# © Copyright 2008 Randal A. Koene <randalk@netmorph.org>
# 
# With design assistance from J. van Pelt & A. van Ooyen, and support
# from the Netherlands Organization for Scientific Research (NWO)
# Program Computational Life Sciences grant CLS2003 (635.100.005) and
# from the EC Marie Curie Research and Training Network (RTN)
# NEURoVERS-it 019247.

# This file is part of NETMORPH.

# NETMORPH is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.

# NETMORPH is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with NETMORPH.  If not, see <http://www.gnu.org/licenses/>.

#
# Makefile for NETMORPH
# (by Randal A. Koene, randalk@minduploading.org)

##########################################################
## Compiler
## --------
CC=gcc
CCPP=g++ 
##########################################################

INCLUDES= -I$(HOME)/src/include
LIB_PATH= -L$(HOME)/src/lib

##########################################################
## Machine selection
## -----------------
## aurora (x86):
MACHSPEC=
MACHSTR=
MACHOPT=
#MACHOPT=-march=pentium4 -mtune=pentium4 -mfpmath=sse
##
## kenji (SUN Ultra):
#MACHSPEC= -DSUN_RX
#MACHSTR=SUN
##
##########################################################
### Attempting a temporary fix for gcc 4.x compilation of dil2al
### (This should be replaced by actual source code modification.)
CPPTEMPWORKAROUND=-fno-access-control

##########################################################
## Regular Expression Library
## --------------------------
## (Suggestion: Using regex-gnu.h guarantees the greatest
## amount of compatibility and identical behaviour on all
## platforms, since it is included with the dil2al source
## code and has been adapted for reliable use with C++.)
##
## regex-gnu.h adapted for integration with C++:
GCC3FXTRA=$(if $(shell gcc -v 2>&1 | grep "^gcc version[^0-9]*[3-9][.]"),-Wno-unused-function)
ALT_REGEX=regex-gnu.o
ALT_REGEX_H=\"regex-gnu.h\"
MEMTESTS=
#MEMTESTS=-DMEMTESTS
#PROFILING=
PROFILING=-DEVALUATE_POSSIBLE_CONNECTION_PROFILING
#SYNAPSEINVENTORY=
SYNAPSEINVENTORY=-DSYNAPTOGENESIS_AND_LOSS_INVENTORY
#STATISTICSVERBOSITY=-DVERBOSE_EMPTY_DATA_SAMPLE_WARNINGS
#STATISTICS=-DSAMPLES_INCLUDE_NETWORK_GENERATED_STATISTICS $(STATISTICSVERBOSITY)
STATISTICS=-DSAMPLES_INCLUDE_NETWORK_STATISTICS_BASE $(STATISTICSVERBOSITY)
#STATISTICS=-DSAMPLES_INCLUDE_NETWORK_STATISTICS_BASE
MEMORYSAVING=
#MEMORYSAVING=-DREDUCED_MEMORY_PTSEM
#RNGCHOICE=-DFAST_RNG
RNGCHOICE=-DPRECISE_RNG
#MODELCHOICES=-DADM_PRIORITIZE_SPEED_OVER_SPACE -DTESTING_SIMPLE_ATTRACTION -DENABLE_APICAL_TUFTING_TRIGGER_DISTANCE $(RNGCHOICE) $(MEMORYSAVING) -DINCLUDE_SIMPLE_FIBER_DIAMETER
MODELCHOICES=-DADM_PRIORITIZE_SPEED_OVER_SPACE -DTESTING_SIMPLE_ATTRACTION $(RNGCHOICE) $(MEMORYSAVING) -DINCLUDE_SIMPLE_FIBER_DIAMETER
OUTPUTCHOICES=-DCHECK_XFIG_RANGES
#-DTESTING_SPIKING
#-DLEGACY_ELONGATION
SIMULATIONMETHODS=-DENABLE_FIXED_STEP_SIMULATION -DFIXED_STEP_SIMULATION_START_AT_DT -DTESTING_SPIKING
DEBUGGING=
#DEBUGGING=-DDEBUG_SPHERICAL_BOUNDARY
#DEBUGGING=-DTESTING_ELONGATION_TOTAL
#DEBUGGING=-DTEST_FOR_NAN
#DEBUGGING=-DINCLUDE_PDF_SAMPLING
#-DDEBUGGING_ELONGATION -DDEBUGGING_DIRECTION -DINCLUDE_PDF_SAMPLING
## Put conditional defines, such as -D__SPATIAL_SEGMENT_SUBSET_TEST into
## the variable NIBRCONDITIONAL and export before running make.
CFXTRA= -D__DIL2AL__ -DSTDC_HEADERS -pedantic -Wall -Wno-char-subscripts $(GCC3FXTRA) $(MEMTESTS) $(PROFILING) $(SYNAPSEINVENTORY) $(STATISTICS) $(MODELCHOICES) $(SIMULATIONMETHODS) $(DEBUGGING) $(OUTPUTCHOICES)
CPPXTRA= -D__DIL2AL__ -D_ALT_REGEX_H=$(ALT_REGEX_H) -D_USE_ALT_REGEX -D_CPP_REGEX $(NIBRCONDITIONAL) $(MACHOPT) -mieee-fp -ffast-math -pedantic -Wall $(GCC3FXTRA) $(MEMTESTS) $(PROFILING) $(SYNAPSEINVENTORY) $(STATISTICS) $(MODELCHOICES) $(SIMULATIONMETHODS) $(DEBUGGING) $(CPPTEMPWORKAROUND) $(OUTPUTCHOICES)
REGEXSTR=regex-gnu_for_C++
FIG2DEV=$(shell which fig2dev)
##
## rx.h:
#ALT_REGEX=rx.o
#ALT_REGEX_H=
#CFXTRA= -D__DIL2AL__
#CPPXTRA= -D__DIL2AL__ -D_BIGREGEX_HAS_RM_SPEP
#REGEXSTR=rx
##
## generic GNU regex (Linux/GNU specific):
#ALT_REGEX=regex.o
#ALT_REGEX_H=regex.h
#CFXTRA=
#CPPXTRA= -D_ALT_REGEX_H=$(ALT_REGEX_H) -D_USE_ALT_REGEX -D__DIL2AL__ -D_BIGREGEX_HAS_RM_SPEP
#REGEXSTR=regex
##
## system <regex.h> (SUN specific):
#ALT_REGEX=
#ALT_REGEX_H=
#CFXTRA= -DSYSTEM_RX
#CPPXTRA= -D__DIL2AL__ -DSYSTEM_RX
#REGEXSTR=system
##########################################################

