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revision 1.33, Wed Sep 14 13:26:27 2005 UTC revision 1.36, Wed Sep 14 13:52:34 2005 UTC
# Line 767  Line 767 
767          # 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
768          # before putting it in the return value.          # before putting it in the return value.
769          my ($start, $stop);          my ($start, $stop);
770          Trace("Parsed location is $beg$dir$len.") if T(SDNA => 4);          Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
771          if ($dir eq "+") {          if ($dir eq "+") {
772              $start = $beg;              $start = $beg;
773              $stop = $beg + $len - 1;              $stop = $beg + $len;
774          } else {          } else {
775              $start = $beg - $len + 1;              $start = $beg - $len;
776              $stop = $beg;              $stop = $beg + 1;
777          }          }
778          Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);          Trace("Looking for sequences containing $start to $stop.") if T(SDNA => 4);
779          my $query = $self->Get(['IsMadeUpOf','Sequence'],          my $query = $self->Get(['IsMadeUpOf','Sequence'],
780              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
781              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",              " IsMadeUpOf(start-position) < ? ORDER BY IsMadeUpOf(start-position)",
782              [$contigID, $start, $stop]);              [$contigID, $start, $stop]);
783          # Loop through the sequences.          # Loop through the sequences.
784          while (my $sequence = $query->Fetch()) {          while (my $sequence = $query->Fetch()) {

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