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1 package Bio::Graphics::Util;
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2
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3 # $Id: Util.pm,v 1.2.2.2 2003/07/06 21:53:55 heikki Exp $
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4 # Non object-oriented utilities used here-and-there in Bio::Graphics modules
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5
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6 use strict;
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7 require Exporter;
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8 use vars '@ISA','@EXPORT','@EXPORT_OK';
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9 @ISA = 'Exporter';
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10 @EXPORT = 'frame_and_offset';
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11
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12
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13 =over 4
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14
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15 =item ($frame,$offset) = frame_and_offset($pos,$strand,$phase)
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16
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17 Calculate the reading frame for a given genomic position, strand and
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18 phase. The offset is the offset from $pos to the first nucleotide
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19 of the reading frame.
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20
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21 In a scalar context, returns the frame only.
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22
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23 =back
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24
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25 =cut
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26
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27 sub frame_and_offset {
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28 my ($pos,$strand,$phase) = @_;
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29 $strand ||= +1;
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30 $phase ||= 0;
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31 my $frame = $strand >= 0
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32 ? ($pos - $phase - 1) % 3
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33 : (1 - $pos - $phase) % 3;
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34 my $offset = -$phase % 3;
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35 $offset *= -1 if $strand < 0;
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36 return wantarray ? ($frame,$offset) : $frame;
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37 }
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38
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39
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40 1;
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