Changes between Version 2 and Version 3 of BioRuby

Timestamp:

2008/02/15 14:25:55 (16 years ago)

Author:

ngoto

Comment:

--

BioRuby

@@ -10 +10 @@
    * mailing list (already available)
    * preparation of MediaWiki by OBF server administrators ... Done
-   * moving contents from wiki.bioruby.org to bioruby.open-bio.org/wiki/
-   * migration from CVS to SVN
+   * moving contents from wiki.bioruby.org to bioruby.open-bio.org/wiki/ ... in progress
+   * (future work) migration from CVS to SVN
  * bioruby.org
    * moving wiki to bioruby.open-bio.org/Wiki
    * moving RDoc to bioruby.rubyforge.org ... Done
-   * moving toppage to Wiki
-   * tar.gz should move to ???
-   * www.bioruby.org and bioruby.org should point bioruby.open-bio.org/wiki/Main_Page (redirection?)
+   * moving toppage to Wiki ... in progress
+   * (future work) tar.gz should move to ???
+   * (future work) www.bioruby.org and bioruby.org should point bioruby.open-bio.org/wiki/Main_Page (redirection?)
 
 == Bio::Sequence improvements for round trip ==
 
+=== Input (creation of Bio::Sequence object) ===
+   * Bio::Sequence#read(str ~~or file?~~~) ... Done
+     * (or Bio::Sequence#input(str or file?) ???)
+     * Bio::*#to_biosequence is automatically called ... Done
+   * Bio::*#to_biosequence implementation
+     * Bio::EMBL ... Done (jan)
+     * Bio::GenBank ... Done (ngoto)
+
 === Output (formatting) ===
    * Bio::Sequence#output(format = ''anything'')
-     * ERB templates
-       * Bio::Sequence#output(format = :embl)
-       * Bio::Sequence#output(format = :genbank)
-
-=== Input (creation of Bio::Sequence object) ===
-   * Bio::Sequence#read(str or file?) or Bio::Sequence#input(str or file?)
-     * Bio::*#to_biosequence is automatically called?
-   * Bio::*#to_biosequence implementation?
+     * using ERB templates
+       * Bio::Sequence#output(format = :embl) ... in progress (jan)
+       * Bio::Sequence#output(format = :genbank) ... in progress (ngoto)
 
 === Easy access to Bio::Sequence inside BioRuby ===
    * Bio::Sequence#embl, Bio::Sequence#gb
-     * can access as if it is Bio::EMBL or Bio::GenBank objects
-     * delegates to Bio::Sequence objects (or translation/conversion may be needed)
-     * Bio::EMBL changed to Bio::Sequence delegation objects?
-       * delayed evaluation?
+     * (idea only) can access as if it is Bio::EMBL or Bio::GenBank objects
+     * (idea only) delegates to Bio::Sequence objects (or translation/conversion may be needed)
+     * (idea only) Bio::EMBL (and GenBank etc.) changed to Bio::Sequence delegation objects?
+       * jan's idea: BiorubyFormats
+       * problem with lazy evaluation?
 
 === Internal structure of Bio::Sequence ===
-   * generated from / compatible with XML Schema?
+   * (future work?) generated from / compatible with XML Schema
+
+== NEXML parser in BioRuby ==
+   * (future work) generate parser code from XML schema