[Bio] / Sprout / Sprout.pm Repository: Repository Listing Bio

# Diff of /Sprout/Sprout.pm

revision 1.33, Wed Sep 14 13:26:27 2005 UTC revision 1.39, Wed Sep 14 14:04:13 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 - 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) + 1 - \$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);

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 Removed from v.1.33 changed lines Added in v.1.39