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revision 1.52, Mon Dec 12 21:48:57 2005 UTC revision 1.55, Mon Apr 3 18:33:58 2006 UTC
# Line 92  Line 92 
92                                                          # database type                                                          # database type
93                         dataDir      => $FIG_Config::sproutData,                         dataDir      => $FIG_Config::sproutData,
94                                                          # data file directory                                                          # data file directory
95                         xmlFileName  => "$FIG_Config::sproutData/SproutDBD.xml",                         xmlFileName  => "$FIG_Config::fig/SproutDBD.xml",
96                                                          # database definition file name                                                          # database definition file name
97                         userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",                         userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",
98                                                          # user name and password                                                          # user name and password
# Line 740  Line 740 
740  should be of the form returned by L</featureLocation> when in a list context. In other words,  should be of the form returned by L</featureLocation> when in a list context. In other words,
741  each location is of the form I<contigID>C<_>I<begin>I<dir>I<end>.  each location is of the form I<contigID>C<_>I<begin>I<dir>I<end>.
742    
743    For example, the following would return the DNA sequence for contig C<83333.1:NC_000913>
744    between positions 1401 and 1532, inclusive.
745    
746        my $sequence = $sprout->DNASeq('83333.1:NC_000913_1401_1532');
747    
748  =over 4  =over 4
749    
750  =item locationList  =item locationList
751    
752  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<end> (see  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<len> or
753  L</FeatureLocation> for more about this format).  I<contigID>C<_>I<begin>C<_>I<end> (see L</FeatureLocation> for more about this format).
754    
755  =item RETURN  =item RETURN
756    
# Line 3221  Line 3226 
3226      return $retVal;      return $retVal;
3227  }  }
3228    
3229    =head3 DeleteGenome
3230    
3231    C<< my $stats = $sprout->DeleteGenome($genomeID, $testFlag); >>
3232    
3233    Delete a genome from the database.
3234    
3235    =over 4
3236    
3237    =item genomeID
3238    
3239    ID of the genome to delete
3240    
3241    =item testFlag
3242    
3243    If TRUE, then the DELETE statements will be traced, but no deletions will occur.
3244    
3245    =item RETURN
3246    
3247    Returns a statistics object describing the rows deleted.
3248    
3249    =back
3250    
3251    =cut
3252    #: Return Type $%;
3253    sub DeleteGenome {
3254        # Get the parameters.
3255        my ($self, $genomeID, $testFlag) = @_;
3256        # Perform the delete for the genome's features.
3257        my $retVal = $self->{_erdb}->Delete('Feature', "fig|$genomeID.%", $testFlag);
3258        # Perform the delete for the primary genome data.
3259        my $stats = $self->{_erdb}->Delete('Genome', $genomeID, $testFlag);
3260        $retVal->Accumulate($stats);
3261        # Return the result.
3262        return $retVal;
3263    }
3264    
3265  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3266    
3267  =head3 ParseAssignment  =head3 ParseAssignment

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