# Makefile for staden X programs (Silicon Graphics version)
# ---------------------------------------------------------

# This makefile generates the following staden programs which
# run under xterm (normal, `N') and those which run directly under X.
NPROGS=      mep  nip   pip   dap  sap  sip   splitp1 splitp2 splitp3 gip sethelp convert_project sapf nipf vep rep lip
LPROGS=           nipl  pipl            sipl
XPROGS=     xmep xnip  xpip  xdap xsap xsip
PROGS= $(NPROGS) $(LPROGS) $(XPROGS)







#
# ``Interesting'' suffices that make needs to know about
#
.SUFFIXES: .a $(SUFFIXES)


#
# Where the wild things are
#
SRC=.
TEDSRC=$(SRC)/../ted
MISCSRC=$(SRC)/../Misc
MISCBIN=$(MISCSRC)
INCLUDES= -I$(SRC) -I$(TEDSRC) -I$(MISCSRC)


#
# Compilers and flags
#
CC= cc
CFLAGS= -g -ansi -prototypes $(INCLUDES)
F77= f77
FFLAGS=  -g -c -old_rl

FLIBS= -lF77 -lU77 -lm -lI77 -lisam
XLIBS= -lXaw -lXt -lXmu -lXext -lX11
LFLAGS= $(FLIBS)
XLFLAGS= $(XLIBS) $(FLIBS)

LD = cc
LDFLAGS = -g 

#
# Shell to perform make commands
#
SHELL=/bin/sh

#
# Sequence library handling routines
#
SEQLIB=\
	seqlibsubs.o
#	/usr/lib/fixade.o


#
# The C objects, needed by every X program
#
CCORE=\
	postscript.o\
	Graph.o\
	plotLog.o\
	help.o\
	dialogues.o\
	userfacecom.o\
	helpnmenu.o\
	xmenu.o\
	FtoC.o\
	mcspec.o\
	locks.o

COBJS=\
	main.o\
	$(CCORE)

XDAPCOBJS=\
	xdapmain.o\
	$(CCORE)


#
# Common objects, needed by every program
#
COMMONOBJSB=\
	fmain.o\
	seeme-sg.o\
	nxspec.o\
	userface.o\
	userfacecom.o\
	nxhelpmenu.o\
	helpnmenu.o\
	FtoC.o\
	subs89.a

COMMONOBJS=\
	$(COMMONOBJSB)\
	postscript.o

SCOMMONOBJS=\
	$(COMMONOBJSB)

XCOMMONOBJS=\
	seeme-sg.o\
	xspec.o\
	subs89.a\
	$(COBJS)

XDAPCOMMONOBJS=\
	seeme-sg.o\
	xspec.o\
	subs89.a\
	$(XDAPCOBJS)


#
# Building the programs
# This should be just a linking phase because all of the object
# files and library files are generated using implicit rules.
# We use the fortran compiler to do linking.
#
GIP=\
	gip.o

GIPOBJS=\
	$(GIP)\
	$(SCOMMONOBJS)

gip: $(GIPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(GIPOBJS) $(LFLAGS)


LIP=\
	lip.o
 
LIPOBJS=\
	$(LIP)\
	$(SEQLIB)\
	$(COMMONOBJS)
 
lip: $(LIPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(LIPOBJS) $(LFLAGS)




MEP=\
	mep.o\
	mepsub.o\
	asubs89.a\
	plot92.a

MEPOBJS=\
	$(MEP)\
	$(COMMONOBJS)\
	pl4010.o

XMEPOBJS=\
	$(MEP)\
	$(XCOMMONOBJS)\
	plX.o\
	textOutput.o 

mep: $(MEPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(MEPOBJS)  $(LFLAGS)

xmep: $(XMEPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(XMEPOBJS) $(XLFLAGS)




NIP=\
	nip.o\
	patternn.a\
	patternnc.a\
	anals89.a\
	asubs89.a\
	plot92.a \
	$(SEQLIB)

NIPOBJS=\
	$(NIP)\
	$(COMMONOBJS)\
	pl4010.o

XNIPOBJS=\
	$(NIP)\
	$(XCOMMONOBJS)\
	plX.o\
	textOutput.o 

nip: $(NIPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(NIPOBJS) $(LFLAGS)

xnip: $(XNIPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(XNIPOBJS) $(XLFLAGS)




NIPL=\
	nipl.o\
	patternnc.a\
	anals89.a\
	asubs89.a\
	$(SEQLIB)

NIPLOBJS=\
	$(NIPL)\
	$(SCOMMONOBJS)

nipl: $(NIPLOBJS)
	$(LD) $(LDFLAGS) -o $@ $(NIPLOBJS) $(LFLAGS)



NIPF=\
	nipf.o\
	asubs89.a\
	plot92.a

NIPFOBJS=\
	$(NIPF)\
	$(COMMONOBJS)\
	pl4010.o


nipf: $(NIPFOBJS)
	$(LD) $(LDFLAGS) -o $@ $(NIPFOBJS) $(LFLAGS)





PIP=\
	pip.o\
	analps89.a\
	patternp.a\
	patternpc.a\
	asubs89.a\
	plot92.a\
	$(SEQLIB)

PIPOBJS=\
	$(PIP)\
	$(COMMONOBJS)\
	pl4010.o

XPIPOBJS=\
	$(PIP)\
	$(XCOMMONOBJS)\
	plX.o\
	textOutput.o 

pip: $(PIPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(PIPOBJS)  $(LFLAGS)

xpip:$(XPIPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(XPIPOBJS) $(XLFLAGS)




PIPL=\
	pipl.o\
	patternpc.a\
	analps89.a\
	asubs89.a\
	$(SEQLIB)

