nclbindings/README at master · pascalin/nclbindings · GitHub

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NCL Bindings 1.0
(c) 2007 David Suarez Pascal <david.suarez@yahoo.com>


README

 NCL Bindings provides a set of wrappers for the classes in the NEXUS
Class Library (http://sourceforge.net/projects/ncl/). These wrappers
were created employing SWIG (http://www.swig.org).

 With NCL Bindings it is very simple to process NEXUS data from
programs written in the languages Perl, Python and Ruby. You just need
to import/include the ncl package from your program and use the
classes provided by NCL or (with some restrictions) create your own
subclasses.

 Basically, NCL use requires two core classes: NxsReader and
NxsToken. NxsReader in conjunction with NxsToken can parse a NEXUS
file and process each type of NEXUS block if an adequate processor has
been registered with NxsReader.

 A common block processor is NxsTaxa. It extracts taxonomic
information from the TAXA block in a NEXUS file and this info can be
employed by other block processors.

 All NCL classes are well documented in the NCL source. Small changes
to the specification have been made. Only API changes are documented
in this file.


NCL wrapped classes

 Core classes

  * NxsReader
    No significant changes were made.

  * NxsToken
    NxsToken constructor receives the a string containing the
    NEXUS data instead of just a file name.

  * NxsBlock
    Report method in NxsBlock and its derived classes return a string
    instead of receiving a writable object.

 Derived classes

  * NxsAssumptionsBlock
  * NxsCharactersBlock
  * NxsDataBlock
  * NxsDistancesBlock
  * NxsTaxaBlock
  * NxsTreesBlock
  * NxsEmptyBlock
  * NxsUnalignedBlock

 The remaining changes will pass, with luck, unnoticed since these
intend to provide the most natural translation between NCL classes and
each language particulars. An example of this is the capitalization of
constant elements in NCL made automatically by SWIG when generating
Ruby wrappers. The same case is with NCL methods returning a Boolean
value, whose names have been modified by appending a question sign (?)
as with Ncl::NxsBlock.IsEmpty?


Installation

 Please check the INSTALL file included with NCL Bindings.


Use

 Once installed, you can employ NCL Bindings from your scripting
language of choice calling one of the following instructions:

 Perl

  use ncl;

 Python

  import ncl

 Ruby

  require 'ncl';


About NCL Bindings

 Development of NCL Bindings was funded by Google through its Summer
of Code 2007 and occurred under mentorship of Mark Holder
(http://www.csit.fsu.edu/~mholder/), one of the developers of NCL.