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

[Mark Holder]

Note, that too use some of the newest features mentioned in the docs,  
someone with phylobase write access will have to sync the version of  
the NCL code in phylobase with what is now in NCL's repo.


all the best,

Mark



On Mar 29, 2010, at 9:34 AM, Brian O'Meara wrote:

> 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
>

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
==============================================








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