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revision 1.1, Sat Sep 10 07:40:17 2005 UTC revision 1.2, Thu Dec 6 14:58:03 2007 UTC
# Line 23  Line 23 
23    
24  =head3 new  =head3 new
25    
26  C<< my $cdna = ContigDNA->new($genID1 => $file1, $genID2 => $file, ... $genIDN => $fileN ); >>      my $cdna = ContigDNA->new($genID1 => $file1, $genID2 => $file, ... $genIDN => $fileN );
27    
28  Construct a new pseudo-FIG object from a set of FASTA files. The incoming parameters come  Construct a new pseudo-FIG object from a set of FASTA files. The incoming parameters come
29  in pairs. The first of each pair is the ID of a genome; the second is the name of a FASTA  in pairs. The first of each pair is the ID of a genome; the second is the name of a FASTA
# Line 62  Line 62 
62    
63  =head3 dna_seq  =head3 dna_seq
64    
65  C<< my $sequence = $sfxlate->dna_seq($genomeID, @locations); >>      my $sequence = $sfxlate->dna_seq($genomeID, @locations);
66    
67  Return the sequence represented by a list of locations. The locations  Return the sequence represented by a list of locations. The locations
68  should be in the standard form I<contigID>C<_>I<begin>I<dir>I<end>.  should be in the standard form I<contigID>C<_>I<begin>I<dir>I<end>.
# Line 105  Line 105 
105    
106  =head3 contig_ln  =head3 contig_ln
107    
108  C<< my $length = $sfxlate->contig_ln($genomeID, $contig); >>      my $length = $sfxlate->contig_ln($genomeID, $contig);
109    
110  Return the length of the specified contig.  Return the length of the specified contig.
111    
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