# CMake script for Bio++ Sequence Library
# Author: Sylvain Gaillard and Julien Dutheil
# Created: 30/07/2012

# File list
SET(CPP_FILES
  Bpp/Seq/Io/Fastq.cpp
  Bpp/Seq/Io/Maf/MafParser.cpp
  Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.cpp
  Bpp/Seq/Io/Maf/MafIterator.cpp
  Bpp/Seq/Io/Maf/SequenceFilterMafIterator.cpp
  Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.cpp
  Bpp/Seq/Io/Maf/ChromosomeMafIterator.cpp
  Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.cpp
  Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp
  Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp
  Bpp/Seq/Io/Maf/FullGapFilterMafIterator.cpp
  Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
  Bpp/Seq/Io/Maf/EntropyFilterMafIterator.cpp
  Bpp/Seq/Io/Maf/MaskFilterMafIterator.cpp
  Bpp/Seq/Io/Maf/QualityFilterMafIterator.cpp
  Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp
  Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp
  Bpp/Seq/Io/Maf/OutputMafIterator.cpp
  Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp
  Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp
  Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.cpp
  Bpp/Seq/Io/Maf/WindowSplitMafIterator.cpp
  Bpp/Seq/Io/Maf/MafSequence.cpp
  Bpp/Seq/Io/Maf/MafStatistics.cpp
  Bpp/Seq/Io/Maf/IterationListener.cpp
  Bpp/Seq/Feature/SequenceFeature.cpp
  Bpp/Seq/Feature/SequenceFeatureTools.cpp
  Bpp/Seq/Feature/Gff/GffFeatureReader.cpp
  Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp
  )

SET(H_FILES
  Bpp/Seq/Io/Fastq.h
  Bpp/Seq/Io/Maf/MafSequence.h
  Bpp/Seq/Io/Maf/MafParser.h
  Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.h
  Bpp/Seq/Io/Maf/MafIterator.h
  Bpp/Seq/Io/Maf/BlockLengthMafIterator.h
  Bpp/Seq/Io/Maf/BlockSizeMafIterator.h
  Bpp/Seq/Io/Maf/SequenceFilterMafIterator.h
  Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.h
  Bpp/Seq/Io/Maf/ChromosomeMafIterator.h
  Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.h
  Bpp/Seq/Io/Maf/BlockMergerMafIterator.h
  Bpp/Seq/Io/Maf/ConcatenateMafIterator.h
  Bpp/Seq/Io/Maf/FullGapFilterMafIterator.h
  Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h
  Bpp/Seq/Io/Maf/EntropyFilterMafIterator.h
  Bpp/Seq/Io/Maf/MaskFilterMafIterator.h
  Bpp/Seq/Io/Maf/QualityFilterMafIterator.h
  Bpp/Seq/Io/Maf/FeatureFilterMafIterator.h
  Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h
  Bpp/Seq/Io/Maf/OutputMafIterator.h
  Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h
  Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
  Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.h
  Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
  Bpp/Seq/Io/Maf/MafStatistics.h
  Bpp/Seq/Io/Maf/IterationListener.h
  Bpp/Seq/Feature/SequenceFeature.h
  Bpp/Seq/Feature/SequenceFeatureTools.h
  Bpp/Seq/Feature/FeatureReader.h
  Bpp/Seq/Feature/Gff/GffFeatureReader.h
  Bpp/Seq/Feature/Gtf/GtfFeatureReader.h
  )

# Build the static lib
ADD_LIBRARY(bppseqomics-static STATIC ${CPP_FILES})
SET_TARGET_PROPERTIES(bppseqomics-static
  PROPERTIES OUTPUT_NAME bpp-seq-omics
  CLEAN_DIRECT_OUTPUT 1
  )
TARGET_LINK_LIBRARIES(bppseqomics-static ${LIBS})

# Build the shared lib
ADD_LIBRARY(bppseqomics-shared SHARED ${CPP_FILES})
SET_TARGET_PROPERTIES(bppseqomics-shared
  PROPERTIES OUTPUT_NAME bpp-seq-omics
  CLEAN_DIRECT_OUTPUT 1
  VERSION ${BPPSEQOMICS_VERSION}
  SOVERSION ${BPPSEQOMICS_VERSION_MAJOR}
  )
TARGET_LINK_LIBRARIES(bppseqomics-shared ${LIBS})

# Install libs
INSTALL(TARGETS bppseqomics-static bppseqomics-shared DESTINATION lib${LIB_SUFFIX})

# Install headers
INSTALL(DIRECTORY Bpp/ DESTINATION include/Bpp FILES_MATCHING PATTERN "*.h")

# Generate generic include files (.all)
INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_SOURCE_DIR}/genIncludes.sh ${CMAKE_PREFIX_PATH}/include/Bpp)")