[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.
Directory listing
This subdirectory contains java code for NeXML processing. Specifically, the directory structure is as follows:
- src/* contains source code for the following
subprojects:
-
src/org/* contains the DOM-based core java 5 NeXML
reading/writing API developed by a
subgroup of the
database interoperability hackathon held at
NESCent March 8-13 2009. The API contains
interfaces in the
org.nexml.modelpackage and their implementations in theorg.nexml.model.implpackage. -
src/mesquite/* contains classes for
mesquite.
These classes use the
org.nexml.model.*architecture, and so function to illustrate how to use it in an application. Written and maintained by Rutger Vos with some help from Wayne Maddison. - src/validator/* contains a Xerces-J-based validator written by Terri Liebowitz of the San Diego Supercomputing Center, with modifications by Mark Holder. It is used to validate nexml instance documents against the schema (or, indeed, any xml instance document against any schema).
-
src/org/* contains the DOM-based core java 5 NeXML
reading/writing API developed by a
subgroup of the
database interoperability hackathon held at
NESCent March 8-13 2009. The API contains
interfaces in the
-
test/* contains
JUnit tests for the
org.nexml.model.*API. - jars/* contains dependencies for the code in the src/ and validator/ folders. Not all these jars are required at present, it seems.
mvn test, mvn compile,
mvn install and mvn clean. For more info, consult the pom.xml.
In addition to using mvn to build and install the code here, you can also use the nexml maven
repository at:
<repository> <id>m2.nexml.repos</id> <name>NeXML Remote Repository</name> <url>http://nexml-dev.nescent.org/.m2/repository/</url> </repository>From where you can download nexml as:
<dependency> <groupId>org.nexml.model</groupId> <artifactId>nexml</artifactId> <version>1.5-SNAPSHOT</version> </dependency>
To download the contents of this folder using
svn:
svn co \
https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java/ \
java
https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java/ \
java
Name Last modified Size Description
Parent Directory - Folder
README.html 26-Jun-2009 06:47 3.3K HTML document
build.sh 26-Jun-2009 06:47 291 Unix shell script
build.xml 10-Jun-2009 03:43 1.9K XML instance document
jars/ 10-Feb-2010 03:15 - Folder
mesquite/ 05-Mar-2008 18:00 - Folder
org/ 07-Feb-2008 00:28 - Folder
pom.xml 09-Dec-2009 11:37 2.3K XML instance document
src/ 26-Jun-2009 06:47 - Folder
test/ 10-Mar-2009 10:43 - Folder
validate_nexml.sh 26-Jun-2009 06:47 1.1K Unix shell script
validator/ 26-Jun-2009 06:47 - Folder