[nexml]
phylogenetic data in xmlThe 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.
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| Fri Jul 4 10:07:21 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.
For example, if
XERCES_HOME=~/xerces-c_2_8_0-x86-macosx-gcc_4_0, compile with-I$XERCES_HOME/includeand link with-L$XERCES_HOME/lib -lxerces-c. -
Generate the headers and binding sources 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.
Name Last modified Size Description
Parent Directory 19-May-2008 13:30 - Folder
build.sh 07-Feb-2008 00:28 1k Unix shell script
driver.cxx 07-Feb-2008 00:28 2k C code
makefile 07-Feb-2008 00:28 1k Make file