[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 / java

| Wed Mar 10 01:48:04 2010 —

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.model package and their implementations in the org.nexml.model.impl package.
- 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).
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.

As of 26/6/09 the NeXML/Java project uses maven for building and dependency management. This means that you can run goals such as 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

 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

nexml - index of /nexml/java/

[nexml]

The future data exchange standard is here!

Directory listing

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