#  %W% %G%
#################################################################
############### acedb: R.Durbin and J.Thierry-Mieg ##############
######### wstaden/makefile.staden  Feb 2000        ##############
#################################################################
#
# ATTENTION:
#   Define in this file machine independant directives
#   to compile staden codes linked against acelib
#
#   The makefile is decomposed into 2 parts
#     makefile: which selects the machine and creates ./bin.*
#     then copies the present file into ../bin.*
#     and the present file which gives details on the linking
#  
#   Machine specific choices, like linker and compiler
#     are specified in ../wmake/*_DEF
#
#   Object modules and exe are created in ../bin.*
#     to keep the present directory clean and allow
#     multiple architectures
#
###########################################################
## Compile Time Variants
## A single source code will produce several object modules
## Rules are given below
###########################################################

# add any new special suffix here - do not have multiple .SUFFIXES lines 
.SUFFIXES: .o .c .o 

#################################################################
# Before running the make command
# setenv ACEDB_MACHINE to indicate one of the predefined
# Machine dependant option files, or write your own.
# These files are called  $(ACEDB_SRC)/wmake/$(ACEDB_MACHINE)_DEF
#
# See the explanation at the top of ../wmake/truemake
#################################################################

COMPI = $(COMPILER)  -DACEDB -D$(NAME) -I.. -I../wh -I../wstaden  -I.
ACELIBS =   $(LIBS) -L. -lfree -lm

.KEEP_STATE: 
## Different platforms use CC or COMPILE.c
CC =        $(COMPI)  -c
COMPILE.c = $(COMPI)  -c


# suppress auto SCCS extraction
.SCCS_GET:

#define defaults  overridable in $(ACEDB_MACHINE)_DEF
RANLIB_NEEDED = true	
AR_OPTIONS = rlu

LINKER = cc
COMPILER = cc

CCFLAGS =  ## to undefine any rubbish
GCFLAGS =  ## to undefine any rubbish

#################################################################
# include your choice froma machine dependant file
# do not edit the present makefile for this purpos
# this simplifies multiple architecture maintainance

include deffile

# Note that you can keep different DEF files for the same machine
# setting  various compiler  options

#################################################################
#################################################################
# Add here your definitions
#################################################################
#################################################################

all: libstaden.a makeSCF scf2ctf ctf2scf

# Rodger Staden's code to read his scf files
LIBSTADEN = wstaden

## acedb specific build for libstaden.a compiled with -DACEDB

LIBSTADEN_OBJS = read_alloc.o Read.o filecompress.o \
		st_translate.o read_scf.o \
		find.o mach-io.o dummy.o \
		traceType.o misc_scf.o \
		xalloc.o error.o files.o \
		stadenarray.o fpoint.o \
		write_scf.o  \
		seqIOALF.o seqIOABI.o seqIOCTF.o \
		seqIOPlain.o expFileIO.o ctfCompress.o 

MAKESCF_OBJS = makeSCF.o dnaacecode.o

SCF2CTF_OBJS = scf2ctf.o dnaacecode.o

CTF2SCF_OBJS = ctf2scf.o dnaacecode.o

STADEN_SOURCES =  $(LIBSTADEN_OBJS:.o=.c)  \
	makeSCF.c dnaacecode.c scf2ctf.c ctf2scf.c

$(STADEN_SOURCES): 
	ln -s ../$(LIBSTADEN)/$@ .

###########################################################
###### Staden library #####################################
## all modules here were copied form Roger Staden distribution
## io_lib-1.7.tar.gz
## with just a few modifications of file names to prevent name conflicts
## for example between staden's array.h and acedb array.h

libstaden.a: $(LIBSTADEN_OBJS)
	ar $(AR_OPTIONS) libstaden.a $?
	if ( $(RANLIB_NEEDED) ) then ranlib libstaden.a; fi

makeSCF: libstaden.a $(MAKESCF_OBJS)
	$(LINKER)  -o makeSCF $(MAKESCF_OBJS) -L. -lstaden -lfree $(LIBS)

scf2ctf: libstaden.a $(SCF2CTF_OBJS)
	$(LINKER)  -o scf2ctf $(SCF2CTF_OBJS) -L. -lstaden -lfree $(LIBS)

ctf2scf: libstaden.a $(CTF2SCF_OBJS)
	$(LINKER)  -o ctf2scf $(CTF2SCF_OBJS) -L. -lstaden -lfree $(LIBS)

###########################################################
######## end of     acedb makefile.staden  ################
###########################################################