Commit 7ace6193 authored by Elias Dohmen's avatar Elias Dohmen 🎓

initial commit

parents
# Compiled Object files
*.slo
*.lo
*.o
# Compiled Dynamic libraries
*.so
*.dylib
# Compiled Static libraries
*.lai
*.la
*.a
# Compiled source #
###################
*.com
*.class
*.dll
*.exe
*.o
*.so
# CMAKE PRODUCED FILES #
########################
build/
doc/html
# Latex helper files #
######################
*~
*.out
*.toc
*.backup
*.aux
*.log
*.dvi
*.toc
# Eclipse files #
#################
.cproject
.project
.settings
# Packages #
############
# it's better to unpack these files and commit the raw source
# git has its own built in compression methods
*.7z
*.dmg
*.gz
*.iso
*.jar
*.rar
*.tar
*.zip
# Logs and databases #
######################
*.log
*.sql
*.sqlite
# OS generated files #
######################
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
Icon?
ehthumbs.db
Thumbs.db
[submodule "libs/BioSeqDataLib"]
path = libs/BioSeqDataLib
url = https://ebbgit.uni-muenster.de/domainWorld/BioSeqDataLib.git
cmake_minimum_required(VERSION 2.6)
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
message(STATUS "Setting build type to 'Release' as none was specified.")
set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
endif()
project (domRates C CXX)
if (UNIX)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wunreachable-code -Wall -pedantic -Wextra -Wunused -lpthread ")
set(Boost_USE_STATIC_LIBS OFF)
set(Boost_USE_MULTITHREADED OFF)
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.7")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x")
endif()
if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "4.6")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
endif()
endif()
endif(UNIX)
################################################
# find necessary libraries #
################################################
# boost
FIND_PACKAGE(Boost 1.46 COMPONENTS system program_options filesystem iostreams REQUIRED)
INCLUDE_DIRECTORIES(SYSTEM ${Boost_INCLUDE_DIR})
link_directories(${Boost_LIBRARY_DIRS})
ADD_DEFINITIONS( "-DHAS_BOOST" )
# OpenMP
find_package(OpenMP)
if (OPENMP_FOUND)
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
endif()
################################################
# domRates #
################################################
include_directories(${CMAKE_CURRENT_BINARY_DIR})
set (BSDL_PATH ./libs/BioSeqDataLib/src/)
set (BSDL_src ${BSDL_PATH}/external/Input.cpp ${BSDL_PATH}/external/Output.cpp ${BSDL_PATH}/domain/Domain.cpp ${BSDL_PATH}/domain/PfamDomain.cpp ${BSDL_PATH}/domain/DomainExt.cpp ${BSDL_PATH}/domain/SFDomain.cpp ${BSDL_PATH}/domain/DomainArrangement.cpp ${BSDL_PATH}/domain/DomainArrangementSet.cpp ${BSDL_PATH}/phylogeny/PhylogeneticTree.cpp ${BSDL_PATH}/phylogeny/fitch.cpp ${BSDL_PATH}/phylogeny/dollo.cpp ${BSDL_PATH}/utility/stringHelpers.cpp)
SET(domRates_src src/domRates.cpp ${BSDL_src})
SET(domRates_exe domRates)
ADD_EXECUTABLE(${domRates_exe} ${domRates_src})
target_link_libraries(${domRates_exe}
${Boost_LIBRARIES}
)
domRates
=========
Requirements
------------
We try to keep the dependencies as little as possible. Current dependencies are:
- BioSeqDataLib
- boost
- OpenMP (optional for multi-thread support)
Installation
------------
Change into the domRates and run the follwing commands:
`mkdir build
cd build
cmake ..
make`
Problems, Bugs & Suggestions
----------------------------
We try our best not to have any bugs in the code, unfortunately some will
probably avoid us. If you encounter one, please be so kind and let us know. The
easiest way would be to use the issue webpage of the gitlab repository:
http://ebbgit.uni-muenster.de/ckeme_01/domRates/issues
If you have any questions/suggestions please contact
Carsten Kemena (c.kemena[ at ]uni-muenster.de).
Developers
----------
Please stick to the format (intention etc.) used in this project. Please
document each function using doxygen and write a unit test using the Boost
framework.
\ No newline at end of file
Subproject commit 682f82828c443b1f3849c5e954ea5c86cebd0c69
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