">595</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Args : CODE </td>
</tr>
<tr>
<td class="h" >
<a name="596">596</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="597">597</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =cut </td>
</tr>
<tr>
<td class="h" >
<a name="598">598</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="599">599</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub introduction { </td>
</tr>
<tr>
<td class="h" >
<a name="600">600</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#600-1">
1
</a>
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#600-1">
1
</a>
</td>
<td >
2
</td>
<td class="s"> my( $self, $code ) = @_; </td>
</tr>
<tr>
<td class="h" >
<a name="601">601</a>
</td>
<td class="c3" >
1
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#601-1">
50
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
3
</td>
<td class="s"> if ($code) { </td>
</tr>
<tr>
<td class="h" >
<a name="602">602</a>
</td>
<td class="c0" >
<a href="#683">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> $self->{'_introduction'} = $code; </td>
</tr>
<tr>
<td class="h" >
<a name="603">603</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="604">604</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--condition.html#604-1">
50
</a>
</td>
<td >
</td>
<td >
</td>
<td >
7
</td>
<td class="s"> return $self->{'_introduction'} || \&default_introduction; </td>
</tr>
<tr>
<td class="h" >
<a name="605">605</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="606">606</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="607">607</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =head2 default_introduction </td>
</tr>
<tr>
<td class="h" >
<a name="608">608</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="609">609</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Title : default_introduction </td>
</tr>
<tr>
<td class="h" >
<a name="610">610</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Usage : $self->default_introduction($result) </td>
</tr>
<tr>
<td class="h" >
<a name="611">611</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Function: Outputs HTML to provide the query </td>
</tr>
<tr>
<td class="h" >
<a name="612">612</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> and the database information </td>
</tr>
<tr>
<td class="h" >
<a name="613">613</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns : string containing HTML </td>
</tr>
<tr>
<td class="h" >
<a name="614">614</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Args : First argument is a Bio::Search::Result::ResultI </td>
</tr>
<tr>
<td class="h" >
<a name="615">615</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Second argument is string holding literature citation </td>
</tr>
<tr>
<td class="h" >
<a name="616">616</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="617">617</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =cut </td>
</tr>
<tr>
<td class="h" >
<a name="618">618</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="619">619</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub default_introduction { </td>
</tr>
<tr>
<td class="h" >
<a name="620">620</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#620-1">
1
</a>
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#620-1">
1
</a>
</td>
<td >
5
</td>
<td class="s"> my ($result) = @_; </td>
</tr>
<tr>
<td class="h" >
<a name="621">621</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="622">622</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
5
</td>
<td class="s"> return sprintf( </td>
</tr>
<tr>
<td class="h" >
<a name="623">623</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> qq{ </td>
</tr>
<tr>
<td class="h" >
<a name="624">624</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Query= %s </td>
</tr>
<tr>
<td class="h" >
<a name="625">625</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> (%s letters) </td>
</tr>
<tr>
<td class="h" >
<a name="626">626</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="627">627</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Database: %s </td>
</tr>
<tr>
<td class="h" >
<a name="628">628</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> %s sequences; %s total letters </td>
</tr>
<tr>
<td class="h" >
<a name="629">629</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> }, </td>
</tr>
<tr>
<td class="h" >
<a name="630">630</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> &_linewrap($result->query_name . " " . </td>
</tr>
<tr>
<td class="h" >
<a name="631">631</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> $result->query_description), </td>
</tr>
<tr>
<td class="h" >
<a name="632">632</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> &_numwithcommas($result->query_length), </td>
</tr>
<tr>
<td class="h" >
<a name="633">633</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> $result->database_name(), </td>
</tr>
<tr>
<td class="h" >
<a name="634">634</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> &_numwithcommas($result->database_entries()), </td>
</tr>
<tr>
<td class="h" >
<a name="635">635</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> &_numwithcommas($result->database_letters()), </td>
</tr>
<tr>
<td class="h" >
<a name="636">636</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> ); </td>
</tr>
<tr>
<td class="h" >
<a name="637">637</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="638">638</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="639">639</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =head2 end_report </td>
</tr>
<tr>
<td class="h" >
<a name="640">640</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="641">641</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Title : end_report </td>
</tr>
<tr>
<td class="h" >
<a name="642">642</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Usage : $self->end_report() </td>
</tr>
<tr>
<td class="h" >
