[BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.8,0.58.2.9

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv20752/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
Added documents for attributes added during Biohackathon2008.


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.8
retrieving revision 0.58.2.9
diff -C2 -d -r0.58.2.8 -r0.58.2.9
*** sequence.rb	4 Mar 2008 11:10:28 -0000	0.58.2.8
--- sequence.rb	27 Mar 2008 13:07:19 -0000	0.58.2.9
***************
*** 73,78 ****
    include Format
  
-   attr_accessor :sequence_version, :topology, :molecule_type, :data_class, :division, :primary_accession, :secondary_accessions, :date_created, :date_modified, :species, :classification
- 
    # Create a new Bio::Sequence object
    #
--- 73,76 ----
***************
*** 154,158 ****
--- 152,196 ----
    # but could be a simple String
    attr_accessor :seq
+ 
+   #---
+   # Attributes below have been added during BioHackathon2008
+   #+++
    
+   # Version number of the sequence (String).
+   attr_accessor :sequence_version
+ 
+   # Topology (String). "circular" or "linear".
+   attr_accessor :topology
+ 
+   # molecular type (String). "DNA" or "RNA" for nucleotide sequence.
+   attr_accessor :molecule_type
+ 
+   # Data Class defined by EMBL (String)
+   # See http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_1
+   attr_accessor :data_class
+ 
+   # Taxonomic Division defined by EMBL/GenBank/DDBJ (String)
+   # See http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_2
+   attr_accessor :division
+ 
+   # Primary accession number (String)
+   attr_accessor :primary_accession
+ 
+   # Secondary accession numbers (Array of String)
+   attr_accessor :secondary_accessions
+ 
+   # Created date of the sequence entry (String)
+   attr_accessor :date_created
+ 
+   # Last modified date of the sequence entry (String)
+   attr_accessor :date_modified
+ 
+   # Organism species (String). For example, "Escherichia coli".
+   attr_accessor :species
+ 
+   # Organism classification, taxonomic classification of the source organism.
+   # (Array of String)
+   attr_accessor :classification
+ 
    # Guess the type of sequence, Amino Acid or Nucleic Acid, and create a 
    # new sequence object (Bio::Sequence::AA or Bio::Sequence::NA) on the basis