NEXUS Class Library (NCL) / News: Recent posts

A new release of NCL has been posted. The release includes bug-fixes to the library as well as the addition of new example programs for reading and writing a variety of data formats.

Below are the parts of the changelog that reflect changes since version 2.1.01

2.1.08 (relative to 2.1.06)

Bug fixes:
- updated nexml writing to deal with changes in the schema
- fixed bug causing mis-indexing of taxa in trees if there is no taxa block
but a translate command. This involves support for illegal nexus files.
I believe that the bug would have showed diagnosable pathologies if it
had affected any analysis (the highest number in the tree would have been
1 too high resulting in exceptions when the taxa block was queried).
- bug fix when trees are followed by labels that contain tokens that have to
be quoted
- fixed behavior of GetNamedStateSetOfColumn and GetObsStates so that they
are sensitive to the current gapmode for the char block
- explicit inclusion of cstdlib where needed... read more

A branch has been created at that supports configuration of NCL so that it can be used to generate swig bindings for languages other than C++. This work builds on an excellent version of SWIG bindings for NCL version 2.0.x by David Suarez Pascal who was employed in the NESCent Google Summer of Code project in the summer of 2007.

Currently the bindings have only been tested on python, but only minor changes should be required to get them working in other languages. ... read more

To obtain this version, use the svn url https://ncl.svn.sourceforge.net/svnroot/ncl/branches/v2.1
to obtain this version (see the "Code" tab in the Sourceforge page for NCL to see instructions).

This version significant upgrade to NCL in terms of ease of use for programmers and the coverage of variants of NEXUS files. This version naturally supports multiple instances of blocks (common in files from Mesquite) and the Mixed datatype used by MrBayes. Support for the UNALIGNED and ASSUMPTIONS block has been dramatically improved. The SETS and CODONS blocks are now handled (they are treated as special forms of the ASSUMPTIONS block to tolerate the inclusion of many of the same commands in different block types). Almost all of the changes in this version were made by Mark Holder, so please direct bug reports, questions, and feature requests to him (though the sourceforge page is the best place to report these).... read more