<a name="643">643</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Function: The method to call when ending a report, this is </td>
</tr>
<tr>
<td class="h" >
<a name="644">644</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> mostly for cleanup for formats which require you to </td>
</tr>
<tr>
<td class="h" >
<a name="645">645</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> have something at the end of the document (</BODY></HTML>) </td>
</tr>
<tr>
<td class="h" >
<a name="646">646</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> for HTML </td>
</tr>
<tr>
<td class="h" >
<a name="647">647</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns : string </td>
</tr>
<tr>
<td class="h" >
<a name="648">648</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Args : none </td>
</tr>
<tr>
<td class="h" >
<a name="649">649</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="650">650</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =cut </td>
</tr>
<tr>
<td class="h" >
<a name="651">651</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="652">652</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub end_report { </td>
</tr>
<tr>
<td class="h" >
<a name="653">653</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#653-1">
1
</a>
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#653-1">
1
</a>
</td>
<td >
3
</td>
<td class="s"> return ""; </td>
</tr>
<tr>
<td class="h" >
<a name="654">654</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="655">655</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="656">656</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="657">657</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> # copied from Bio::Index::Fasta </td>
</tr>
<tr>
<td class="h" >
<a name="658">658</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> # useful here as well </td>
</tr>
<tr>
<td class="h" >
<a name="659">659</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="660">660</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =head2 id_parser </td>
</tr>
<tr>
<td class="h" >
<a name="661">661</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="662">662</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Title : id_parser </td>
</tr>
<tr>
<td class="h" >
<a name="663">663</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Usage : $index->id_parser( CODE ) </td>
</tr>
<tr>
<td class="h" >
<a name="664">664</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Function: Stores or returns the code used by record_id to </td>
</tr>
<tr>
<td class="h" >
<a name="665">665</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> parse the ID for record from a string. Useful </td>
</tr>
<tr>
<td class="h" >
<a name="666">666</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> for (for instance) specifying a different </td>
</tr>
<tr>
<td class="h" >
<a name="667">667</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> parser for different flavours of FASTA file. </td>
</tr>
<tr>
<td class="h" >
<a name="668">668</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns \&default_id_parser (see below) if not </td>
</tr>
<tr>
<td class="h" >
<a name="669">669</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> set. If you supply your own id_parser </td>
</tr>
<tr>
<td class="h" >
<a name="670">670</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> subroutine, then it should expect a fasta </td>
</tr>
<tr>
<td class="h" >
<a name="671">671</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> description line. An entry will be added to </td>
</tr>
<tr>
<td class="h" >
<a name="672">672</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> the index for each string in the list returned. </td>
</tr>
<tr>
<td class="h" >
<a name="673">673</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Example : $index->id_parser( \&my_id_parser ) </td>
</tr>
<tr>
<td class="h" >
<a name="674">674</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns : ref to CODE if called without arguments </td>
</tr>
<tr>
<td class="h" >
<a name="675">675</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Args : CODE </td>
</tr>
<tr>
<td class="h" >
<a name="676">676</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="677">677</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =cut </td>
</tr>
<tr>
<td class="h" >
<a name="678">678</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="679">679</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub id_parser { </td>
</tr>
<tr>
<td class="h" >
<a name="680">680</a>
</td>
<td class="c3" >
20
</td>
<td >
</td>
<td >
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#680-1">
20
</a>
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#680-1">
1
</a>
</td>
<td >
32
</td>
<td class="s"> my( $self, $code ) = @_; </td>
</tr>
<tr>
<td class="h" >
<a name="681">681</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="682">682</a>
</td>
<td class="c3" >
20
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#682-1">
50
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
32
</td>
<td class="s"> if ($code) { </td>
</tr>
<tr>
<td class="h" >
<a name="683">683</a>
</td>
<td class="c0" >
<a href="#706">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> $self->{'_id_parser'} = $code; </td>
</tr>
<tr>
<td class="h" >
<a name="684">684</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="685">685</a>
</td>
<td class="c3" >
20
</td>
<td >
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--condition.html#685-1">
50
</a>
</td>
<td >
</td>
<td >
</td>
<td >
80
</td>
<td class="s"> return $self->{'_id_parser'} || \&default_id_parser; </td>
</tr>
<tr>
<td class="h" >
<a name="686">686</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="687">687</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="688">688</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="689">689</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="690">690</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =head2 default_id_parser </td>