##########################################################
## Safe Regular Expressions
## ------------------------
## assume '\0' within String length and rm structure has
## no sp/ep pointers:
#SAFEREGEX=
## make no assumptions:
SAFEREGEX= -D_BIGREGEX_SAFE_MATCHES
##########################################################

##########################################################
## Compiler Options
## ----------------
# Normal:
COMPOPT=-O3
OPTSTR=optimized
## debugging information:
# For gprof:
#GPROF=-pg
# For Valgrind:
#COMPOPT=-g -O0 -Wall
#OPTSTR=Valgrind
# For gprof:
#COMPOPT=-pg -O3
#OPTSTR=Gprof
#COMPOPT= -g
#OPTSTR=debugging_info
##########################################################

##########################################################
## C++ Specific Compiler Options
## -----------------------------
## debugging information:
#CPPOPT=
## generate profile information for use with gprof:
#CPPOPT=
## optimized:
CPPOPT= -felide-constructors
##########################################################

CFLAGS= $(COMPOPT) $(MACHSPEC) $(CFXTRA)
CPPFLAGS= $(COMPOPT) $(CPPOPT) $(MACHSPEC) $(CPPXTRA) $(SAFEREGEX) $(INCLUDES)

.INIT:
	@echo '-------------------------------------------------------------------'
	@echo 'Compilation options: $(MACHSTR), $(OPTSTR), $(REGEXSTR)'
	@echo '-------------------------------------------------------------------'

all: nibr nibr2D wizard

diagnostic.o: diagnostic.cc diagnostic.hh file.hh BigString.hh BigRegex.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -c diagnostic.cc -o diagnostic.o

state_storable.o: state_storable.cc state_storable.hh global.hh BigString.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -c state_storable.cc -o state_storable.o

mtprng.o: mtprng.cc mtprng.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -c mtprng.cc -o mtprng.o

global.o: global.cc global.hh file.hh Fig_Object.hh Command_Line_Parameters.hh mtprng.hh BigString.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -c global.cc -o global.o

file.o: file.cc file.hh BigString.hh global.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -c file.cc -o file.o

