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|
project (jGraphMolJava Java)
include_directories( ${RDKit_ExternalDir} )
find_package(Java REQUIRED)
find_package(JNI REQUIRED)
# Make sure we can access the junit.jar -- needed for compiling/running tests
find_file(JUNIT_JAR junit.jar ${RDKit_JavaLibDir})
if (NOT JUNIT_JAR)
MESSAGE ("junit.jar is not found in ${RDKit_JavaLibDir}. Please add it to this directory and rerun cmake.")
MESSAGE(FATAL_ERROR "Cannot find required JUnit library (junit.jar)")
endif (NOT JUNIT_JAR)
# Likewise for javadoc
find_program(JAVADOC_EXE javadoc PATH _JAVA_PATHS _JAVA_HINTS /usr/bin /usr/local/bin)
if (NOT JAVADOC_EXE)
MESSAGE ("javadoc (executable) is not found. Please add it to PATH and rerun cmake.")
MESSAGE(FATAL_ERROR "Cannot find required javadoc executable (javadoc)")
endif (NOT JAVADOC_EXE)
INCLUDE_DIRECTORIES(${JNI_INCLUDE_DIRS})
SET_SOURCE_FILES_PROPERTIES(GraphMolJava.i PROPERTIES CPLUSPLUS ON )
FILE(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../*.java COPY_SOURCE)
FILE(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/org/RDKit COPY_DEST)
# Setup a few variables for environment-specific things
if(WIN32)
ADD_DEFINITIONS("/W3 /wd4716 /bigobj")
SET(PATH_SEP ";")
SET(COPY_CMD xcopy ${COPY_SOURCE} ${COPY_DEST} /Y /I)
else()
SET(PATH_SEP ":")
SET(COPY_CMD cp -p ${COPY_SOURCE} ${COPY_DEST})
endif()
# Coax SWIG into playing nicely with Apple environments
if(APPLE)
SET(CMAKE_SIZEOF_VOID_P 4)
endif(APPLE)
if(CMAKE_SIZEOF_VOID_P MATCHES 4)
SET(CMAKE_SWIG_FLAGS -package "org.RDKit")
else()
SET(CMAKE_SWIG_FLAGS -package "org.RDKit" "-DSWIGWORDSIZE64")
endif()
SET(CMAKE_SWIG_OUTDIR ${CMAKE_CURRENT_SOURCE_DIR}/src/org/RDKit )
if(RDK_BUILD_INCHI_SUPPORT)
SET(CMAKE_SWIG_FLAGS "-DBUILD_INCHI_SUPPORT" ${CMAKE_SWIG_FLAGS} )
endif()
if(RDK_BUILD_AVALON_SUPPORT)
SET(CMAKE_SWIG_FLAGS "-DBUILD_AVALON_SUPPORT" ${CMAKE_SWIG_FLAGS} )
endif()
# enable this line to build the ErrorGenerator class for testing handling of C++ errors in the JNI layer
#SET(CMAKE_SWIG_FLAGS ${CMAKE_SWIG_FLAGS} "-D INCLUDE_ERROR_GENERATOR" )
FILE(GLOB SWIG_SRC_FILES "${CMAKE_CURRENT_SOURCE_DIR}/../*.i")
# we added all source files, now remove the ones that we're not supporting in this build:
if(NOT RDK_BUILD_AVALON_SUPPORT)
LIST(REMOVE_ITEM SWIG_SRC_FILES "${CMAKE_CURRENT_SOURCE_DIR}/../AvalonLib.i")
endif()
if(NOT RDK_BUILD_INCHI_SUPPORT)
LIST(REMOVE_ITEM SWIG_SRC_FILES "${CMAKE_CURRENT_SOURCE_DIR}/../Inchi.i")
endif()
SET(SWIG_MODULE_GraphMolWrap_EXTRA_DEPS ${SWIG_SRC_FILES} )
SWIG_ADD_MODULE(GraphMolWrap "java" GraphMolJava.i )
SWIG_LINK_LIBRARIES(GraphMolWrap ${RDKit_Wrapper_Libs} )
# code adapted from the wrapper code for
# GDCM: http://gdcm.svn.sf.net/viewvc/gdcm/trunk/Wrapping/Java/CMakeLists.txt?view=markup
ADD_CUSTOM_COMMAND(
OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar
## Add in our own Java sources
#COMMAND ${COPY_CMD}
## 1. run this custom command only after swig has been run.
COMMAND ${JAVA_COMPILE} -d build "src/org/RDKit/*.java"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
## 2. now that the *.class have been generated construct the jar file.
COMMAND ${JAVA_ARCHIVE} cf
${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar -C ${CMAKE_CURRENT_SOURCE_DIR}/build
org/RDKit
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
#DEPENDS GraphMolWrap
DEPENDS "${swig_generated_file_fullname}"
COMMENT "javac *.java; jar cf -> .jar"
OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKitDoc.jar
## Run Javadoc against newly created .java files to create docs
COMMAND ${JAVADOC_EXE} -tag notes -tag example -d ${CMAKE_CURRENT_SOURCE_DIR}/doc -sourcepath ${CMAKE_CURRENT_SOURCE_DIR}/src org.RDKit