</tr>
<tr>
<td class="h" >
<a name="691">691</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="692">692</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Title : default_id_parser </td>
</tr>
<tr>
<td class="h" >
<a name="693">693</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Usage : $id = default_id_parser( $header ) </td>
</tr>
<tr>
<td class="h" >
<a name="694">694</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Function: The default Fasta ID parser for Fasta.pm </td>
</tr>
<tr>
<td class="h" >
<a name="695">695</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns $1 from applying the regexp /^>\s*(\S+)/ </td>
</tr>
<tr>
<td class="h" >
<a name="696">696</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> to $header. </td>
</tr>
<tr>
<td class="h" >
<a name="697">697</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns : ID string </td>
</tr>
<tr>
<td class="h" >
<a name="698">698</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Args : a fasta header line string </td>
</tr>
<tr>
<td class="h" >
<a name="699">699</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="700">700</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =cut </td>
</tr>
<tr>
<td class="h" >
<a name="701">701</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="702">702</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub default_id_parser { </td>
</tr>
<tr>
<td class="h" >
<a name="703">703</a>
</td>
<td class="c3" >
20
</td>
<td >
</td>
<td >
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#703-1">
20
</a>
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#703-1">
1
</a>
</td>
<td >
30
</td>
<td class="s"> my ($string) = @_; </td>
</tr>
<tr>
<td class="h" >
<a name="704">704</a>
</td>
<td class="c3" >
20
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
25
</td>
<td class="s"> my ($gi,$acc); </td>
</tr>
<tr>
<td class="h" >
<a name="705">705</a>
</td>
<td class="c3" >
20
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#705-1">
50
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
62
</td>
<td class="s"> if( $string =~ s/gi\|(\d+)\|?// ) </td>
</tr>
<tr>
<td class="h" >
<a name="706">706</a>
</td>
<td class="c0" >
<a href="# ">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> { $gi = $1; $acc = $1;} </td>
</tr>
<tr>
<td class="h" >
<a > </a>
</td>
<td class="c0" >
<a href="#711">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="707">707</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="708">708</a>
</td>
<td class="c3" >
20
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#708-1">
50
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
118
</td>
<td class="s"> if( $string =~ /(\w+)\|([A-Z\d\.\_]+)(\|[A-Z\d\_]+)?/ ) { </td>
</tr>
<tr>
<td class="h" >
<a name="709">709</a>
</td>
<td class="c3" >
20
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#709-1">
50
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
75
</td>
<td class="s"> $acc = defined $2 ? $2 : $1; </td>
</tr>
<tr>
<td class="h" >
<a name="710">710</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } else { </td>
</tr>
<tr>
<td class="h" >
<a name="711">711</a>
</td>
<td class="c0" >
<a href="#712">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> $acc = $string; </td>
</tr>
<tr>
<td class="h" >
<a name="712">712</a>
</td>
<td class="c0" >
<a href="#713">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> $acc =~ s/^\s+(\S+)/$1/; </td>
</tr>
<tr>
<td class="h" >
<a name="713">713</a>
</td>
<td class="c0" >
<a href="#718">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> $acc =~ s/(\S+)\s+$/$1/; </td>
</tr>
<tr>
<td class="h" >
<a name="714">714</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="715">715</a>
</td>
<td class="c3" >
20
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
48
</td>
<td class="s"> return ($gi,$acc); </td>
</tr>
<tr>
<td class="h" >
<a name="716">716</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="717">717</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="718">718</a>
</td>
<td class="c0" >
<a href="#719">
0
</a>
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#718-1">
0
</a>
</td>
<td >
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#718-1">
0
</a>
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#718-1">
0
</a>
</td>
<td >
0
</td>
<td class="s"> sub MIN { $a <=> $b ? $a : $b; } </td>
</tr>
<tr>
<td class="h" >
<a name="719">719</a>
</td>
<td class="c0" >
<a href="#735">
0
</a>
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#719-1">
0
</a>
</td>
<td >
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#719-1">
0
</a>
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#719-1">
0
</a>
</td>
<td >
0
</td>
<td class="s"> sub MAX { $a <=> $b ? $b : $a; } </td>
</tr>
<tr>
<td class="h" >
<a name="720">720</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="721">721</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="722">722</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =head2 algorithm_reference </td>
</tr>
<tr>
<td class="h" >
<a name="723">723</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="724">724</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Title : algorithm_reference </td>
</tr>
<tr>
<td class="h" >
<a name="725">725</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Usage : my $reference = $writer->algorithm_reference($result); </td>
</tr>
<tr>
<td class="h" >
<a name="726">726</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Function: Returns the appropriate Bibliographic reference for the </td>
</tr>
<tr>
<td class="h" >
<a name="727">727</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> algorithm format being produced </td>
</tr>
<tr>
<td class="h" >
<a name="728">728</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns : String </td>
</tr>
<tr>
<td class="h" >
