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# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
if ( Java_FOUND )
include(UseJava)
########################################
# ngs-java.jar
# java API
set( NGS_SRC
ngs/ErrorMsg.java
ngs/Statistics.java
ngs/Fragment.java
ngs/FragmentIterator.java
ngs/Read.java
ngs/ReadIterator.java
ngs/ReadGroup.java
ngs/ReadGroupIterator.java
ngs/Alignment.java
ngs/AlignmentIterator.java
ngs/PileupEvent.java
ngs/PileupEventIterator.java
ngs/Pileup.java
ngs/PileupIterator.java
ngs/Reference.java
ngs/ReferenceIterator.java
ngs/ReadCollection.java
ngs/Package.java
)
# java language bindings
set( ITF_SRC
ngs/itf/Refcount.java
ngs/itf/StatisticsItf.java
ngs/itf/FragmentItf.java
ngs/itf/FragmentIteratorItf.java
ngs/itf/ReadItf.java
ngs/itf/ReadIteratorItf.java
ngs/itf/ReadGroupItf.java
ngs/itf/ReadGroupIteratorItf.java
ngs/itf/AlignmentItf.java
ngs/itf/AlignmentIteratorItf.java
ngs/itf/PileupEventItf.java
ngs/itf/PileupEventIteratorItf.java
ngs/itf/PileupItf.java
ngs/itf/PileupIteratorItf.java
ngs/itf/ReferenceItf.java
ngs/itf/ReferenceIteratorItf.java
ngs/itf/ReadCollectionItf.java
)
# NCBI engine bindings
set( NCBI_SRC
gov/nih/nlm/ncbi/ngs/DownloadManager.java
gov/nih/nlm/ncbi/ngs/FileCreator.java
gov/nih/nlm/ncbi/ngs/HttpManager.java
gov/nih/nlm/ncbi/ngs/LibDependencies.java
gov/nih/nlm/ncbi/ngs/LibManager.java
gov/nih/nlm/ncbi/ngs/LibPathIterator.java
gov/nih/nlm/ncbi/ngs/LibVersionChecker.java
gov/nih/nlm/ncbi/ngs/LMProperties.java
gov/nih/nlm/ncbi/ngs/Logger.java
gov/nih/nlm/ncbi/ngs/Manager.java
gov/nih/nlm/ncbi/ngs/NGS.java
gov/nih/nlm/ncbi/ngs/Version.java
gov/nih/nlm/ncbi/ngs/error/LibraryLoadError.java
gov/nih/nlm/ncbi/ngs/error/LibraryNotFoundError.java
gov/nih/nlm/ncbi/ngs/error/LibraryIncompatibleVersionError.java
gov/nih/nlm/ncbi/ngs/error/cause/ConnectionProblemCause.java
gov/nih/nlm/ncbi/ngs/error/cause/DownloadDisabledCause.java
gov/nih/nlm/ncbi/ngs/error/cause/InvalidLibraryCause.java
gov/nih/nlm/ncbi/ngs/error/cause/JvmErrorCause.java
gov/nih/nlm/ncbi/ngs/error/cause/LibraryLoadCause.java
gov/nih/nlm/ncbi/ngs/error/cause/OutdatedJarCause.java
gov/nih/nlm/ncbi/ngs/error/cause/PrereleaseReqLibCause.java
gov/nih/nlm/ncbi/ngs/error/cause/UnsupportedArchCause.java
)
find_package(JNI)
if ( JNI_FOUND )
add_jar( ngs-java
SOURCES ${NGS_SRC} ${ITF_SRC} ${NCBI_SRC}
OUTPUT_DIR ${CMAKE_JAR_OUTPUT_DIRECTORY}
GENERATE_NATIVE_HEADERS ngs-jni-headers DESTINATION ./jni
)
else()
add_jar( ngs-java
SOURCES ${NGS_SRC} ${ITF_SRC} ${NCBI_SRC}
OUTPUT_DIR ${CMAKE_JAR_OUTPUT_DIRECTORY}
)
endif()
install_jar( ngs-java ${CMAKE_INSTALL_PREFIX}/jar/ )
#TODO: add symlinks
########################################
# examples
add_subdirectory( examples )
########################################
# javadoc
if ( Java_JAVADOC_EXECUTABLE )
create_javadoc( ngs-doc
PACKAGES gov.nih.nlm.ncbi.ngs ngs
SOURCEPATH ${CMAKE_CURRENT_SOURCE_DIR}
)
foreach(f ${NGS_SRC})
set(SRC_FILES "${SRC_FILES} ${f}")
endforeach()
foreach(f ${ITF_SRC})
set(SRC_FILES "${SRC_FILES} ${f}")
endforeach()
foreach(f ${NCBI_SRC})
set(SRC_FILES "${SRC_FILES} ${f}")
endforeach()
set( NGS_JAVADOC_DIR ${CMAKE_BINARY_DIR}/ngs/ngs-java/javadoc/ngs-doc )
if ( Java_JAR_EXECUTABLE AND NOT (${OS} STREQUAL "windows") )
add_custom_target(
ngs-doc-jar ALL COMMAND
sh -c "${Java_JAR_EXECUTABLE} -cf ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-doc.jar ."
DEPENDS ngs-doc_javadoc
WORKING_DIRECTORY ${NGS_JAVADOC_DIR}
)
install( FILES ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-doc.jar DESTINATION ${CMAKE_INSTALL_PREFIX}/jar/ )
add_custom_target(
ngs-src-jar ALL COMMAND
sh -c "${Java_JAR_EXECUTABLE} -cf ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-src.jar ${SRC_FILES}"
DEPENDS ngs-doc_javadoc
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
)
install( FILES ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-src.jar DESTINATION ${CMAKE_INSTALL_PREFIX}/jar/ )
elseif ( Java_JAR_EXECUTABLE AND ${OS} STREQUAL "windows" )
add_custom_target(
ngs-doc-jar ALL COMMAND
"${Java_JAR_EXECUTABLE}" -cf "${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-doc.jar" .
DEPENDS ngs-doc_javadoc
WORKING_DIRECTORY ${NGS_JAVADOC_DIR}
)
install( FILES ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-doc.jar DESTINATION ${CMAKE_INSTALL_PREFIX}/jar/ )
# https://jira.ncbi.nlm.nih.gov/browse/VDB-4761 - temporarily disabling
# add_custom_target(
# ngs-src-jar ALL COMMAND
# "${Java_JAR_EXECUTABLE}" -cf "${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-src.jar" ${SRC_FILES}
# WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
# )
# install( FILES ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-src.jar DESTINATION ${CMAKE_INSTALL_PREFIX}/jar/ )
endif()
endif()
endif()
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