armanbilge/B3

Issues

• Support an XML templating language

  #26 opened 10 years ago by armanbilge
  0

• Make main() methods into JUnit tests

  #25 opened 10 years ago by armanbilge
  0

• Using resume does not continue writing log file

  #24 opened 10 years ago by armanbilge
  1

• Reinforce separation of Likelihood vs. Model interfaces

  #11 opened 10 years ago by armanbilge
  0

• Deserialization for resume fails because plugins are not reloaded

  #23 opened 10 years ago by armanbilge
  0

• Create SimpleXMLObjectParser Automatically

  #20 opened 10 years ago by armanbilge
  0

• Potential bug where threads do not terminate

  #19 opened 10 years ago by armanbilge
  1

• Consider using JNA to interface with BEAGLE

  #22 opened 10 years ago by armanbilge
  0

• BeagleTreeLikelihood with multiple instances on multiple threads returns -Inf

  #21 opened 10 years ago by armanbilge
  1

• Clever initialization of epsilon/L for HamiltonUpdate

  #15 opened 10 years ago by armanbilge
  0

• Aggressive Initialization

  #16 opened 10 years ago by armanbilge
  0

• Improve Performance of State Serialization for Resume

  #18 opened 10 years ago by armanbilge
  0

• NumberFormatter is evil

  #17 opened 10 years ago by genomescale
  0

• Separate calculations and states in the framework

  #1 opened 10 years ago by walterxie
  0

• Replace Citable/Citation interface/class with annotation

  #10 opened 10 years ago by armanbilge
  0

• Log files created prematurely

  #13 opened 10 years ago by armanbilge
  0

• Serialization fails due to ConcurrentModificationException

  #14 opened 10 years ago by armanbilge
  0

• Simplify and merge tree classes

  #2 opened 10 years ago by walterxie
  0

• Merge beast.evomodel and beast.beagle

  #8 opened 10 years ago by armanbilge
  1

• Remove unused Interfaces, Classes, and Methods

  #12 opened 10 years ago by armanbilge
  0

• Remove references to BEAST from xml package

  #9 opened 10 years ago by armanbilge
  0

• Namespaces for XML parsers

  #7 opened 10 years ago by armanbilge
  0

• Use Dirichlet prior for frequencies and relative rates

  #6 opened 10 years ago by armanbilge
  0

• Don't require a tree to call functions on Nodes

  #5 opened 10 years ago by armanbilge
  0

• Merge Coalescent Populations with Coalescent Population Models

  #4 opened 10 years ago by walterxie
  0

• Incompatibility to BEAST 1

  #3 opened 10 years ago by walterxie
  0