Difference between revisions of "Project Plan for NeXML and RDF API in BioRuby"

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(Week 3)
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== Week 1 ==
 
== Week 1 ==
 
Development of the NeXML parser.
 
Development of the NeXML parser.
* Design classes to encapsulate:
+
* Design classes to encapsulate, and parse and return corresponding objects for:
 
** Taxa( <code>otu</code> )
 
** Taxa( <code>otu</code> )
 
** Taxa block( <code>otus</code> ) and
 
** Taxa block( <code>otus</code> ) and
 
** Sets( <code>class</code> )
 
** Sets( <code>class</code> )
* Parse <code>otu</code>, <code>otus</code> and <code>class</code> and return objects of the corresponding class.
+
 
 
== Week 2 ==
 
== Week 2 ==
* Design classes to encapsulate:
+
* Design classes to encapsulate, and parse and return corresponding objects for:
 
** Trees( <code>trees</code> )
 
** Trees( <code>trees</code> )
 
** Tree( <code>tree</code> ), Network( <code>network</code> ), Node( <code>node</code> ) and Edge( <code>edge</code> )
 
** Tree( <code>tree</code> ), Network( <code>network</code> ), Node( <code>node</code> ) and Edge( <code>edge</code> )
* Parse <code>trees</code>, <code>tree</code>, <code>node</code>, <code>edge</code> and return objects of the corresponding class.
+
 
 
== Week 3 ==
 
== Week 3 ==
 
* Design classes to encapsulate, and parse and return corresponding objects for:
 
* Design classes to encapsulate, and parse and return corresponding objects for:
Line 18: Line 18:
  
 
== Week 4 ==
 
== Week 4 ==
 +
Make sure that the API for the parser is in place, with software development iterations, tests and documents.
 +
 
== Week 5 ==
 
== Week 5 ==
 +
Development of the NeXML serializer
 +
* Extend the already designed classes to serialize:
 +
** Taxa( <code>otu</code> )
 +
** Taxa block( <code>otus</code> ) and
 +
** Sets( <code>class</code> )
 +
 
== Week 6 ==
 
== Week 6 ==
 +
* Extend the already designed classes to serialize:
 +
** Trees( <code>trees</code> )
 +
** Tree( <code>tree</code> ), Network( <code>network</code> ), Node( <code>node</code> ) and Edge( <code>edge</code> )
 +
 
== Week 7 ==
 
== Week 7 ==
 +
* Extend the already designed classes to serialize:
 +
** Character block( <code>characters</code> )
 +
** <code>format</code>, <code>states</code>, <code>state</code>, <code>char</code>
 +
** <code>matrix</code>, <code>row</code>
 +
 
== Week 8 ==
 
== Week 8 ==
 +
Make sure that the API for the NeXML serializer is in place, with software development iterations, tests and documents.
 +
 
== Week 9 ==
 
== Week 9 ==
 +
Design classes for semantic annotation.
 +
 
== Week 10 ==
 
== Week 10 ==
 +
 
== Week 11 ==
 
== Week 11 ==
 +
 
== Week 12 ==
 
== Week 12 ==
  

Revision as of 00:34, 26 May 2010

Week 1

Development of the NeXML parser.

  • Design classes to encapsulate, and parse and return corresponding objects for:
    • Taxa( otu )
    • Taxa block( otus ) and
    • Sets( class )

Week 2

  • Design classes to encapsulate, and parse and return corresponding objects for:
    • Trees( trees )
    • Tree( tree ), Network( network ), Node( node ) and Edge( edge )

Week 3

  • Design classes to encapsulate, and parse and return corresponding objects for:
    • Character block( characters )
    • format, states, state, char
    • matrix, row

Week 4

Make sure that the API for the parser is in place, with software development iterations, tests and documents.

Week 5

Development of the NeXML serializer

  • Extend the already designed classes to serialize:
    • Taxa( otu )
    • Taxa block( otus ) and
    • Sets( class )

Week 6

  • Extend the already designed classes to serialize:
    • Trees( trees )
    • Tree( tree ), Network( network ), Node( node ) and Edge( edge )

Week 7

  • Extend the already designed classes to serialize:
    • Character block( characters )
    • format, states, state, char
    • matrix, row

Week 8

Make sure that the API for the NeXML serializer is in place, with software development iterations, tests and documents.

Week 9

Design classes for semantic annotation.

Week 10

Week 11

Week 12

A discussion on API can be found here - NeXML and RDF API for BioRuby