Show CDNApgs.pm syntax highlighted
package CDNApgs;
use base "SequenceTrack";
use base "GeneSeqerSequence";
do 'SITEDEF.pl';
sub _init{
my $self = shift;
$self->SUPER::_init(@_);
$self->{sequenceTYPE} = 'cDNA';
$self->{gsqATYPE} = 'C';
$self->{db_table} = (exists($self->{db_table})) ? $self->{db_table} : 'cdna';
$self->{trackname} = (exists($self->{trackname}))? $self->{trackname}: 'cDNA';
my $DB_TABLE = $self->{db_table};
my $DISPLAY_LIMITS = (exists($self->{QUERYLIMIT}))? $self->{QUERYLIMIT} : '';
$self->{SQL_BASE} = qq{SELECT c.gi,c.description,p.uid,p.gseg_uid,p.E_O,p.sim,p.cov,p.G_O,p.chr,p.l_pos,p.r_pos,p.pgs,p.isCognate,c.acc,c.seq,c.version,p.mlength,p.pgs_lpos,p.pgs_rpos,p.gseg_gaps,p.pgs_gaps FROM ${DB_TABLE}_good_pgs as p INNER JOIN ${DB_TABLE} as c USING (gi) };
$self->{gsegSQL_BASE} = qq{SELECT c.gi,c.description,gp.uid,gp.E_O,gp.sim,gp.cov,gp.gseg_gi,gp.G_O,gp.l_pos,gp.r_pos,gp.pgs,gp.isCognate,gp.mergeNOTE,c.acc,c.seq,c.version,gp.mlength,gp.pgs_lpos,gp.pgs_rpos,gp.gseg_gaps,gp.pgs_gaps FROM gseg_${DB_TABLE}_good_pgs as gp INNER JOIN ${DB_TABLE} as c USING (gi) };
$self->{gsqPGS_QUERY} = qq{$self->{SQL_BASE} WHERE (p.uid=?) };
$self->{gsqPGS_EX_QUERY} = qq{SELECT num,gseg_start,gseg_stop,pgs_start,pgs_stop,score,pgs_uid FROM ${DB_TABLE}_good_pgs_exons WHERE (pgs_uid=?) };
$self->{gsqPGS_IN_QUERY} = qq{SELECT num,gseg_start,gseg_stop,Dscore,Dsim,Ascore,Asim,pgs_uid FROM ${DB_TABLE}_good_pgs_introns WHERE (pgs_uid=?) };
$self->{gseggsqPGS_QUERY} = qq{$self->{gsegSQL_BASE} WHERE (gp.uid=?) };
$self->{gseggsqPGS_EX_QUERY} = qq{SELECT num,gseg_start,gseg_stop,pgs_start,pgs_stop,score,pgs_uid FROM gseg_${DB_TABLE}_good_pgs_exons WHERE (pgs_uid=?) };
$self->{gseggsqPGS_IN_QUERY} = qq{SELECT num,gseg_start,gseg_stop,Dscore,Dsim,Ascore,Asim,pgs_uid FROM gseg_${DB_TABLE}_good_pgs_introns WHERE (pgs_uid=?) };
$self->{chrREGION_QUERY} = qq{$self->{SQL_BASE} WHERE (p.chr=?)&&(p.r_pos>=?)&&(p.l_pos<=?) ${DISPLAY_LIMITS} };
$self->{gsegREGION_QUERY} = qq{$self->{gsegSQL_BASE} WHERE (gp.gseg_gi=?)&&(gp.r_pos>=?)&&(gp.l_pos<=?) ${DISPLAY_LIMITS} };
$self->{chrDESC_QUERY} = qq{$self->{SQL_BASE} WHERE MATCH (description) AGAINST ( ? IN BOOLEAN MODE) };
$self->{gsegDESC_QUERY} = qq{$self->{gsegSQL_BASE} WHERE MATCH (description) AGAINST ( ? IN BOOLEAN MODE) };
$self->{chrUID_QUERY} = qq{SELECT p.gi FROM ${DB_TABLE}_good_pgs as p WHERE (p.uid=?) };
$self->{gsegUID_QUERY} = qq{SELECT gp.gi FROM gseg_${DB_TABLE}_good_pgs as gp WHERE (gp.uid=?) };
$self->{seqQUERY} = qq{SELECT c.gi,c.acc,c.version,c.description,c.seq FROM ${DB_TABLE} as c WHERE (?) IN (c.gi,c.acc) };
$self->{chrQUERY} = qq{SELECT p.uid,p.gseg_uid,p.E_O,p.sim,p.cov,p.G_O,p.chr,p.l_pos,p.r_pos,p.pgs,p.isCognate,p.gi FROM ${DB_TABLE}_good_pgs as p WHERE (p.gi=?) };
$self->{gsegQUERY} = qq{SELECT gp.uid,gp.E_O,gp.sim,gp.cov,gp.gseg_gi,gp.G_O,gp.l_pos,gp.r_pos,gp.pgs,gp.isCognate,gp.mergeNOTE,gp.gi FROM gseg_${DB_TABLE}_good_pgs as gp WHERE (gp.gi=?) };
$self->{MULTI_ID_QUERY} = sub {
my ($BASE,$idlist) = @_;
return $BASE . "WHERE (c.gi IN ($idlist))||(acc IN ($idlist))||(clone IN ($idlist))";
};
}
1;
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