Makefile

# use g++ compiler
CXX=g++
CXXFLAGS?=-Wall -pedantic -std=c++11

# flag specifications for release and debug
RELEASEFLAGS?=$(CXXFLAGS) -O3
DEBUGFLAGS?=$(CXXFLAGS) -O0 -g #-pg

# relevant constants
CPP_FILES=main.cpp common.cpp coalescent.cpp
HEADER_FILES=common.h coalescent.h
GLOBAL_DEPS=$(CPP_FILES) $(HEADER_FILES)
EXE_PREFIX=coatran

## constant effective population size
CONSTANT=constant
CONSTANT_EXE=$(EXE_PREFIX)_$(CONSTANT)
CONSTANT_DEBUG=$(CONSTANT)_debug
CONSTANT_DEBUG_EXE=$(EXE_PREFIX)_$(CONSTANT_DEBUG)

## exponential effective population size growth
EXPGROWTH=expgrowth
EXPGROWTH_EXE=$(EXE_PREFIX)_$(EXPGROWTH)
EXPGROWTH_DEBUG=$(EXPGROWTH)_debug
EXPGROWTH_DEBUG_EXE=$(EXE_PREFIX)_$(EXPGROWTH_DEBUG)

## latest possible coalescence (time of transmission)
TRANSTREE=transtree
TRANSTREE_EXE=$(EXE_PREFIX)_$(TRANSTREE)
TRANSTREE_DEBUG=$(TRANSTREE)_debug
TRANSTREE_DEBUG_EXE=$(EXE_PREFIX)_$(TRANSTREE_DEBUG)

## earliest possible coalescence (time of infection)
INFTIME=inftime
INFTIME_EXE=$(EXE_PREFIX)_$(INFTIME)
INFTIME_DEBUG=$(INFTIME)_debug
INFTIME_DEBUG_EXE=$(EXE_PREFIX)_$(INFTIME_DEBUG)

# compile all executables
RELEASE_EXES=$(CONSTANT_EXE) $(EXPGROWTH_EXE) $(TRANSTREE_EXE) $(INFTIME_EXE)
DEBUG_EXES=$(CONSTANT_DEBUG_EXE) $(EXPGROWTH_DEBUG_EXE) $(TRANSTREE_DEBUG_EXE) $(INFTIME_DEBUG_EXE)
all: $(RELEASE_EXES)
debug: $(DEBUG_EXES)

## constant effective population size
$(CONSTANT_EXE): $(GLOBAL_DEPS)
	$(CXX) $(RELEASEFLAGS) -o $(CONSTANT_EXE) $(CPP_FILES)
$(CONSTANT_DEBUG_EXE): $(GLOBAL_DEPS)
	$(CXX) $(DEBUGFLAGS) -o $(CONSTANT_DEBUG_EXE) $(CPP_FILES)

## exponential effective population size growth
EXPGROWTH_FLAG=-DEXPGROWTH
$(EXPGROWTH_EXE): $(GLOBAL_DEPS)
	$(CXX) $(RELEASEFLAGS) $(EXPGROWTH_FLAG) -o $(EXPGROWTH_EXE) $(CPP_FILES)
$(EXPGROWTH_DEBUG_EXE): $(GLOBAL_DEPS)
	$(CXX) $(DEBUGFLAGS) $(EXPGROWTH_FLAG) -o $(EXPGROWTH_DEBUG_EXE) $(CPP_FILES)

## latest possible coalescence (time of transmission)
TRANSTREE_FLAG=-DTRANSTREE
$(TRANSTREE_EXE): $(GLOBAL_DEPS)
	$(CXX) $(RELEASEFLAGS) $(TRANSTREE_FLAG) -o $(TRANSTREE_EXE) $(CPP_FILES)
$(TRANSTREE_DEBUG_EXE): $(GLOBAL_DEPS)
	$(CXX) $(DEBUGFLAGS) $(TRANSTREE_FLAG) -o $(TRANSTREE_DEBUG_EXE) $(CPP_FILES)

## earliest possible coalescence (time of infection)
INFTIME_FLAG=-DINFTIME
$(INFTIME_EXE): $(GLOBAL_DEPS)
	$(CXX) $(RELEASEFLAGS) $(INFTIME_FLAG) -o $(INFTIME_EXE) $(CPP_FILES)
$(INFTIME_DEBUG_EXE): $(GLOBAL_DEPS)
	$(CXX) $(DEBUGFLAGS) $(INFTIME_FLAG) -o $(INFTIME_DEBUG_EXE) $(CPP_FILES)

# clean things up
clean:
	$(RM) $(RELEASE_EXES) $(DEBUG_EXES) *.o