lib/CXGN/BioTools/SearchIOHTMLWriter.pm

   1 package CXGN::BioTools::SearchIOHTMLWriter;
   2 use strict;
   3 use warnings;
   4
   5 use CXGN::Tools::Identifiers;
   6 use CXGN::BlastDB;
   7
   8 use base qw/Bio::SearchIO::Writer::HTMLResultWriter/;
   9
  10 sub new {
  11   my ($class,$db_id, @args) = @_;
  12   my $self = $class->SUPER::new(@args);
  13
  14
  15
  16   $self->id_parser( sub {
  17                         my ($idline) = @_;
  18                         my ($ident,$acc) = Bio::SearchIO::Writer::HTMLResultWriter::default_id_parser($idline);
  19                         #The default implementation checks for NCBI-style identifiers in the given string ('gi|12345|AA54321').
  20                         #For these IDs, it extracts the GI and accession and
  21                         #returns a two-element list of strings (GI, acc).
  22
  23                         return ($ident,$acc) if $acc;
  24                         return CXGN::Tools::Identifiers::clean_identifier($ident) || $ident;
  25                       });
  26   my $hit_link = sub {
  27     my ($self, $hit, $result) = @_;
  28     #see if we can link it as a CXGN identifier.  Otherwise,
  29     #use the default bioperl link generator
  30     my $url = CXGN::Tools::Identifiers::link_identifier($hit->name())
  31         || $self->default_hit_link_desc($hit,$result,$db_id);
  32
  33     return $url;
  34   };
  35   $self->hit_link_desc($hit_link);
  36   $self->hit_link_align($hit_link);
  37   $self->start_report(sub {''});
  38   return $self;
  39 }
  40
  41 sub end_report {
  42   return '';
  43 }
  44
  45
  46 sub default_hit_link_desc {
  47     my $self = shift;
  48     my $hit = shift;
  49     my $result = shift;
  50     my $db_id = shift;
  51
  52     my $coords_string =
  53         "hilite_coords="
  54        .join ',',
  55         map $_->start('subject').'-'.$_->end('subject'),
  56         $hit->hsps;
  57
  58     my $id = $hit->name();
  59     return qq{<a href="show_match_seq.pl?blast_db_id=$db_id&amp;id=$id&amp;$coords_string">$id</a>};
  60 }
  61
  62 ###
  63 1;#do not remove
  64 ###
  65
  66