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revision 1.29, Wed Nov 21 20:41:05 2007 UTC revision 1.30, Fri Nov 30 21:35:51 2007 UTC
# Line 17  Line 17 
17  #  #
18  ########################################################################  ########################################################################
19    
20    =head1 TODO
21    
22    =over 4
23    
24    =item Null arg to ContigO::dna_seq() should return entire contig seq.
25    
26    =item Add method to access "FIG::crude_estimate_of_distance()"
27    
28    =back
29    
30    =cut
31    
32  =head1 Overview  =head1 Overview
33    
34  This module is a set of packages encapsulating the SEED's core methods  This module is a set of packages encapsulating the SEED's core methods
35  using an "OOP-like" style.  using an "OOP-like" style.
36    
37  There are several modules clearly related to "individual genomes:"  There are several modules clearly related to "individual genomes:"
38  FIGO, GenomeO, ContigO, FeatureO (and I<maybe> AnnotationO).  GenomeO, ContigO, FeatureO (and I<maybe> AnnotationO).
39    
40  There are also modules that deal with complex relationships between  There are also modules that deal with complex relationships between
41  pairs or sets of features in one, two, or more genomes,  pairs or sets of features in one, two, or more genomes,
# Line 32  Line 44 
44    
45  Finally, the methods in "Attribute" might in principle attach  Finally, the methods in "Attribute" might in principle attach
46  "atributes" to any type of object.  "atributes" to any type of object.
47  (Likewise, in principle one might like to attach an "annotation"  (Likewise, in principle one might also want to attach an "annotation"
48  to any type of object  to any type of object,
49    although currently we only support annotations of "features.")
50    
51  The four modules dealing with "genomes" have a reasonable clear  The three modules that act on "individual genomes" have a reasonable clear
52  "implied heirarchy:"  "implied heirarchy" relative to FIGO:
53    
54  =over 4  =over 4
55    
# Line 693  Line 706 
706    
707  =item RETURNS:  =item RETURNS:
708    
709      string of DNA sequence running from $beg to $end  String containing DNA subsequence running from $beg to $end
710      (NOTE: if $beg > $end, returns reverse complement of DNA subsequence.)      (NOTE: if $beg > $end, returns reverse complement of DNA subsequence.)
711    
712  =back  =back

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