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
## Put the doc files into their own separate archive.
COMMAND ${JAVA_ARCHIVE} cf
${CMAKE_CURRENT_SOURCE_DIR}/org.RDKitDoc.jar
doc
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
#DEPENDS GraphMolWrap
DEPENDS "${swig_generated_file_fullname}"
COMMENT "jar cf org.RDKitDoc.jar -d doc"
)
ADD_CUSTOM_TARGET(GraphMolWrapJar ALL
DEPENDS GraphMolWrap ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar
COMMENT "building jar"
)
## Tests -- note that building/rebuilding them keys on the file WrapperTests.class
SET(CMAKE_JAVA_TEST_OUTDIR ${CMAKE_CURRENT_SOURCE_DIR}/build-test )
FILE(GLOB JAVA_TEST_FILES "${CMAKE_CURRENT_SOURCE_DIR}/src-test/org/RDKit/*.java")
# we added all source files, now remove the ones that we're not supporting in this build:
if(NOT RDK_BUILD_AVALON_SUPPORT)
LIST(REMOVE_ITEM JAVA_TEST_FILES "${CMAKE_CURRENT_SOURCE_DIR}/src-test/org/RDKit/AvalonLibTests.java")
endif()
if(NOT RDK_BUILD_INCHI_SUPPORT)
LIST(REMOVE_ITEM JAVA_TEST_FILES "${CMAKE_CURRENT_SOURCE_DIR}/src-test/org/RDKit/InchiTests.java")
endif()
ADD_CUSTOM_COMMAND(
OUTPUT ${CMAKE_JAVA_TEST_OUTDIR}/org/RDKit/WrapperTests.class
COMMAND ${JAVA_COMPILE} -d ${CMAKE_JAVA_TEST_OUTDIR} -cp "${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar${PATH_SEP}${JUNIT_JAR}" ${JAVA_TEST_FILES}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar ${JAVA_TEST_FILES}
)
ADD_CUSTOM_TARGET(BuildJavaWrapperTests ALL
DEPENDS ${CMAKE_JAVA_TEST_OUTDIR}/org/RDKit/WrapperTests.class GraphMolWrap
COMMENT "building test classes"
)
ADD_CUSTOM_TARGET(RunJavaWrapperTests
DEPENDS BuildJavaWrapperTests
COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/runUnitTests.sh
)
ADD_TEST(JavaAromaticTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.AromaticTests)
ADD_TEST(JavaAtomPairsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.AtomPairsTests)
ADD_TEST(JavaBasicMoleculeTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.BasicMoleculeTests)
ADD_TEST(JavaBasicMolecule2Tests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.BasicMolecule2Tests)
ADD_TEST(JavaChemAtomTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ChemAtomTests)
ADD_TEST(JavaChemBondTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ChemBondTests)
ADD_TEST(JavaChemReactionTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ChemReactionTests)
ADD_TEST(JavaChemSmartsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ChemSmartsTests)
ADD_TEST(JavaChemTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ChemTests)
ADD_TEST(JavaChemv2Tests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.Chemv2Tests)
ADD_TEST(JavaConformerTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ConformerTests)
ADD_TEST(JavaDescriptorTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.DescriptorTests)
ADD_TEST(JavaDistanceGeometryTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.DistanceGeometryTests)
ADD_TEST(JavaErrorHandlingTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ErrorHandlingTests)
ADD_TEST(JavaFingerprintsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.FingerprintsTests)
ADD_TEST(JavaForceFieldsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ForceFieldsTests)
ADD_TEST(JavaHManipulationsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.HManipulationsTests)
ADD_TEST(JavaLipinskiTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.LipinskiTests)
ADD_TEST(JavaPicklingTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.PicklingTests)
ADD_TEST(JavaSmilesCreationTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.SmilesCreationTests)
ADD_TEST(JavaSmilesDetailsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.SmilesDetailsTests)
ADD_TEST(JavaSmilesTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.SmilesTests)
ADD_TEST(JavaSuppliersTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.SuppliersTests)
ADD_TEST(JavaWrapperTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.WrapperTests)
if(RDK_BUILD_AVALON_SUPPORT)
ADD_TEST(JavaAvalonTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.AvalonLibTests)
endif(RDK_BUILD_AVALON_SUPPORT)
if (RDK_BUILD_INCHI_SUPPORT)
ADD_TEST(JavaInchiTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.InchiTests)
endif (RDK_BUILD_INCHI_SUPPORT)
#ADD_TEST(JavaMemoryTests
# java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
# -cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
# org.RDKit.MemoryTests)
INSTALL(TARGETS GraphMolWrap
DESTINATION ${CMAKE_CURRENT_SOURCE_DIR} )
|