StringList.o: StringList.cc StringList.hh BigString.hh BigRegex.hh regex-gnu.h
	$(CCPP) $(CPPFLAGS) $(COLORS) -c StringList.cc -o StringList.o

event.o event2D.o: event.cc event.hh network.hh global.hh Command_Line_Parameters.hh state_storable.hh
	$(CCPP) $(CPPFLAGS) -DVECTOR3D -c event.cc -o event.o
	$(CCPP) $(CPPFLAGS) -DVECTOR2D -c event.cc -o event2D.o

spatial.o spatial2D.o: spatial.cc spatial.hh Spatial_Presentation.hh global.hh
	$(CCPP) $(CPPFLAGS) -DVECTOR3D -c spatial.cc -o spatial.o
	$(CCPP) $(CPPFLAGS) -DVECTOR2D -c spatial.cc -o spatial2D.o

network.o network2D.o: network.cc network.hh Network_Statistics.hh synapse.hh synapse_formation_model.hh global.hh file.hh Command_Line_Parameters.hh Network_Generated_Statistics.hh Sampled_Output.hh Network_Statistics.hh Spatial_Segment_Subset.hh Results.hh Connection_Statistics.hh dendritic_growth_model.hh neurite_diameter_model.hh spatial.hh event.hh state_storable.hh Txt_Object.hh VRML_Object.hh Catacomb_Object.hh slice.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c network.cc -o network.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c network.cc -o network2D.o

neuron.o neuron2D.o: neuron.cc neuron.hh network.hh prepost_structure.hh connection.hh fibre_elongation_model.hh axon_direction_model.hh Color_Table.hh spatial.hh event.hh global.hh Network_Generated_Statistics.hh Sampled_Output.hh Command_Line_Parameters.hh BigString.hh state_storable.hh Txt_Object.hh VRML_Object.hh Catacomb_Object.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c neuron.cc -o neuron.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c neuron.cc -o neuron2D.o

IFactivity.o IFactivity2D.o: IFactivity.cc IFactivity.hh neuron.hh connection.hh Sampled_Output.hh event.hh
	$(CCPP) $(CPPFLAGS) -DVECTOR3D -c IFactivity.cc -o IFactivity.o
	$(CCPP) $(CPPFLAGS) -DVECTOR2D -c IFactivity.cc -o IFactivity2D.o

synapse.o synapse2D.o: synapse.cc synapse.hh connection.hh synapse_structure.hh Fig_Object.hh Color_Table.hh global.hh state_storable.hh Txt_Object.hh VRML_Object.hh Catacomb_Object.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c synapse.cc -o synapse.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c synapse.cc -o synapse2D.o

connection.o connection2D.o: connection.cc connection.hh neuron.hh Fig_Object.hh Sampled_Output.hh state_storable.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c connection.cc -o connection.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c connection.cc -o connection2D.o

generic_synapse.o: generic_synapse.cc generic_synapse.hh nibr.hh BigString.hh BigRegex.hh regex-gnu.h
	$(CCPP) $(CPPFLAGS) $(COLORS) -c generic_synapse.cc -o generic_synapse.o

synapse_formation_model.o synapse_formation_model2D.o: synapse_formation_model.cc synapse_formation_model.hh fibre_structure.hh synapse_structure.hh synapse.hh Connection_Statistics.hh neuron.hh spatial.hh Command_Line_Parameters.hh diagnostic.hh global.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c synapse_formation_model.cc -o synapse_formation_model.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c synapse_formation_model.cc -o synapse_formation_model2D.o

branching_models.o branching_models2D.o: branching_models.cc branching_models.hh dendritic_growth_model.hh fibre_structure.hh neuron.hh spatial.hh Command_Line_Parameters.hh global.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c branching_models.cc -o branching_models.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c branching_models.cc -o branching_models2D.o

turning_models.o turning_models2D.o: turning_models.cc turning_models.hh dendritic_growth_model.hh fibre_structure.hh neuron.hh spatial.hh Command_Line_Parameters.hh global.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c turning_models.cc -o turning_models.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c turning_models.cc -o turning_models2D.o

