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Viewing changes to Bio/DB/GFF/Adaptor/dbi/pg_fts.pm

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
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package Bio::DB::GFF::Adaptor::dbi::pg_fts;
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# $Id: pg_fts.pm,v 1.2.4.1 2006/10/02 23:10:16 sendu Exp $
 
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# $Id: pg_fts.pm 11724 2007-10-16 19:28:22Z lstein $
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=head1 NAME
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use base qw(Bio::DB::GFF::Adaptor::dbi::pg);
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use constant FULLTEXTSEARCH => <<END;
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SELECT distinct gclass,gname,fattribute_value
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    FROM fgroup,fattribute_to_feature,fdata
 
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SELECT distinct gclass,gname,fattribute_value,fmethod,fsource
 
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    FROM fgroup,fattribute_to_feature,fdata,ftype
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     WHERE fgroup.gid=fdata.gid
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       AND fdata.fid=fattribute_to_feature.fid
 
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       AND fdata.ftypeid=ftype.ftypeid
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       AND (fattribute_to_feature.idxfti @@ to_tsquery('default', ?))
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END
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;
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use constant FULLTEXTWILDCARD => <<END;
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SELECT distinct gclass,gname,fattribute_value
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    FROM fgroup,fattribute_to_feature,fdata
 
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SELECT distinct gclass,gname,fattribute_value,fmethod,fsource
 
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    FROM fgroup,fattribute_to_feature,fdata,ftype
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     WHERE fgroup.gid=fdata.gid
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       AND fdata.fid=fattribute_to_feature.fid
 
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       AND fdata.ftypeid=ftype.ftypeid
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       AND lower(fattribute_to_feature.fattribute_value) LIKE lower(?)
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END
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;
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  } 
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  my @results;
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  while (my ($class,$name,$note) = $sth->fetchrow_array) {
 
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  while (my ($class,$name,$note,$method,$source) = $sth->fetchrow_array) {
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     next unless $class && $name;    # sorry, ignore NULL objects
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     my $featname = Bio::DB::GFF::Featname->new($class=>$name);
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     push @results,[$featname,$note,0]; #gbrowse expects a score, but
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                                        #pg doesn't give one, thus the 0
 
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     my $type     = Bio::DB::GFF::Typename->new($method,$source);
 
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     push @results,[$featname,$note,0,$type]; #gbrowse expects a score, but
 
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                                              #pg doesn't give one, thus the 0
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  }
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  return @results;