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revision 1.25, Sun Sep 11 17:29:52 2005 UTC revision 1.31, Wed Sep 14 13:14:12 2005 UTC
# Line 765  Line 765 
765          # the start point is the ending. Note that in the latter case we must reverse the DNA string          # the start point is the ending. Note that in the latter case we must reverse the DNA string
766          # before putting it in the return value.          # before putting it in the return value.
767          my ($start, $stop);          my ($start, $stop);
768            Trace("Parsed location is $beg$dir$len.") if T(SDNA => 4);
769          if ($dir eq "+") {          if ($dir eq "+") {
770              $start = $beg;              $start = $beg;
771              $stop = $beg + $len - 1;              $stop = $beg + $len - 1;
772          } else {          } else {
773              $start = $beg + $len + 1;              $start = $beg - $len + 1;
774              $stop = $beg;              $stop = $beg;
775          }          }
776            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
777          my $query = $self->Get(['IsMadeUpOf','Sequence'],          my $query = $self->Get(['IsMadeUpOf','Sequence'],
778              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
779              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 783  Line 785 
785                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
786                                     'IsMadeUpOf(len)']);                                     'IsMadeUpOf(len)']);
787              my $stopPosition = $startPosition + $sequenceLength;              my $stopPosition = $startPosition + $sequenceLength;
788                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
789              # Figure out the start point and length of the relevant section.              # Figure out the start point and length of the relevant section.
790              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
791              my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;
792                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
793              # Add the relevant data to the location data.              # Add the relevant data to the location data.
794              $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
795          }          }
796          # Add this location's data to the return string. Note that we may need to reverse it.          # Add this location's data to the return string. Note that we may need to reverse it.
797          if ($dir eq '+') {          if ($dir eq '+') {
798              $retVal .= $locationDNA;              $retVal .= $locationDNA;
799          } else {          } else {
800              $locationDNA = join('', reverse split //, $locationDNA);              $retVal .= FIG::reverse_comp($locationDNA);
             $retVal .= $locationDNA;  
801          }          }
802      }      }
803      # Return the result.      # Return the result.
# Line 2048  Line 2051 
2051      # Get the parameters.      # Get the parameters.
2052      my ($self, $entityName, $entityID) = @_;      my ($self, $entityName, $entityID) = @_;
2053      # Check for the entity instance.      # Check for the entity instance.
2054        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2055      my $testInstance = $self->GetEntity($entityName, $entityID);      my $testInstance = $self->GetEntity($entityName, $entityID);
2056      # Return an existence indicator.      # Return an existence indicator.
2057      my $retVal = ($testInstance ? 1 : 0);      my $retVal = ($testInstance ? 1 : 0);

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