axon_direction_model.o axon_direction_model2D.o: axon_direction_model.cc axon_direction_model.hh dendritic_growth_model.hh fibre_structure.hh neuron.hh spatial.hh Command_Line_Parameters.hh global.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c axon_direction_model.cc -o axon_direction_model.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c axon_direction_model.cc -o axon_direction_model2D.o

fibre_elongation_model.o fibre_elongation_model2D.o: fibre_elongation_model.cc fibre_elongation_model.hh dendritic_growth_model.hh axon_direction_model.hh fibre_structure.hh neuron.hh event.hh Command_Line_Parameters.hh global.hh diagnostic.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c fibre_elongation_model.cc -o fibre_elongation_model.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c fibre_elongation_model.cc -o fibre_elongation_model2D.o

dendritic_growth_model.o dendritic_growth_model2D.o: dendritic_growth_model.cc dendritic_growth_model.hh axon_direction_model.hh fibre_structure.hh network.hh neuron.hh Connection_Statistics.hh Sampled_Output.hh Command_Line_Parameters.hh global.hh BigString.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c dendritic_growth_model.cc -o dendritic_growth_model.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c dendritic_growth_model.cc -o dendritic_growth_model2D.o

neurite_diameter_model.o: neurite_diameter_model.cc neurite_diameter_model.hh fibre_structure.hh network.hh Command_Line_Parameters.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c neurite_diameter_model.cc -o neurite_diameter_model.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c neurite_diameter_model.cc -o neurite_diameter_model2D.o

environment_physics.o: environment_physics.cc environment_physics.hh neuron.hh network.hh event.hh Command_Line_Parameters.hh spatial.hh global.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c environment_physics.cc -o environment_physics.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c environment_physics.cc -o environment_physics2D.o

synapse_structure.o synapse_structure2D.o: synapse_structure.cc synapse_structure.hh fibre_structure.hh Fig_Object.hh Sampled_Output.hh spatial.hh global.hh state_storable.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c synapse_structure.cc -o synapse_structure.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c synapse_structure.cc -o synapse_structure2D.o

fibre_structure.o fibre_structure2D.o: fibre_structure.cc fibre_structure.hh dendritic_growth_model.hh axon_direction_model.hh branching_models.hh fibre_elongation_model.hh environment_physics.hh neuron.hh event.hh Network_Generated_Statistics.hh Sampled_Output.hh Fig_Object.hh spatial.hh global.hh diagnostic.hh state_storable.hh Txt_Object.hh VRML_Object.hh Catacomb_Object.hh Command_Line_Parameters.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c fibre_structure.cc -o fibre_structure.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c fibre_structure.cc -o fibre_structure2D.o

prepost_structure.o prepost_structure2D.o: prepost_structure.cc prepost_structure.hh neuron.hh network.hh axon_direction_model.hh spatial.hh fibre_structure.hh Network_Generated_Statistics.hh global.hh state_storable.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c prepost_structure.cc -o prepost_structure.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c prepost_structure.cc -o prepost_structure2D.o

Connection_Statistics.o Connection_Statistics2D.o: Connection_Statistics.cc Connection_Statistics.hh neuron.hh BigString.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c Connection_Statistics.cc -o Connection_Statistics.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c Connection_Statistics.cc -o Connection_Statistics2D.o

Network_Statistics.o Network_Statistics2D.o: Network_Statistics.cc Network_Statistics.hh BigString.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c Network_Statistics.cc -o Network_Statistics.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c Network_Statistics.cc -o Network_Statistics2D.o

Spatial_Segment_Subset.o Spatial_Segment_Subset2D.o: Spatial_Segment_Subset.cc Spatial_Segment_Subset.hh fibre_structure.hh synapse_formation_model.hh Fig_Object.hh Color_Table.hh spatial.hh global.hh diagnostic.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c Spatial_Segment_Subset.cc -o Spatial_Segment_Subset.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c Spatial_Segment_Subset.cc -o Spatial_Segment_Subset2D.o

Command.o: Command.cc BigString.hh global.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -c Command.cc -o Command.o

