New Features:

1. Data support.

2. Maximum Likelihood Estimation (MLE)
3. Modify existing data set and create new data set.

Jobs Added:

Maximum Likelihood Estimation (MLE)

For Infinite-Alleles Model.

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Issues Coalescent 1.4.0:

Bug

• [COALESCENT-24] - IllegalStateException in ExactRecursionListener
• [COALESCENT-29] - Genealogy Probability work-around Fixed

Design

• [COALESCENT-28] - Statistic.alleles() from Set to Iterable

Feature

• [COALESCENT-12] - Data support
• [COALESCENT-14] - Statistic: Allele based Iteration
• [COALESCENT-19] - Acceptance Test
• [COALESCENT-22] - Console application
• [COALESCENT-31] - MLE (Exact) of theta for K69
• [COALESCENT-40] - MLE (Exact) of theta for KC64

Refactor

• [COALESCENT-20] - Builder and Provider-Impls Updated
• [COALESCENT-27] - BigDecimal in Statistic

Task

• [COALESCENT-41] - GeneTree Test Updated

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.

Data Life Cycle

1. When a job is run, the URL of the data set is given in the output 

   window.

2. Use Favorites to add the folder/file. Edit the data set and run 

   jobs using the drop-down data combo box.

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.

For Infinite-Sites Model

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Issues Commons 1.2.2:

Feature

• [COMMONS-61] - Likelihood with Estimators
• [COMMONS-62] - Compute Model Likelihood
• [COMMONS-63] - Model Estimation
• [COMMONS-67] - Key-Value Combo Builder Property

Task

• [COMMONS-53] - Model & Data Simulation Interface
• [COMMONS-64] - A StringList2 Provider: WHITE-SPACE
• [COMMONS-65] - A StringList Provider: WHITE-SPACE