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

Diff of /Sprout/Sprout.pm

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

revision 1.32, Wed Sep 14 13:24:14 2005 UTC revision 1.38, Wed Sep 14 14:02:44 2005 UTC
# Line 625  Line 625 
625          # Compute the initial base pair.          # Compute the initial base pair.
626          my $start = ($dir eq "+" ? $beg : $beg + $len - 1);          my $start = ($dir eq "+" ? $beg : $beg + $len - 1);
627          # Add the specifier to the list.          # Add the specifier to the list.
628          push @retVal, "${contigID}_$beg$dir$len";          push @retVal, "${contigID}_$start$dir$len";
629      }      }
630      # Return the list in the format indicated by the context.      # Return the list in the format indicated by the context.
631      return (wantarray ? @retVal : join(',', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
# Line 767  Line 767 
767          # the start point is the ending. Note that in the latter case we must reverse the DNA string          # the start point is the ending. Note that in the latter case we must reverse the DNA string
768          # before putting it in the return value.          # before putting it in the return value.
769          my ($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 - 1;
# 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) - $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.1.32  
changed lines
  Added in v.1.38

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3