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revision 1.5, Fri Jan 13 07:00:28 2006 UTC revision 1.7, Mon Feb 13 15:42:48 2006 UTC
# Line 213  Line 213 
213      my ($class, $dbname, $dbType, $port) = @_;      my ($class, $dbname, $dbType, $port) = @_;
214      # Plug in the default values.      # Plug in the default values.
215      if (! $dbname) {      if (! $dbname) {
216          $dbname = $FIG_Config::simBlocksDB;          $dbname = DBName();
217      }      }
218      if (! $dbType) {      if (! $dbType) {
219          $dbType = $FIG_Config::dbms;          $dbType = $FIG_Config::dbms;
# Line 231  Line 231 
231      return $retVal;      return $retVal;
232  }  }
233    
234    =head3 DBName
235    
236    C<< my $name = SimBlocks::DBName; >>
237    
238    Return the name of the database. This is set from a config variable, but if the
239    variable is undefined a default value is used.
240    
241    =cut
242    
243    sub DBName {
244        my $retVal;
245        if (defined $FIG_Config::simBlocksDB) {
246            $retVal = $FIG_Config::simBlocksDB;
247        } else {
248            $retVal = "Blocks";
249        }
250        return $retVal;
251    }
252    
253  =head3 DefaultDistances  =head3 DefaultDistances
254    
255  C<< my $distances = DefaultDistances(); >>  C<< my $distances = DefaultDistances(); >>
# Line 1183  Line 1202 
1202      Trace("Searching for regions near " . $loc->String) if T(4);      Trace("Searching for regions near " . $loc->String) if T(4);
1203      # Ask for the regions in the section we want.      # Ask for the regions in the section we want.
1204      my @regions = $self->GetAll(['Region', 'IncludesRegion', 'GroupBlock'],      my @regions = $self->GetAll(['Region', 'IncludesRegion', 'GroupBlock'],
1205                                  'Region(end) >= ? AND Region(position) <= ? AND Region(contigID) = ?',                                  'Region(endpoint) >= ? AND Region(position) <= ? AND Region(contigID) = ?',
1206                                  [$left, $right, $contigID],                                  [$left, $right, $contigID],
1207                                  ['GroupBlock(id)', 'GroupBlock(pattern)',                                  ['GroupBlock(id)', 'GroupBlock(pattern)',
1208                                   'GroupBlock(len)',                                   'GroupBlock(len)',
1209                                   'Region(position)', 'Region(end)',                                   'Region(position)', 'Region(endpoint)',
1210                                   'Region(content)']);                                   'Region(content)']);
1211      # Loop through the regions found. For each region we will output a location string.      # Loop through the regions found. For each region we will output a location string.
1212      for my $regionData (@regions) {      for my $regionData (@regions) {

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