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@melkebir
melkebir committed Mar 27, 2015
1 parent a0de71f commit 5d33b83
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10 changes: 10 additions & 0 deletions .gitignore
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*.exe
*.out
*.app

# Mac stuff
.DS_Store

# Python things
*.pyc

# Build directory
build/
src/config.h
294 changes: 294 additions & 0 deletions CMakeLists.txt
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cmake_minimum_required( VERSION 2.8 )

project( AncesTree )

set( analyse_solution_prob_hdr
src/utils.h
src/matrix.h
src/ppmatrix.h
src/realmatrix.h
src/maxsolution.h
src/solutiongraph.h
src/clonaltree.h
src/ancestrymatrix.h
src/baseancestrygraph.h
src/probancestrygraph.h
src/readcountmatrix.h
src/realintervalmatrix.h
src/probcomparison.h
)

set( analyse_solution_prob_src
src/analysesolutionprob.cpp
src/utils.cpp
src/matrix.cpp
src/ppmatrix.cpp
src/realmatrix.cpp
src/maxsolution.cpp
src/solutiongraph.cpp
src/clonaltree.cpp
src/ancestrymatrix.cpp
src/baseancestrygraph.cpp
src/probancestrygraph.cpp
src/readcountmatrix.cpp
src/realintervalmatrix.cpp
src/probcomparison.cpp
)

set( analyse_solution_hdr
src/utils.h
src/matrix.h
src/ppmatrix.h
src/realmatrix.h
src/maxsolution.h
src/solutiongraph.h
src/clonaltree.h
src/ancestrymatrix.h
src/baseancestrygraph.h
src/probancestrygraph.h
src/readcountmatrix.h
src/realintervalmatrix.h
src/comparison.h
)

set( analyse_solution_src
src/analysesolution.cpp
src/utils.cpp
src/matrix.cpp
src/ppmatrix.cpp
src/realmatrix.cpp
src/maxsolution.cpp
src/solutiongraph.cpp
src/clonaltree.cpp
src/ancestrymatrix.cpp
src/baseancestrygraph.cpp
src/probancestrygraph.cpp
src/readcountmatrix.cpp
src/realintervalmatrix.cpp
src/comparison.cpp
)

set( visualize_solution_src
src/visualizesolution.cpp
src/utils.cpp
src/matrix.cpp
src/ppmatrix.cpp
src/realmatrix.cpp
src/maxsolution.cpp
src/solutiongraph.cpp
src/clonaltree.cpp
)

set( visualize_solution_hdr
src/utils.h
src/matrix.h
src/ppmatrix.h
src/realmatrix.h
src/maxsolution.h
src/solutiongraph.h
src/clonaltree.h
)

set( analyse_src
src/analyse.cpp
src/probancestrygraph.cpp
src/baseancestrygraph.cpp
src/ancestrymatrix.cpp
src/utils.cpp
src/matrix.cpp
src/readcountmatrix.cpp
src/realintervalmatrix.cpp
src/realmatrix.cpp
)

set( analyse_hdr
src/probancestrygraph.h
src/baseancestrygraph.h
src/ancestrymatrix.h
src/utils.h
src/matrix.h
src/readcountmatrix.h
src/realintervalmatrix.h
src/realmatrix.h
)

set( ancestree_ilp_src
src/ancestreeilp.cpp
src/intmaxilpsolver.cpp
src/probancestrygraph.cpp
src/baseancestrygraph.cpp
src/ancestrymatrix.cpp
src/utils.cpp
src/matrix.cpp
src/ppmatrix.cpp
src/realmatrix.cpp
src/realintervalmatrix.cpp
src/readcountmatrix.cpp
src/maxsolution.cpp
src/clonaltree.cpp
)

set( ancestree_ilp_hdr
src/intmaxilpsolver.h
src/probancestrygraph.h
src/ancestrymatrix.h
src/baseancestrygraph.h
src/utils.h
src/matrix.h
src/ppmatrix.h
src/realmatrix.h
src/realintervalmatrix.h
src/readcountmatrix.h
src/maxsolution.h
src/clonaltree.h
)

set( constructancestrymatrix_src
src/constructancestrymatrix.cpp
src/utils.cpp
src/readcountmatrix.cpp
src/matrix.cpp
src/ancestrymatrix.cpp
src/realintervalmatrix.cpp
src/realmatrix.cpp
)

set( constructancestrymatrix_hdr
src/utils.h
src/readcountmatrix.h
src/matrix.h
src/realintervalmatrix.h
src/realmatrix.h
src/ancestrymatrix.h
)

set( ancestree_src
src/ancestree.cpp
src/solutiongraph.cpp
src/intmaxilpsolver.cpp
src/probancestrygraph.cpp
src/baseancestrygraph.cpp
src/ppmatrix.cpp
src/maxsolution.cpp
src/clonaltree.cpp
src/utils.cpp
src/readcountmatrix.cpp
src/matrix.cpp
src/realintervalmatrix.cpp
src/realmatrix.cpp
src/ancestrymatrix.cpp
)

set( ancestree_hdr
src/solutiongraph.h
src/intmaxilpsolver.h
src/probancestrygraph.h
src/baseancestrygraph.h
src/ppmatrix.h
src/maxsolution.h
src/clonaltree.h
src/utils.h
src/readcountmatrix.h
src/matrix.h
src/realintervalmatrix.h
src/realmatrix.h
src/ancestrymatrix.h
src/config.h
)

set( LIBLEMON_ROOT "$ENV{HOME}/lemon" CACHE PATH "Additional search directory for lemon library" )

