protein stuff is now only on with -DUSE_CMAPLE_AA=ON

Author: bqminh

CMakeLists.txt

@@ -246,7 +246,7 @@ include_directories("${PROJECT_BINARY_DIR}")
 #include_directories("${PROJECT_BINARY_DIR}/zlib-1.2.7")
 
 
-if (NOT CMAPLE_FLAGS MATCHES "nozlib")
+if (NOT CMAPLE_FLAGS MATCHES "nozlib" AND NOT CMAPLE_FLAGS MATCHES "static")
     find_package(ZLIB)
 endif()
 
@@ -300,28 +300,35 @@ add_subdirectory(unittest)
 # the main executable
 ##################################################################
 add_executable(cmaple main/main.cpp)
-add_executable(cmaple-aa main/main.cpp)
+if (USE_CMAPLE_AA)
+    add_executable(cmaple-aa main/main.cpp)
+endif()
 
 if(Backtrace_FOUND)
   include_directories(${Backtrace_INCLUDE_DIR})
   target_link_libraries(cmaple PRIVATE ${Backtrace_LIBRARY})
-  target_link_libraries(cmaple-aa PRIVATE ${Backtrace_LIBRARY})
+    if (USE_CMAPLE_AA)
+      target_link_libraries(cmaple-aa PRIVATE ${Backtrace_LIBRARY})
+    endif()
 endif(Backtrace_FOUND)
 
 ##################################################################
 # setup linking flags
 ##################################################################
 
 target_link_libraries(cmaple PUBLIC maple cmaple_tree cmaple_alignment cmaple_model ncl nclextra cmaple_utils)
-target_link_libraries(cmaple-aa PUBLIC maple-aa cmaple_tree-aa cmaple_alignment-aa cmaple_model-aa ncl nclextra cmaple_utils)
-
+if (USE_CMAPLE_AA)
+    target_link_libraries(cmaple-aa PUBLIC maple-aa cmaple_tree-aa cmaple_alignment-aa cmaple_model-aa ncl nclextra cmaple_utils)
+endif()
 
 ##############################################################
 # add the install targets
 ##############################################################
 if (INSTALL_CMAPLE)
     install (TARGETS cmaple DESTINATION bin)
-    install (TARGETS cmaple-aa DESTINATION bin)
+    if (USE_CMAPLE_AA)
+        install (TARGETS cmaple-aa DESTINATION bin)
+    endif()
     install (FILES "${PROJECT_SOURCE_DIR}/example/example.maple" DESTINATION .)
     install (FILES "${PROJECT_SOURCE_DIR}/example/tree.nwk" DESTINATION .)
     #install (FILES "${PROJECT_BINARY_DIR}/cmaple_config.h" DESTINATION "include")
@@ -333,7 +340,9 @@ if (INSTALL_CMAPLE)
 
     if (WIN32)
         install (FILES "${BINARY_DIR}/cmaple${EXE_SUFFIX}-click.exe" DESTINATION bin)
-        install (FILES "${BINARY_DIR}/cmaple-aa${EXE_SUFFIX}-click.exe" DESTINATION bin)
+        if (USE_CMAPLE_AA)
+            install (FILES "${BINARY_DIR}/cmaple-aa${EXE_SUFFIX}-click.exe" DESTINATION bin)
+        endif()
     endif()
 endif()
 

alignment/CMakeLists.txt

@@ -9,13 +9,15 @@ alignment.h alignment.cpp
 target_compile_definitions(cmaple_alignment PUBLIC NUM_STATES=4)
 target_link_libraries(cmaple_alignment cmaple_utils)
 
-# Protein data
-add_library(cmaple_alignment-aa
-mutation.h mutation.cpp
-seqregion.h seqregion.cpp
-seqregions.h seqregions.cpp
-sequence.h sequence.cpp
-alignment.h alignment.cpp
-)
-target_compile_definitions(cmaple_alignment-aa PUBLIC NUM_STATES=20)
-target_link_libraries(cmaple_alignment-aa cmaple_utils)
+if (USE_CMAPLE_AA)
+    # Protein data
+    add_library(cmaple_alignment-aa
+    mutation.h mutation.cpp
+    seqregion.h seqregion.cpp
+    seqregions.h seqregions.cpp
+    sequence.h sequence.cpp
+    alignment.h alignment.cpp
+    )
+    target_compile_definitions(cmaple_alignment-aa PUBLIC NUM_STATES=20)
+    target_link_libraries(cmaple_alignment-aa cmaple_utils)
+endif()

maple/CMakeLists.txt

@@ -4,9 +4,11 @@ cmaple.h cmaple.cpp
 )
 target_link_libraries(maple cmaple_tree cmaple_alignment cmaple_model cmaple_utils)
 
-# Protein data
-add_library(maple-aa
-cmaple.h cmaple.cpp
-)
-target_link_libraries(maple-aa cmaple_tree-aa cmaple_alignment-aa cmaple_model-aa cmaple_utils)
 
+if (USE_CMAPLE_AA)
+    # Protein data
+    add_library(maple-aa
+    cmaple.h cmaple.cpp
+    )
+    target_link_libraries(maple-aa cmaple_tree-aa cmaple_alignment-aa cmaple_model-aa cmaple_utils)
+endif()

model/CMakeLists.txt

@@ -7,11 +7,13 @@ model_aa.h model_aa.cpp
 )
 target_link_libraries(cmaple_model cmaple_alignment cmaple_utils ncl nclextra)
 
-# Protein data
-add_library(cmaple_model-aa
-model.h model.cpp
-modelbase.h modelbase.cpp
-model_dna.h model_dna.cpp
-model_aa.h model_aa.cpp
-)
-target_link_libraries(cmaple_model-aa cmaple_alignment-aa cmaple_utils ncl nclextra)
+if (USE_CMAPLE_AA)
+    # Protein data
+    add_library(cmaple_model-aa
+    model.h model.cpp
+    modelbase.h modelbase.cpp
+    model_dna.h model_dna.cpp
+    model_aa.h model_aa.cpp
+    )
+    target_link_libraries(cmaple_model-aa cmaple_alignment-aa cmaple_utils ncl nclextra)
+endif()

tree/CMakeLists.txt

@@ -11,15 +11,17 @@ altbranch.h
 )
 target_link_libraries(cmaple_tree cmaple_model cmaple_alignment cmaple_utils)
 
-# Protein data
-add_library(cmaple_tree-aa
-tree.h tree.cpp
-rootcandidate.h
-updatingnode.h updatingnode.cpp
-traversingnode.h traversingnode.cpp
-phylonode.h phylonode.cpp
-leaf.h
-internal.h
-altbranch.h
-)
-target_link_libraries(cmaple_tree-aa cmaple_model-aa cmaple_alignment-aa cmaple_utils)
+if (USE_CMAPLE_AA)
+    # Protein data
+    add_library(cmaple_tree-aa
+    tree.h tree.cpp
+    rootcandidate.h
+    updatingnode.h updatingnode.cpp
+    traversingnode.h traversingnode.cpp
+    phylonode.h phylonode.cpp
+    leaf.h
+    internal.h
+    altbranch.h
+    )
+    target_link_libraries(cmaple_tree-aa cmaple_model-aa cmaple_alignment-aa cmaple_utils)
+endif()