This section explains the implementation of the first iteration of the project; it also explains some of the technologies used during the creation of the initial stages of the program.
Before any work can be carried out the main project base needs to be set up, this project will be using Maven. As the project will be using external dependencies such as the open source molecule viewer "Jmol" these dependencies can change over time, maven will be able to help with this problem as it will be able to update these external sources for you on the fly once they have been added to the maven project properties. Maven also simplifies with the testing of the project as a whole with the deep integration with the java unit-testing platform "Junit". The main project configuration file can be seen in the appendices under the heading "pom.xml". The other options for build systems include Make files or Ant scripts. Maven is the better choice due to it's excellent dependency management and it's close integration with source control management and issue control software.
The main documentation for the project will be recorded within this document. However, I will also be using JavaDoc to document the java source code to provide information about the public interfaces to the system. JavaDoc is able to generate HTML API documentation just from the comments of the source code; this makes it ideal for an open source project such as this as it will allow the source code to be easily understood by the community. The JavaDoc comments will be compiled into a searchable HTML file that will be uploaded to the projects website at Google Code.