coalescent Files

Release notes for coalescent application version 1.4.0

Date: Dec 30, 2012

Project website: http://coalescent.sourceforge.net

Features:

1. Data support. 
   Jobs can select data from a drop-down combo box. Only relevant data sets are shown. The application is preloaded with data sets.

2. Maximum Likelihood Estimation (MLE). 
   1.1 For Infinite-Alleles Model. 
   1.2 For Infinite-Sites Model.

3. Modify existing data set and create new data set. 
   2.1 When a job is run, the URL of the data set is given in the output window
   2.2 Use Favorites to add the folder/file. Edit the data set and run jobs using the drop-down data combo box.
   2.3 Create a copy of the data set in the Favorites window; restart application to see the data in the drop-down data combo box.
   
Improvements:

1.  XML Console Properties.
    The format of the console properties file has been replaced from being simple properties file to
	XML. This allows greater flexibility. As before, the GUI is compatible with the current version of
	the console properties, ensuring that all jobs that run on the GUI will also run from the console
	and vice versa.
	
2.  Recursion Traversal More Efficient.
    2.1 Cut sets are now stored in HashSet (from ArrayList) making the lookup almost instant.
	2.2 HashCode and Non-HashCode (tree checking) based equals implementation. HashCode based equals
	    implementation is much faster and is accurate mostly (no test failures).
		
3.  API Improvements
    3.1 GeneTree$Tracker related work-around with Genealogy has been resolved.
	3.2 Redesigned Builder, Provider & Provider-Impl. Builders are more compact and flexible using
	    annonymous classes. 
    3.3 Acceptance Tests for all commands has been adopted as a build policy.