# used to use  -include @CIPHYCAS_PREFIX_FILE@ before we added #include "phycas/phycas.h" to every file.
AM_CXXFLAGS =  $(CIPRES_LIB_CXXFLAGS) $(CIPRES_LIB_INC_DIRS) @CXXFLAGS@ @CXXFLAGS_OPTIM_SPEED@ @CXXFLAGS_WARNINGS@
lib_LIBRARIES = libCiphycas.a
libCiphycas_a_SOURCES = \
	@NCL_ROOT@/ncl/nxs_basic_manager.cpp \
	@NCL_ROOT@/ncl/nxs_block.cpp \
	@NCL_ROOT@/ncl/nxs_exception.cpp \
	@NCL_ROOT@/ncl/nxs_reader.cpp \
	@NCL_ROOT@/ncl/nxs_token.cpp \
	@NCL_ROOT@/ncl/characters/nxs_char_listener.cpp \
	@NCL_ROOT@/ncl/characters/nxs_characters_block.cpp \
	@NCL_ROOT@/ncl/characters/nxs_characters_block_commands.cpp \
	@NCL_ROOT@/ncl/characters/nxs_characters_manager.cpp \
	@NCL_ROOT@/ncl/command/nxs_auto_command.cpp \
	@NCL_ROOT@/ncl/command/nxs_choice_cmd_param.cpp \
	@NCL_ROOT@/ncl/command/nxs_cmd_param.cpp \
	@NCL_ROOT@/ncl/command/nxs_command.cpp \
	@NCL_ROOT@/ncl/command/nxs_command_manager.cpp \
	@NCL_ROOT@/ncl/command/nxs_command_output.cpp \
	@NCL_ROOT@/ncl/command/nxs_file_cmd_param.cpp \
	@NCL_ROOT@/ncl/command/nxs_mixed_cmd_param.cpp \
	@NCL_ROOT@/ncl/command/nxs_primitive_cmd_param.cpp \
	@NCL_ROOT@/ncl/command/nxs_restricted_string_cmd_param.cpp \
	@NCL_ROOT@/ncl/command/nxs_set_cmd_param.cpp \
	@NCL_ROOT@/ncl/misc/arg_stream.cpp \
	@NCL_ROOT@/ncl/misc/nxs_data_type.cpp \
	@NCL_ROOT@/ncl/misc/eliminated_index_slider.cpp \
	@NCL_ROOT@/ncl/misc/nxs_discrete_matrix.cpp \
	@NCL_ROOT@/ncl/misc/nxs_file_path.cpp \
	@NCL_ROOT@/ncl/misc/nxs_index_set.cpp \
	@NCL_ROOT@/ncl/misc/nxs_test.cpp \
	@NCL_ROOT@/ncl/misc/string_extensions.cpp \
	@NCL_ROOT@/ncl/output/nxs_output_stream_wrapper.cpp \
	@NCL_ROOT@/ncl/output/generic_output_classes.cpp \
	@NCL_ROOT@/ncl/output/nxs_console_out_stream_impl.cpp \
	@NCL_ROOT@/ncl/output/nxs_input.cpp \
	@NCL_ROOT@/ncl/output/nxs_table.cpp \
	@NCL_ROOT@/ncl/output/nxs_table_cell.cpp \
	@NCL_ROOT@/ncl/output/nxs_typist.cpp \
	@NCL_ROOT@/ncl/output/nxs_user_query.cpp \
	@NCL_ROOT@/ncl/taxa/base_taxa_manager.cpp \
	@NCL_ROOT@/ncl/taxa/nxs_alternative_taxa_block.cpp \
	@NCL_ROOT@/ncl/taxa/nxs_taxa_block.cpp \
	@NCL_ROOT@/ncl/taxa/nxs_taxa_listener.cpp \
	@NCL_ROOT@/ncl/taxa/nxs_taxa_manager.cpp \
	@NCL_ROOT@/ncl/trees/newick_verifier.cpp \
	@NCL_ROOT@/ncl/trees/nxs_tree_listener.cpp \
	@NCL_ROOT@/ncl/trees/nxs_trees_block.cpp \
	@NCL_ROOT@/ncl/trees/nxs_trees_manager.cpp \
	@PHYCAS_ROOT@/phycas/characters/characters_manager.cpp \
	@PHYCAS_ROOT@/phycas/likelihood/const_site_info.cpp \
	@PHYCAS_ROOT@/phycas/misc/multiline_bound.cpp \
	@PHYCAS_ROOT@/phycas/rand/cdf.cpp \
	@PHYCAS_ROOT@/phycas/rand/distribution_command_param.cpp \
	@PHYCAS_ROOT@/phycas/rand/distribution_description.cpp \
	@PHYCAS_ROOT@/phycas/rand/probability_distribution.cpp \
	@PHYCAS_ROOT@/phycas/rand/lot.cpp \
	@PHYCAS_ROOT@/phycas/taxa/taxa_manager.cpp \
	@PHYCAS_ROOT@/phycas/trees/draw_context.cpp \
	@PHYCAS_ROOT@/phycas/trees/draw_tree.cpp \
	@PHYCAS_ROOT@/phycas/trees/tree_manip.cpp \
	@PHYCAS_ROOT@/phycas/trees/tree_node.cpp \
	@PHYCAS_ROOT@/phycas/trees/tree.cpp \
	@PHYCAS_ROOT@/phycas/trees/trees_manager.cpp \
	@PHYCAS_ROOT@/phycas/trees/split.cpp