getTree and github

I've got the openTree functions working in the getTree class. openTree takes in a tree file and returns an array of phylogeny objects. These objects can be accessed by storeTree.

The csv parsers seem to be working as well. I'm thinking about replacing these with parsers from the GeoTools library. There's tons of stuff there, so I'll need to spend time picking out what I need for phyloGeoRef.

A side note, I'm having some problems with git and github so if you're watching the repo I wouldn't rely on anything that shows up there until I give the OK on this blog.

UPDATE: everything in the github repo should be good to go now :-)

CSV Parsers

I've been working on the parseCoord class. This class contains several parsers for parsing delimited files. There are built in csv and tsv parsers and a function to define your own delimiter. These will be utilized to parse files containing the latitude and longitude coordinates. I've been using the opencsv library of csv parsers extensively.

Day 1: Tree classes

A brief summary of day 1:

I'm currently focusing on crating the tree classes. getTree and storeTree are the two I'm working on now. Currently I'm relying on the forester package for my parsers. This package is part of the biojava library. I'm currently implementing newick, nexus and phyloxml parsers. More will come as time permits, but these three are the priority right now.

storeTree, as the name suggests, is the class that defines how a tree object is stored in the library. It mainly defines a tree objects and holds information such as parent-child relationships, number of nodes, branch lengths and leafs.

getTree deals with the parsers and outlines functions that call the appropriate parser. It will probably end up interacting heavily with storeTree.

Hello Code

An update of what I've been doing during the SoC bonding period.

First of all, information about the project will be kept mainly in 3 places:

Github will host the actual code and a rough draft of the documentation will be kept on the github wiki.

This blog will have updates of what I'm currently working on and the current state of the project.

Phyloinformatics wiki is a semi-static page that has general info about the project and the project plan. This will be updated as I complete tasks, but this blog should be considered the most up to date record of the project.

IDE
Currently trying to decide between NetBeans and Eclipse, any suggestions are welcome.

Open source java libraries
Jak is a java API for kml
BioJava has methods for reading and building phylogenetic trees
GeoPhyloBuilder implements trees in 3D space
freegis has many open source java libraries and applications
java-source has some more open source geo-java libraries and programs