[Phylobase-devl] Fwd: Nexus class library v2.1 finally has some documentation about what has changed since v2.0

[Brian O'Meara]

Mark Holder has updated the documentation for NCL, which should make  
using it in phylobase easier. Thanks, Mark!

Brian

Begin forwarded message:

> From: Mark Holder <mtholder at ku.edu>
> Date: March 27, 2010 3:17:38 PM EDT
> To: Brandon Chisham <bchisham at cs.nmsu.edu>, "Brian O'Meara" <bcomeara at nescent.org 
> >, Dave Swofford <david.swofford at duke.edu>, Paul Lewis <paul.lewis at uconn.edu 
> >, dz <zwickl at ku.edu>, Jeet Sukumaran <jeet at ku.edu>, Paul van der  
> Mark <paulvdm at scs.fsu.edu>, Peter Cowan <pdc at berkeley.edu>, Michael  
> Sanderson <sanderm at email.arizona.edu>, Arlin Stoltzfus <arlin.stoltzfus at nist.gov 
> >, William Piel <william.piel at yale.edu>, Rutger Vos <rutgeraldo at gmail.com 
> >, David Maddison <beetle at ag.arizona.edu>, Wayne Maddison <wmaddisn at interchange.ubc.ca 
> >, Hilmar Lapp <hlapp at duke.edu>, Fredrik Ronquist <ronquist at csit.fsu.edu 
> >, John Huelsenbeck <johnh at berkeley.edu>
> Subject: Nexus class library v2.1 finally has some documentation  
> about what has changed since v2.0
>
> Hi NCL users (and other folks who may be interested in NEXUS parsing),
>
> Short message:
> 	- I have finally forced myself to update the NCL documentation to  
> reflect the changes to the API that accompanied the v2.1 branch.
>
> 	- Check out the high level overview at: http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/index.html
>
> 	- Checkout the example code at:
> 		http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/simpleNCLClient/simpleNCLClient.cpp
> 	  and its Makefile:
> 		http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/simpleNCLClient/Makefile
>
> 	- Please let me know if you find errors/typos in the docs ( mtholder at gmail.com 
>  ).  I'm sure there are plenty of typos.
>
> 	- I pushed a new release to sourceforge (v2.1.11). Some of the docs  
> refer to convenience functions that I just added to the library, so  
> you'll need that version of the library.
>
>
>
>
>
> Longer message:
>
> As you probably know the currently-developed branches of NCL (https://ncl.svn.sourceforge.net/svnroot/ncl/branches/v2.1
> and https://ncl.svn.sourceforge.net/svnroot/ncl/branches/v2.2) have  
> changed considerably since version 2.0 of the library.
>
> Paul Lewis is the author of NCL, and for a few years now I've been  
> helping expand and maintain the library. Unfortunately, while Paul  
> is very disciplined about documenting his code, I'm not a very good  
> commenter/documenter.  So the documentation has become much less  
> useful of late because of my additions to the library.
>
> We have really tried to make the new API backward compatible, so  
> Paul's docs are still useful.
>
> However:
> 	- The newer API can be considerably easier to use and more robust  
> for complex NEXUS files (those which contain multiple instances of  
> the same block).
>
> 	- There are some substantial performance improvements in the newer  
> version.  Admittedly most of our software is not limited by parsing  
> time, but if you are writing an application that needs to crunch a  
> lot of files or big files (or both) you should be using NCL v2.1.
>
> 	- v2.1 and later supports quite a few more commands and options  
> (including Mesquite's LINK/TITLE syntax for dealing with multiple  
> blocks, Mesquite's extension to the CHARSET commands, and MrBayes'  
> extensions to NEXUS such as datatype=mixed and dataype=restriction  
> in the FORMAT command).
>
> 	- v2.2 is now generated from v2.1 using a simple script.  v2.2  
> provides support for SWIG bindings to NCL.  Currently only python  
> bindings have been tested, but other languages should be usable  
> without too much tweaking.
>
> So, I think that the jump from 2.0 to 2.1 is worth making.
>
>
> I've just made a push on documenting the newer API at a high level.   
> It is still a work in progress, but if you've been frustrated by my  
> poor documentation of NCL, you should check out:
> 	http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/index.html
>
> The logic of the newer API and new features are described much  
> better than they have been before now.
>
> You may also want to look at the at the example files at:
> 			http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/simpleNCLClient/simpleNCLClient.cpp
>
> which can be built using the Makefile at:
> 		http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/simpleNCLClient/Makefile
> if you use g++, have installed NCL and put NCL_INSTALL_DIR in your  
> env.
>
>
> all the best,
> Mark
>
>
>
>
>
>
>
>
> Mark Holder
>
> mtholder at ku.edu
> http://phylo.bio.ku.edu/mark-holder
>
> ==============================================
> Department of Ecology and Evolutionary Biology
> University of Kansas
> 6031 Haworth Hall
> 1200 Sunnyside Avenue
> Lawrence, Kansas 66045
>
> lab phone:  785.864.5789
>
> fax (shared): 785.864.5860
> ==============================================
>
>
>
>
>
>
>
>

------------------------------------------------------
Brian O'Meara
http://www.brianomeara.info
Assistant Prof.
Dept. Ecology & Evolutionary Biology
U. of Tennessee, Knoxville

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