[Bio] / Sprout / Sprout.pm Repository:
ViewVC logotype

Diff of /Sprout/Sprout.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.37, Wed Sep 14 13:55:54 2005 UTC revision 1.38, Wed Sep 14 14:02:44 2005 UTC
# Line 770  Line 770 
770          Trace("Parse of \"$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;              $stop = $beg + $len - 1;
774          } else {          } else {
775              $start = $beg - $len;              $start = $beg - $len + 1;
776              $stop = $beg + 1;              $stop = $beg;
777          }          }
778          Trace("Looking for sequences containing $start to $stop.") if T(SDNA => 4);          Trace("Looking for sequences containing $start through $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()) {
# Line 790  Line 790 
790              Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);              Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
791              # Figure out the start point and length of the relevant section.              # Figure out the start point and length of the relevant section.
792              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
793              my $len1 = ($stopPosition < $stop ? $stopPosition : $stop - 1) - $startPosition - $pos1;              my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) - $startPosition - $pos1;
794              Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);              Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
795              # Add the relevant data to the location data.              # Add the relevant data to the location data.
796              $locationDNA .= substr($sequenceData, $pos1, $len1);              $locationDNA .= substr($sequenceData, $pos1, $len1);

Legend:
Removed from v.1.37  
changed lines
  Added in v.1.38

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3