########################################################################
#       Generic command-line makefile for NCBI applications
#
#   This assumes the following variables are set in a file called "ncbi.mk"
#     which is included by this one. In this case it resides in a directory
#     set by the environment variable "NCBI"
#
#    NCBI_CC = default compiler to use
#    NCBI_CFLAGS1 = default compiler switches (not optimization)
#    NCBI_LDFLAGS1 = default compiler switches when linking (not optimization)
#    NCBI_OPTFLAG = default optimization (-O)
#    NCBI_INCDIR = default toolkit include paths
#    NCBI_LIBDIR = default toolkit library paths
#    NCBI_ALTLIB  = debugging toolkit library paths
#    NCBI_VIBFLAG = additional include paths/defines for Vibrant apps
#    NCBI_VIBLIBS  = additional libraries needed to link Vibrant apps
#    NCBI_OTHERLIBS = additional libraries needed to link the system
#
#   This enables platform independent makefiles for ncbi toolkit apps. You
#   can change any default behavior by setting the variable on the command
#   line.
#
#   Use gcc complier.   "make NCBI_CC=gcc" or "make CC=gcc"
#   Change optimization to debug
#                "make NCBI_OPTFLAG="-g" NCBI_LIBPATH=$NCBI_ALTLIB"
#                or
#                "make OPTFLAG="-g" LIBPATH=$NCBI_ALTLIB"
#
#   You can also change the behavior permanently in the makefile by changing
#    the assignment of the internal variable to the one from the include
#    file:
#
#   Use gcc compiler.
#    Change   CC=$(NCBI_CC)
#    To       CC=gcc
#    in the makefile itself
#
#   Make debugging version
#    OPTFLAG=-g
#    LIBPATH=$(NCBI_ALTLIB)
#
#   You need to specify the EXE and SRC symbols
#
#######################################################################
#
# default flags for compiling and loading
#
#######################################################################

include $(NCBI)/ncbi.mk

CC = $(NCBI_CC)
#CC = lint
#CC = purify cc -xildoff
CFLAGS1 = $(NCBI_CFLAGS1)
LDFLAGS1 = $(NCBI_LDFLAGS1)
OPTFLAG = -g -D DEBUG_DDV
OTHERLIBS = $(NCBI_OTHERLIBS)
VIBLIBS= $(NCBI_VIBLIBS)
VIBFLAG= $(NCBI_VIBFLAG)
INCPATH = $(NCBI_INCDIR)
LIBPATH = $(NCBI_ALTLIB)
# DEF = -DINTERNAL_NCBI_SEQUIN -DSALSA_DEBUG 
SRC = algorend.o cn3dentr.o cn3dmain.o cn3dmatn.o cn3dmesh.o cn3dmodl.o \
cn3dmsel.o cn3dmsg.o cn3dopen.o cn3dsave.o cn3dshim.o \
cn3dwin.o cn3dxprt.o seqcons.o cn3dstyl.o
EXE = Cn3D


CFLAGS = $(CFLAGS1) $(OPTFLAG) -I. -I$(INCPATH) $(VIBFLAG) $(DEF)
LDFLAGS = -I. -I$(INCPATH) $(OPTFLAG) -L../lib -L$(LIBPATH) $(VIBFLAG) $(DEF)

# all NCBI libraries aliased for easy access here

LIB1 = -lncbi
LIB2 = -lncbiobj
LIB3 = -lncbicdr
LIB4 = -lvibrant
LIB5 = -lncbiacc
LIB6 = -lnetcli
LIB7 = -lnetentr
LIB8 = -lncbiNacc
LIB9 = -lncbiCacc
# LIB10 is reserved for NCSA socket library
#LIB10 =
LIB11 = -lncbimla
LIB12 = -lncbitax1
LIB13 = -lncbiid0
LIB18 = -lncbibls2
LIB19 = -lncbispel
LIB20 = -lncbidesk
LIB21 = -lncbibls2
LIB22 = -lncbimmdb
LIB23 = -lncbitool
LIB29 = -lncbitxc1
LIB31 = -lvibnet
LIB33 = -lsmartnet
LIB36 = -lncbitree
LIB41 = -lncbiid1

## To clean out the directory without removing make
##

## Implicit actions
##
## if need a .o, compile the .c
##

.KEEP_STATE:

.c.o :
	$(CC) $(CFLAGS) $<

#####################################################################
##
## Here is where you set up your own things to make
##
#####################################################################

## Default thing to make will be "all"
##

all : $(EXE)

## make individual applications and components
##

$(EXE) : $(SRC)
	$(CC) -o $(EXE) $(LDFLAGS) $(SRC)  $(LIB31) $(LIB20) $(LIB41) -lnetblast $(LIB22) \
	$(LIB8) $(LIB7) $(LIB6) $(LIB3) $(LIB4) $(LIB23) $(LIB2) $(LIB1) \
	$(NCBI_VIBLIBS) $(LIB36) $(NCBI_OTHERLIBS)