Command_Line_Parameters.o: Command_Line_Parameters.cc Command_Line_Parameters.hh file.hh global.hh BigString.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -c Command_Line_Parameters.cc -o Command_Line_Parameters.o

Results.o: Results.cc Results.hh BigString.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -c Results.cc -o Results.o

Network_Generated_Statistics.o: Network_Generated_Statistics.cc Network_Generated_Statistics.hh Command_Line_Parameters.hh global.hh BigString.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -c Network_Generated_Statistics.cc -o Network_Generated_Statistics.o

Spatial_Presentation.o Spatial_Presentation2D.o: Spatial_Presentation.cc Spatial_Presentation.hh global.hh Command_Line_Parameters.hh spatial.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -DFIG2DEV=\"$(FIG2DEV)\" -c Spatial_Presentation.cc -o Spatial_Presentation.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -DFIG2DEV=\"$(FIG2DEV)\" -c Spatial_Presentation.cc -o Spatial_Presentation2D.o

Sampled_Output.o Sampled_Output2D.o: Sampled_Output.cc Sampled_Output.hh Network_Generated_Statistics.hh Color_Table.hh Spatial_Presentation.hh Command_Line_Parameters.hh spatial.hh global.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -DFIG2DEV=\"$(FIG2DEV)\" -c Sampled_Output.cc -o Sampled_Output.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -DFIG2DEV=\"$(FIG2DEV)\" -c Sampled_Output.cc -o Sampled_Output2D.o

Color_Table.o: Color_Table.cc Color_Table.hh Fig_Object.hh Command_Line_Parameters.hh global.hh BigString.hh 
	$(CCPP) $(CPPFLAGS) $(COLORS) -c Color_Table.cc -o Color_Table.o

Fig_Object.o: Fig_Object.cc Fig_Object.hh BigString.hh diagnostic.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -c Fig_Object.cc -o Fig_Object.o

Txt_Object.o: Txt_Object.cc Txt_Object.hh global.hh BigString.hh diagnostic.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -c Txt_Object.cc -o Txt_Object.o

VRML_Object.o: VRML_Object.cc VRML_Object.hh global.hh spatial.hh BigString.hh diagnostic.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c VRML_Object.cc -o VRML_Object.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c VRML_Object.cc -o VRML_Object2D.o

Catacomb_Object.o: Catacomb_Object.cc Catacomb_Object.hh global.hh network.hh spatial.hh BigString.hh diagnostic.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c Catacomb_Object.cc -o Catacomb_Object.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c Catacomb_Object.cc -o Catacomb_Object2D.o

slice.o: slice.cc slice.hh spatial.hh Command_Line_Parameters.hh global.hh
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c slice.cc -o slice.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c slice.cc -o slice2D.o

nibr.o nibr2D.o: nibr.cc nibr.hh network.hh synapse.hh synapse_formation_model.hh axon_direction_model.hh environment_physics.hh Command_Line_Parameters.hh Sampled_Output.hh Spatial_Presentation.hh file.hh spatial.hh event.hh slice.hh diagnostic.hh BigString.hh BigRegex.hh mtprng.hh regex-gnu.h
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -DFIG2DEV=\"$(FIG2DEV)\" -c nibr.cc -o nibr.o
	$(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -DFIG2DEV=\"$(FIG2DEV)\" -c nibr.cc -o nibr2D.o

wizard.o: wizard.cc wizard.hh StringList.hh BigString.hh BigRegex.hh regex-gnu.h
	$(CCPP) $(CPPFLAGS) $(COLORS) -c wizard.cc -o wizard.o

