Name:           phybin
Version:        0.3
License: BSD3
License-file:   LICENSE
Stability: Beta
Author:			Ryan Newton <rrnewton@gmail.com>
Maintainer:		Ryan Newton <rrnewton@gmail.com>


-- Version history:
-- 0.1.2   -- first significant release
-- 0.1.2.1 -- 
-- 0.1.2.4 -- new release, several new features
-- 0.1.2.5 -- bump for graphviz API changes
-- 0.2 -- Add Robinson-Foulds distance, use Int labels.
-- 0.2.2 -- misc changes and expose library
-- 0.2.4 -- add consensus trees
-- 0.2.6 -- colorization, hashrf, misc improvements
-- 0.2.7 -- Add command line opt --showtrees
-- 0.2.8 -- Add command line opt --highlight
-- 0.2.9 -- Add command line opt --interior
-- 0.2.10 -- Add command line opt --matching
-- 0.2.11 -- Cleanup and windows compatibility.
-- 0.3    -- significant improvements and new functionality.

-- homepage: http://code.haskell.org/phybin
-- homepage: http://people.csail.mit.edu/newton/phybin/
homepage: http://www.cs.indiana.edu/~rrnewton/projects/phybin/

Copyright: Copyright (c) 2010 Ryan Newton
Synopsis: Utility for clustering phylogenetic trees in Newick format based on Robinson-Foulds distance.
Description: 
   This package provides a libary and executable for dealing with Newick tree files.
   .
   It can do simple binning of identical trees or more complex clustering based on 
   an all-to-all Robinson-Foulds distance matrix.
   .
   phybin produces output files that characterize the size and contents of each bin or cluster (including
   generating GraphViz-based visual representations of the tree topologies).

Category: Bioinformatics
Cabal-Version: >= 1.8

Extra-source-files: README.md

Build-type: Simple

Source-repository head
  type:     git
  location: git://github.com/rrnewton/PhyBin.git

Flag hashrf
  description: Use the HashRF algorithm by default instead of the naive one.
  default: True

Flag bitvec
  description: Use bitvectors rather than IntSets for bipartitions.
  default: False

Flag sequential
  description: Don't use any parallelism at all.
  default: False

Library
  Exposed-modules:   Bio.Phylogeny.PhyBin
                     Bio.Phylogeny.PhyBin.Binning
                     Bio.Phylogeny.PhyBin.CoreTypes                     
                     Bio.Phylogeny.PhyBin.Parser
                     Bio.Phylogeny.PhyBin.PreProcessor
                     Bio.Phylogeny.PhyBin.RFDistance  
                     Bio.Phylogeny.PhyBin.Util
                     Bio.Phylogeny.PhyBin.Visualize
  -- Data.BitList
  Build-Depends:     base >= 3 && < 5, directory, process, containers, 
                     async, time,
                     filepath, 
                     graphviz >= 2999.16, 
                     text >= 0.11 && < 0.12,
                     prettyclass, fgl,
                     HUnit, bytestring, 
                     -- For bytestring.lazy support:
                     parsec >= 3.1.0, 
                     vector >= 0.10,
                     hierarchical-clustering >= 0.4, split >= 0.2
--                     lattice-par, 
  GHC-Options: -O2 -funbox-strict-fields -rtsopts

  if flag(hashrf)
     CPP-Options: -DUSE_HASHRF
  if flag(bitvec)
     CPP-Options: -DBITVEC_BIPS
     Build-Depends:  bitvec >= 0.1
  if flag(sequential)
     CPP-Options: -DSEQUENTIALIZE

Executable phybin
  Main-is:           Main.hs
  Build-Depends:     phybin
  -- DUPLICATE:
  Build-Depends:     base >= 3 && < 5, directory, process, containers, 
                     async, time,
                     filepath, 
                     graphviz >= 2999.16, 
                     text >= 0.11 && < 0.12,
                     prettyclass, fgl,
                     HUnit, bytestring, 
                     -- For bytestring.lazy support:
                     parsec >= 3.1.0, 
                     vector >= 0.10,
                     hierarchical-clustering >= 0.4, split >= 0.2
--                     lattice-par, 
  GHC-Options: -O2 -funbox-strict-fields -rtsopts -threaded

  if flag(hashrf)
     CPP-Options: -DUSE_HASHRF
  if flag(bitvec)
     CPP-Options: -DBITVEC_BIPS
     Build-Depends:  bitvec >= 0.1
  if flag(sequential)
     CPP-Options: -DSEQUENTIALIZE


-- DUPLICATED from executable:
Test-Suite test-phybin
  Main-is:           TestAll.hs
  Type:              exitcode-stdio-1.0
--  Build-Depends:     phybin
  Build-Depends:     base >= 3 && < 5, directory, process, containers, 
                     async, time,
                     filepath, 
                     graphviz >= 2999.16, 
                     text >= 0.11 && < 0.12,
                     prettyclass, fgl,
                     HUnit, bytestring, 
                     parsec >= 3.1.0, 
                     vector >= 0.10,
                     hierarchical-clustering >= 0.4, split >= 0.2
  -- Additional depends for test:
  Build-Depends:  HUnit, test-framework, test-framework-hunit, test-framework-th
  GHC-Options: -O2 -funbox-strict-fields -rtsopts -threaded

  if flag(hashrf)
     CPP-Options: -DUSE_HASHRF
  if flag(bitvec)
     CPP-Options: -DBITVEC_BIPS
     Build-Depends:  bitvec >= 0.1
  if flag(sequential)
     CPP-Options: -DSEQUENTIALIZE