coalescent Files

version: 1.0.0
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An exact implementation of the probability recursion for model KC64 and statistic An. It also prints
out the configurations that are computed during the recursion.

1.0.1- RELEASE SCRIPT FOR CONSOLE CLIENT ID: 1011 DATE: 9/7/10 Status: CLOSED

The following are the requirements of the release. There are two types of releases, binary and source. The first step of the build is to do
a fresh compilation to detect any compilation errors. All releases gurantee correct compilation. The binary release is a single .zip file (coalescent_console_bin_<version>.zip) with the following contents. The application jar file console.jar-which contains all the necessary code for the console client, app.properties- contains the application settings for the console application, release_notes.txt which documents the release notes for that version, a 'src' directory that contains source code for all the classes compiled and an 'api' directory that contains the javadoc produced on the 'src' directory. The source release contains only the above mentioned 'src' directory and nothing else and the source release .zip file is named coalescent_console_src_<version>.zip.


1.0.1- Refactoring packages in project coalescent_app ID:1012  Started: 9/9/10 Closed: 10/4/10 Status: CLOSED

We need to re-factor the package structure in coalescent_app so that individual client`s packages do not overlap and they can be easily moved away from the package if needed when they grow big enough. This will also help put the general application framework code in its own package. 

The proposed packaged structure is:

app---CmdEvent.java, Comand.java
console---ConsoleClient.java
console.event---- ConsoleCmdEvent, KC64RRCmdEvent.java
console.command--- ConsoleCommand.java, KC64RRCommand.java

The command-event registration code has been moved from ConsoleClient to a new class Registry in package console. Also, there is now a new class, PropertyKeys, to store some selected application property keys.


1.0.1- Refactoring Recursion ID:1013  Started: 9/9/10 Closed: 10/4/10 Status: CLOSED

The folowing improvements are suggested.
 
 1. Rename ExactKC64AnRecursion to ExactRecursion.
 2. Implement ExactRecursion`s boundary condition in a private method
 3. Change the way presence of a coalescent event is detected. Instead use the better API An.canCoalesce(). 
 4. Improve javadoc 
 5. Change Recursion from Interface to Abstract Class. Use a protected constrcutor with parameter, an object of CompositeModel
 6. Change the type parameter from M extends Model to M extends CompositeModel 
 7. Move the factory method for recursion from Recursions to the abstract class Recursion. Delete Recursions.
 8. Rename the factory method to getNewExactRecursion (CompositeModel model, Class< ? extends Statistic> class) throws NoSuchAlgorithmException
 
 
1.0.1- Refactoring An ID:1014  Started: 9/9/10 Closed: 10/4/10 Status: CLOSED

The folowing improvements are suggested.

 1. Refactor mutationProb(theta) to KC64
 2. Refactor coalescentProb(theta) to KC64
 3. Make applyCoalescent() and applyMutation() immutable and thus making An efectively immutable
 3. The array holding An should eliminate right zeroes

1.0.2- ExactRecursion ID:1021  Started: 10/5/10 Status: OPEN

 1. An.applyCoalescent():Iterator<An> . ExactRecursion is modified to use this feature.
 
1.0.3- Generic Exact Recursion using Events ID: 1031  Started: 10/5/10 Closed: 10/8/10 Status: CLOSED

 1. Implement exact computation of the probability recursion for KC64.