[nexml]

phylogenetic data in xml

The future data exchange standard is here!

nexml is an exchange standard for representing phylogenetic data — inspired by the commonly used NEXUS format, but more robust and easier to process.

Directory listing

~ / nexml / cpp

| Wed Aug 20 22:50:38 2008 —

Prerequisites

C++ bindings are generated from the nexml schema files using the xsd tool from CodeSynthesis, and are then compiled with something like the driver.cxx file to yield an executable that processes nexml instance documents (presumably this would be part of an importer that maps the beans objects created by the xsd tool onto your internal object model). The basic steps are as follows:

Download and install xsd-* for your platform.
Download and install xerces-c, we need to include its headers during compiling and libxerces during linking.
Generate the headers and binding sources from the schema using the xsd tool. The easiest way to do this is to run the configure script in the parent directory and use make from that directory (if you are a developer, you will have to run the bootstrap.sh shell script to create the configure script -- you will also need up-to-date autoconf and automake). You will need to use the --with-xerces= and --with-code-syn-xsd arguments to configure

If you do not want to use the configure-based build, you can also build the C++ bindings using something like this shell script or this Makefile. You may have to tweak these a little depending on your install location and version for xsd and xerces-c. The salient point in these script examples is the command line invocation for xsd.
Create your own mappings between the xsd object model and that of your software. The driver.cxx gives a simple example of where to start with that. Make sure to use the flags to include and link to xsd, and xerces. For example, compile with -I$XERCES_HOME/include -I$XSD_HOME/$XSD_HOME/libxsd and link with -L$XERCES_HOME/lib -lxerces-c.

 Name                 Last modified       Size  Description

 Parent Directory     14-Aug-2008 11:40      -  Folder
 Makefile.am          13-Aug-2008 16:15     4k  Make file
 build.sh             13-Aug-2008 13:00     1k  Unix shell script
 cpp-bindings.tar.gz  13-Aug-2008 00:13    69k  GZIP tar archive
 driver.cxx           13-Aug-2008 14:50     2k  C code
 handwrittenMakefile  13-Aug-2008 14:50     1k  Make file
 makefile             07-Feb-2008 00:28     1k  Make file
 out/                 13-Aug-2008 00:15      -  Folder

nexml - index of /nexml/cpp/

[nexml]

The future data exchange standard is here!

Directory listing

Prerequisites

Quick links:

Bindings:

Goings on:

External links