<a name="729">729</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Args : L<Bio::Search::Result::ResultI> to reference </td>
</tr>
<tr>
<td class="h" >
<a name="730">730</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="731">731</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="732">732</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =cut </td>
</tr>
<tr>
<td class="h" >
<a name="733">733</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="734">734</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub algorithm_reference{ </td>
</tr>
<tr>
<td class="h" >
<a name="735">735</a>
</td>
<td class="c0" >
<a href="#736">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#735-1">
0
</a>
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#735-1">
1
</a>
</td>
<td >
0
</td>
<td class="s"> my ($self,$result) = @_; </td>
</tr>
<tr>
<td class="h" >
<a name="736">736</a>
</td>
<td class="c0" >
<a href="#738">
0
</a>
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#736-1">
0
</a>
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--condition.html#736-1">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> return '' if( ! defined $result || !ref($result) || </td>
</tr>
<tr>
<td class="h" >
<a > </a>
</td>
<td >
</td>
<td >
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--condition.html#-2">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="737">737</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> ! $result->isa('Bio::Search::Result::ResultI')) ; </td>
</tr>
<tr>
<td class="h" >
<a name="738">738</a>
</td>
<td class="c0" >
<a href="#739">
0
</a>
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#738-1">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> if( $result->algorithm =~ /BLAST/i ) { </td>
</tr>
<tr>
<td class="h" >
<a > </a>
</td>
<td >
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#-2">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="739">739</a>
</td>
<td class="c0" >
<a href="#740">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> my $res = $result->algorithm . ' '. $result->algorithm_version. "\n"; </td>
</tr>
<tr>
<td class="h" >
<a name="740">740</a>
</td>
<td class="c0" >
<a href="#741">
0
</a>
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#740-1">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> if( $result->algorithm_version =~ /WashU/i ) { </td>
</tr>
<tr>
<td class="h" >
<a name="741">741</a>
</td>
<td class="c0" >
<a href="#748">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> return $res .qq{ </td>
</tr>
<tr>
<td class="h" >
<a name="742">742</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA. </td>
</tr>
<tr>
<td class="h" >
<a name="743">743</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> All Rights Reserved. </td>
</tr>
<tr>
<td class="h" >
<a name="744">744</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="745">745</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Reference: Gish, W. (1996-2000) http://blast.wustl.edu </td>
</tr>
<tr>
<td class="h" >
<a name="746">746</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> }; </td>
</tr>
<tr>
<td class="h" >
<a name="747">747</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } else { </td>
</tr>
<tr>
<td class="h" >
<a name="748">748</a>
</td>
<td class="c0" >
<a href="#756">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> return $res . qq{ </td>
</tr>
<tr>
<td class="h" >
<a name="749">749</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, </td>
</tr>
<tr>
<td class="h" >
<a name="750">750</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), </td>
</tr>
<tr>
<td class="h" >
<a name="751">751</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> "Gapped BLAST and PSI-BLAST: a new generation of protein database search </td>
</tr>
<tr>
<td class="h" >
<a name="752">752</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> programs", Nucleic Acids Res. 25:3389-3402. </td>
</tr>
<tr>
<td class="h" >
<a name="753">753</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> }; </td>
</tr>
<tr>
<td class="h" >
<a name="754">754</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="755">755</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } elsif( $result->algorithm =~ /FAST/i ) { </td>
</tr>
<tr>
<td class="h" >
<a name="756">756</a>
</td>
<td class="c0" >
<a href="#759">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> return $result->algorithm. " ". $result->algorithm_version . "\n". </td>
</tr>
<tr>
<td class="h" >
<a name="757">757</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> "\nReference: Pearson et al, Genomics (1997) 46:24-36\n"; </td>
</tr>
<tr>
<td class="h" >
<a name="758">758</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } else { </td>
</tr>
<tr>
<td class="h" >
<a name="759">759</a>
</td>
<td class="c0" >
<a href="#774">
0
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> return ''; </td>
</tr>
<tr>
<td class="h" >
<a name="760">760</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="761">761</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="762">762</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="763">763</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> # from Perl Cookbook 2.17 </td>
</tr>
<tr>
<td class="h" >
<a name="764">764</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub _numwithcommas { </td>
</tr>
<tr>
<td class="h" >
<a name="765">765</a>
</td>
<td class="c3" >
23
</td>
<td >
</td>
<td >
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#765-1">
23
</a>
</td>
<td >
</td>
<td >
32
</td>
<td class="s"> my $num = reverse( $_[0] ); </td>
</tr>
<tr>
<td class="h" >
<a name="766">766</a>
</td>
<td class="c3" >
23
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
81
</td>
<td class="s"> $num =~ s/(\d{3})(?=\d)(?!\d*\.)/$1,/g; </td>
</tr>
<tr>
<td class="h" >
<a name="767">767</a>
</td>
<td class="c3" >
23
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