set( GitCommand1 "symbolic-ref HEAD 2> /dev/null | cut -b 12-" )
execute_process( COMMAND git symbolic-ref HEAD WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
COMMAND tail -c -7 COMMAND tr -d "\\n" OUTPUT_VARIABLE GitBranch )
set( GitCommand2 "log --pretty=format:\\\"%h\\\" -1" )
execute_process( COMMAND git log --pretty=format:%h WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
COMMAND head -n 1 COMMAND tr -d "\\n" OUTPUT_VARIABLE GitHashtag )
set( ANCESTREE_VERSION \"${GitBranch}-${GitHashtag}\" )

set( Boost_USE_STATIC_LIBS ON )
find_package( Boost REQUIRED )

if( NOT CPLEX_INC_DIR OR NOT CPLEX_LIB_DIR OR NOT CONCERT_INC_DIR OR NOT CONCERT_LIB_DIR )
set( CPLEX_AUTODETECTION_PREFIXES "$ENV{HOME}/ILOG;/opt/ibm/ILOG;$ENV{HOME}/Applications/IBM/ILOG" CACHE STRING "CPLEX automatic lookup directories" )
foreach( CplexInstallPrefix ${CPLEX_AUTODETECTION_PREFIXES} )
file( GLOB_RECURSE CplexLibraryPaths ${CplexInstallPrefix}/*/cplex/lib/*/libcplex.a )
if( CplexLibraryPaths )
list( LENGTH CplexLibraryPaths NumPath )
if( NumPath GREATER 1 )
message( WARNING "Found multiple CPLEX installations in ${CplexInstallPrefix}, automatically selecting the first one, please set {CPLEX|CONCERT}_{INC|LIB}_DIR manually if this is not the right selection" )
else()
message( "Found CPLEX's installation in ${CPlexInstallPrefix}" )
endif()
list( GET CplexLibraryPaths 0 CplexLibraryPath )

set( MyRegex "${CplexInstallPrefix}/(.*)/cplex/?/lib/(.*)/libcplex.a" )
string( REGEX MATCH "${MyRegex}" ValidatedCplexLibPath ${CplexLibraryPath} )
if( NOT ValidatedCplexLibPath )
message( WARNING "Unable to recognize ${CplexLibraryPath} as a valid CPLEX path" )
else()
string( REGEX REPLACE "${MyRegex}" "\\1" CplexHome ${ValidatedCplexLibPath} )
string( REGEX REPLACE "${MyRegex}" "\\2" CplexArch ${ValidatedCplexLibPath} )

set( CPLEX_INC_DIR "${CplexInstallPrefix}/${CplexHome}/cplex/include" CACHE PATH "CPLEX's include dir" )
set( CPLEX_LIB_DIR "${CplexInstallPrefix}/${CplexHome}/cplex/lib/${CplexArch}" CACHE PATH "CPLEX's library dir" )
set( CONCERT_INC_DIR "${CplexInstallPrefix}/${CplexHome}/concert/include" CACHE PATH "Concert's include dir" )
set( CONCERT_LIB_DIR "${CplexInstallPrefix}/${CplexHome}/concert/lib/${CplexArch}" CACHE PATH "Concert's library dir" )

break()
endif()
else()
message( "Unable to find CPLEX and Concert installation in ${CplexInstallPrefix}" )
endif()
endforeach()

if( NOT CPLEX_INC_DIR OR NOT CPLEX_LIB_DIR OR NOT CONCERT_INC_DIR OR NOT CONCERT_LIB_DIR )
message( "Unable to autodeted CPLEX's and Concert's installation directories, please set {CPLEX|CONCERT}_{INC|LIB}_DIR manually" )
else()
message( "Autodetected CPLEX's include dir : ${CPLEX_INC_DIR}" )
message( "Autodetected CPLEX's library dir : ${CPLEX_LIB_DIR}" )
message( "Autodetected Concert's include dir : ${CONCERT_INC_DIR}" )
message( "Autodetected Concert's library dir : ${CONCERT_LIB_DIR}" )
endif()
endif()

SET(CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LIBRARY "libstdc++")
add_definitions( -DIL_STD )
configure_file( src/config.h.in ${PROJECT_SOURCE_DIR}/src/config.h )

if( ${CMAKE_SYSTEM_NAME} MATCHES "Darwin" )
set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++ " )
endif()

include_directories( ${CPLEX_INC_DIR} ${CONCERT_INC_DIR} "${LIBLEMON_ROOT}/include" "src" ${Boost_INCLUDE_DIRS} )
link_directories( ${CPLEX_LIB_DIR} ${CONCERT_LIB_DIR} "${LIBLEMON_ROOT}/lib" )

set( CommonLibs
m
ilocplex
cplex
concert
pthread
emon
)

add_executable( analyse_solution ${analyse_solution_src} ${analyse_solution_hdr} )
target_link_libraries( analyse_solution ${CommonLibs} )

add_executable( analyse_solution_prob ${analyse_solution_prob_src} ${analyse_solution_prob_hdr} )
target_link_libraries( analyse_solution_prob ${CommonLibs} )

add_executable( visualize_solution ${visualize_solution_src} ${visualize_solution_hdr} )
target_link_libraries( visualize_solution ${CommonLibs} )

add_executable( construct_ancestry_matrix ${constructancestrymatrix_src} ${constructancestrymatrix_hdr} )
target_link_libraries( construct_ancestry_matrix ${CommonLibs} )

add_executable( analyse EXCLUDE_FROM_ALL ${analyse_src} ${analyse_hdr} )
target_link_libraries( analyse ${CommonLibs} )

add_executable( ancestree_ilp ${ancestree_ilp_src} ${ancestree_ilp_hdr} )
target_link_libraries( ancestree_ilp ${CommonLibs} )

add_executable( ancestree ${ancestree_src} ${ancestree_hdr} )
target_link_libraries( ancestree ${CommonLibs} )

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