nibr: nibr.o Txt_Object.o VRML_Object.o Catacomb_Object.o Fig_Object.o Color_Table.o Sampled_Output.o Spatial_Presentation.o Network_Generated_Statistics.o Results.o Command_Line_Parameters.o Command.o Spatial_Segment_Subset.o Network_Statistics.o Connection_Statistics.o prepost_structure.o fibre_structure.o synapse_structure.o generic_synapse.o dendritic_growth_model.o synapse_formation_model.o branching_models.o turning_models.o axon_direction_model.o fibre_elongation_model.o neurite_diameter_model.o environment_physics.o connection.o synapse.o IFactivity.o neuron.o network.o spatial.o event.o slice.o StringList.o file.o state_storable.o global.o diagnostic.o BigString.o BigRegex.o mtprng.o regex-gnu.o
	@echo "Design rule: Add only the physiology required by function."
	@echo "  ___connected neurons (connection)"
	@echo "  _____individual synapses (synapse)"
	@echo "  _______presynaptic and postsynaptic nodes and branches"
	@echo "  _________terminals, receptive zones/spines, soma, axon hillock"
	$(CCPP) $(CPPFLAGS) nibr.o Txt_Object.o VRML_Object.o Catacomb_Object.o Fig_Object.o Color_Table.o Sampled_Output.o Spatial_Presentation.o Network_Generated_Statistics.o Results.o Command_Line_Parameters.o Command.o Spatial_Segment_Subset.o Network_Statistics.o Connection_Statistics.o prepost_structure.o fibre_structure.o synapse_structure.o generic_synapse.o dendritic_growth_model.o synapse_formation_model.o branching_models.o turning_models.o axon_direction_model.o fibre_elongation_model.o neurite_diameter_model.o environment_physics.o connection.o synapse.o IFactivity.o neuron.o network.o spatial.o event.o slice.o StringList.o file.o state_storable.o global.o diagnostic.o BigString.o BigRegex.o mtprng.o regex-gnu.o -lgeometry -o netmorph $(LIB_PATH)
	ln -f -s netmorph nibr

nibr2D: nibr2D.o Txt_Object.o VRML_Object2D.o Catacomb_Object2D.o Fig_Object.o Color_Table.o Sampled_Output2D.o Spatial_Presentation2D.o Network_Generated_Statistics.o Results.o Command_Line_Parameters.o Command.o Spatial_Segment_Subset2D.o Network_Statistics2D.o Connection_Statistics2D.o prepost_structure2D.o fibre_structure2D.o synapse_structure2D.o generic_synapse.o dendritic_growth_model2D.o synapse_formation_model2D.o branching_models2D.o turning_models2D.o axon_direction_model2D.o fibre_elongation_model2D.o neurite_diameter_model2D.o environment_physics2D.o connection2D.o synapse2D.o IFactivity2D.o neuron2D.o network2D.o spatial2D.o event2D.o slice2D.o StringList.o file.o state_storable.o global.o diagnostic.o BigString.o BigRegex.o mtprng.o regex-gnu.o
	@echo "Design rule: Add only the physiology required by function."
	@echo "  ___connected neurons (connection)"
	@echo "  _____individual synapses (synapse)"
	@echo "  _______presynaptic and postsynaptic nodes and branches"
	@echo "  _________terminals, receptive zones/spines, soma, axon hillock"
	$(CCPP) $(CPPFLAGS) nibr2D.o Txt_Object.o VRML_Object2D.o Catacomb_Object2D.o Fig_Object.o Color_Table.o Sampled_Output2D.o Spatial_Presentation2D.o Network_Generated_Statistics.o Results.o Command_Line_Parameters.o Command.o Spatial_Segment_Subset2D.o Network_Statistics2D.o Connection_Statistics2D.o prepost_structure2D.o fibre_structure2D.o synapse_structure2D.o generic_synapse.o dendritic_growth_model2D.o synapse_formation_model2D.o branching_models2D.o turning_models2D.o axon_direction_model2D.o fibre_elongation_model2D.o neurite_diameter_model2D.o environment_physics2D.o connection2D.o synapse2D.o IFactivity2D.o neuron2D.o network2D.o spatial2D.o event2D.o slice2D.o StringList.o file.o state_storable.o global.o diagnostic.o BigString.o BigRegex.o mtprng.o regex-gnu.o -lgeometry -o netmorph2D $(LIB_PATH)
	ln -f -s netmorph2D nibr2D

wizard: wizard.o StringList.o BigString.o BigRegex.o regex-gnu.o
	$(CCPP) $(CPPFLAGS) wizard.o StringList.o BigString.o BigRegex.o regex-gnu.o -o wizard $(LIB_PATH)

clean:
	rm -r -f *.o $(NAME)
	ln -s $(HOME)/src/dil2al/BigString.o
	ln -s $(HOME)/src/dil2al/BigRegex.o
	ln -s $(HOME)/src/dil2al/regex-gnu.o