Changes between Version 2 and Version 3 of BioRuby

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Timestamp:
2008/02/15 14:25:55 (11 years ago)
Author:
ngoto
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  • BioRuby

    v2 v3  
    1010   * mailing list (already available) 
    1111   * preparation of MediaWiki by OBF server administrators ... Done 
    12    * moving contents from wiki.bioruby.org to bioruby.open-bio.org/wiki/ 
    13    * migration from CVS to SVN 
     12   * moving contents from wiki.bioruby.org to bioruby.open-bio.org/wiki/ ... in progress 
     13   * (future work) migration from CVS to SVN 
    1414 * bioruby.org 
    1515   * moving wiki to bioruby.open-bio.org/Wiki 
    1616   * moving RDoc to bioruby.rubyforge.org ... Done 
    17    * moving toppage to Wiki 
    18    * tar.gz should move to ??? 
    19    * www.bioruby.org and bioruby.org should point bioruby.open-bio.org/wiki/Main_Page (redirection?) 
     17   * moving toppage to Wiki ... in progress 
     18   * (future work) tar.gz should move to ??? 
     19   * (future work) www.bioruby.org and bioruby.org should point bioruby.open-bio.org/wiki/Main_Page (redirection?) 
    2020 
    2121== Bio::Sequence improvements for round trip == 
    2222 
     23=== Input (creation of Bio::Sequence object) === 
     24   * Bio::Sequence#read(str ~~or file?~~~) ... Done 
     25     * (or Bio::Sequence#input(str or file?) ???) 
     26     * Bio::*#to_biosequence is automatically called ... Done 
     27   * Bio::*#to_biosequence implementation 
     28     * Bio::EMBL ... Done (jan) 
     29     * Bio::GenBank ... Done (ngoto) 
     30 
    2331=== Output (formatting) === 
    2432   * Bio::Sequence#output(format = ''anything'') 
    25      * ERB templates 
    26        * Bio::Sequence#output(format = :embl) 
    27        * Bio::Sequence#output(format = :genbank) 
    28  
    29 === Input (creation of Bio::Sequence object) === 
    30    * Bio::Sequence#read(str or file?) or Bio::Sequence#input(str or file?) 
    31      * Bio::*#to_biosequence is automatically called? 
    32    * Bio::*#to_biosequence implementation? 
     33     * using ERB templates 
     34       * Bio::Sequence#output(format = :embl) ... in progress (jan) 
     35       * Bio::Sequence#output(format = :genbank) ... in progress (ngoto) 
    3336 
    3437=== Easy access to Bio::Sequence inside BioRuby === 
    3538   * Bio::Sequence#embl, Bio::Sequence#gb 
    36      * can access as if it is Bio::EMBL or Bio::GenBank objects 
    37      * delegates to Bio::Sequence objects (or translation/conversion may be needed) 
    38      * Bio::EMBL changed to Bio::Sequence delegation objects? 
    39        * delayed evaluation? 
     39     * (idea only) can access as if it is Bio::EMBL or Bio::GenBank objects 
     40     * (idea only) delegates to Bio::Sequence objects (or translation/conversion may be needed) 
     41     * (idea only) Bio::EMBL (and GenBank etc.) changed to Bio::Sequence delegation objects? 
     42       * jan's idea: BiorubyFormats 
     43       * problem with lazy evaluation? 
    4044 
    4145=== Internal structure of Bio::Sequence === 
    42    * generated from / compatible with XML Schema? 
     46   * (future work?) generated from / compatible with XML Schema 
     47 
     48== NEXML parser in BioRuby == 
     49   * (future work) generate parser code from XML schema