70
</td>
<td class="s"> return scalar reverse $num; </td>
</tr>
<tr>
<td class="h" >
<a name="768">768</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="769">769</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="770">770</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub _linewrap { </td>
</tr>
<tr>
<td class="h" >
<a name="771">771</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#771-1">
1
</a>
</td>
<td >
</td>
<td >
3
</td>
<td class="s"> my ($str) = @_; </td>
</tr>
<tr>
<td class="h" >
<a name="772">772</a>
</td>
<td class="c3" >
1
</td>
<td class="c0" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#772-1">
50
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
5
</td>
<td class="s"> if($TextWrapLoaded) { </td>
</tr>
<tr>
<td class="h" >
<a name="773">773</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
8
</td>
<td class="s"> return Text::Wrap::wrap("","",$str); # use Text::Wrap </td>
</tr>
<tr>
<td class="h" >
<a name="774">774</a>
</td>
<td class="c0" >
0
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
0
</td>
<td class="s"> } else { return $str; } # cannot wrap </td>
</tr>
<tr>
<td class="h" >
<a name="775">775</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="776">776</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =head2 Methods Bio::SearchIO::SearchWriterI </td>
</tr>
<tr>
<td class="h" >
<a name="777">777</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="778">778</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> L<Bio::SearchIO::SearchWriterI> inherited methods. </td>
</tr>
<tr>
<td class="h" >
<a name="779">779</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="780">780</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =head2 filter </td>
</tr>
<tr>
<td class="h" >
<a name="781">781</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="782">782</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Title : filter </td>
</tr>
<tr>
<td class="h" >
<a name="783">783</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Usage : $writer->filter('hsp', \&hsp_filter); </td>
</tr>
<tr>
<td class="h" >
<a name="784">784</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Function: Filter out either at HSP,Hit,or Result level </td>
</tr>
<tr>
<td class="h" >
<a name="785">785</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns : none </td>
</tr>
<tr>
<td class="h" >
<a name="786">786</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Args : string => data type, </td>
</tr>
<tr>
<td class="h" >
<a name="787">787</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> CODE reference </td>
</tr>
<tr>
<td class="h" >
<a name="788">788</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="789">789</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="790">790</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =cut </td>
</tr>
<tr>
<td class="h" >
<a name="791">791</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="792">792</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =head2 no_wublastlinks </td>
</tr>
<tr>
<td class="h" >
<a name="793">793</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="794">794</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Title : no_wublastlinks </td>
</tr>
<tr>
<td class="h" >
<a name="795">795</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Usage : $obj->no_wublastlinks($newval) </td>
</tr>
<tr>
<td class="h" >
<a name="796">796</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Function: Get/Set boolean value regarding whether or not to display </td>
</tr>
<tr>
<td class="h" >
<a name="797">797</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Link = (1) </td>
</tr>
<tr>
<td class="h" >
<a name="798">798</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> type output in the report output (WU-BLAST only) </td>
</tr>
<tr>
<td class="h" >
<a name="799">799</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Returns : boolean </td>
</tr>
<tr>
<td class="h" >
<a name="800">800</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> Args : on set, new boolean value (a scalar or undef, optional) </td>
</tr>
<tr>
<td class="h" >
<a name="801">801</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="802">802</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="803">803</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> =cut </td>
</tr>
<tr>
<td class="h" >
<a name="804">804</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="805">805</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> sub no_wublastlinks{ </td>
</tr>
<tr>
<td class="h" >
<a name="806">806</a>
</td>
<td class="c3" >
2
</td>
<td >
</td>
<td >
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#806-1">
2
</a>
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--subroutine.html#806-1">
1
</a>
</td>
<td >
3
</td>
<td class="s"> my $self = shift; </td>
</tr>
<tr>
<td class="h" >
<a name="807">807</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="808">808</a>
</td>
<td class="c3" >
2
</td>
<td class="c3" >
<a href="Bio-SearchIO-Writer-TextResultWriter-pm--branch.html#808-1">
100
</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
11
</td>
<td class="s"> return $self->{'no_wublastlinks'} = shift if @_; </td>
</tr>
<tr>
<td class="h" >
<a name="809">809</a>
</td>
<td class="c3" >
1
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
3
</td>
<td class="s"> return $self->{'no_wublastlinks'}; </td>
</tr>
<tr>
<td class="h" >
<a name="810">810</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> } </td>
</tr>
<tr>
<td class="h" >
<a name="811">811</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="812">812</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> </td>
</tr>
<tr>
<td class="h" >
<a name="813">813</a>
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td >
</td>
<td class="s"> 1; </td>
</tr>
</table>
</body>
</html>
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