PIPLOBJS=\
	$(PIPL)\
	$(SCOMMONOBJS)

pipl: $(PIPLOBJS)
	$(LD) $(LDFLAGS) -o $@ $(PIPLOBJS)  $(LFLAGS)



#
# Trace manager objects
#
STDTEDFILES=\
	seq.o\
	seqIOABI.o\
	seqIOALF.o\
	seqIOSCF.o\
	seqIOPlain.o\
	opp.o\
	fpoint.o\
	mach-io.o

TMANOBJS=\
	tman_main.o\
	tman_display.o\
	tman_traceDisplay.o\
	tman_basesDisplay.o\
	tman_context.o\
	tman_gadgets.o\
	$(STDTEDFILES)

# Some versions of X11R4 may have a bug in SmeLine.c
XHACK=\
	SmeLine.o

EDITOR=\
	$(XHACK)\
	xsapConEdit.o\
	contigEditor.o\
	edUtils.o\
	undo.o\
	Sheet.o\
	select.o\
	extend.o\
	searchUtils.o\
	edMenu.o\
	trans.o\
	$(MISCBIN)/misc.a

TAGEDITOR=\
	tagEditor.o\
	tagdbparse.o\
	tagU2.o\
	tagU1.o

DAP=\
	dap.o\
	dbsysnew.o\
	dbsyscommon.o\
	asubs89.a\
	plot92.a

DAPOBJS=\
	$(DAP)\
	$(COMMONOBJS)\
	pl4010.o\
	conEdit.o\
	tagU2.o

XDAPOBJS=\
	$(DAP)\
	$(XDAPCOMMONOBJS)\
	plX.o\
	textOutput.o\
	$(EDITOR)\
	$(TMANOBJS)\
	$(TAGEDITOR)

dap: $(DAPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(DAPOBJS) $(LFLAGS)

xdap: $(XDAPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(XDAPOBJS) $(XLFLAGS)

convert_project: cvt.o
	$(CC) $(CFLAGS) -o $@ cvt.o

SAP=\
	sap.o\
	dbsyscommon.o\
	dbsysold.o\
	asubs89.a\
	plot92.a

SAPOBJS=\
	$(SAP)\
	$(COMMONOBJS)\
	pl4010.o

XSAPOBJS=\
	$(SAP)\
	$(XCOMMONOBJS)\
	plX.o\
	textOutput.o 

sap: $(SAPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(SAPOBJS) $(LFLAGS)

xsap: $(XSAPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(XSAPOBJS) $(XLFLAGS)




SAPF=\
	sapf.o\
	dbsyscommon.o\
	dbsysold.o\
	asubs89.a\
	plot92.a

SAPFOBJS=\
	$(SAPF)\
	sapmen.o\
	$(COMMONOBJS)\
	pl4010.o

sapf: $(SAPFOBJS)
	$(LD) $(LDFLAGS) -o $@ $(SAPFOBJS) $(LFLAGS)






SIP=\
	sip.o\
	dias89.a\
	plot92.a\
	$(SEQLIB)

SIPOBJS=\
	$(SIP)\
	$(COMMONOBJS)\
	pl4010.o

XSIPOBJS=\
	$(SIP)\
	$(XCOMMONOBJS)\
	plX.o\
	textOutput.o 

sip: $(SIPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(SIPOBJS) $(LFLAGS)

xsip: $(XSIPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(XSIPOBJS) $(XLFLAGS)




SIPL=\
	sipl.o\
	dias89.a\
	$(SEQLIB)

SIPLOBJS=\
	$(SIPL)\
	$(SCOMMONOBJS)

sipl: $(SIPLOBJS)
	$(LD) $(LDFLAGS) -o $@ $(SIPLOBJS) $(LFLAGS)




SETHELP=\
	sethelp.o

SETHELPOBJS=\
	$(SETHELP)\

sethelp: $(SETHELPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(SETHELPOBJS) $(LFLAGS)




SPLITP1=\
	splitp1.o
SPLITP1OBJS=\
	$(SPLITP1)\
	$(SCOMMONOBJS)

splitp1: $(SPLITP1OBJS)
	$(LD) $(LDFLAGS) -o $@ $(SPLITP1OBJS) $(LFLAGS)




SPLITP2=\
	splitp2.o
SPLITP2OBJS=\
	$(SPLITP2)\
	$(SCOMMONOBJS)

splitp2: $(SPLITP2OBJS)
	$(LD) $(LDFLAGS) -o $@ $(SPLITP2OBJS) $(LFLAGS)





SPLITP3=\
	splitp3.o
SPLITP3OBJS=\
	$(SPLITP3)\
	$(SCOMMONOBJS)

splitp3: $(SPLITP3OBJS)
	$(LD) $(LDFLAGS) -o $@ $(SPLITP3OBJS) $(LFLAGS)



REP=\
	rep.o\
	dias89.a\
	subs89.a

REPOBJS=\
	$(REP)\
	$(COMMONOBJS)
 
rep:	$(REPOBJS)
	$(F77) $(LDFLAGS) -o $@ $(REPOBJS) $(LFLAGS)





VEP=\
	vep.o\
	dias89.a\
	subs89.a


VEPOBJS=\
	$(VEP)\
	$(SCOMMONOBJS)


vep: $(VEPOBJS)
	$(LD) $(LDFLAGS) -o $@ $(VEPOBJS)  $(LFLAGS)




#
# Special dependencies
#
#

#
# Files requiring simple C compilation (thing.c -> thing.o)
# 
%.o: %.c
	$(CC) $(CFLAGS) -c $<
%.o: $(SRC)/%.c
	$(CC) $(CFLAGS) -c $<
%.o: $(TEDSRC)/%.c
	$(CC) $(CFLAGS) -c $<

# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
# 
%.o: $(SRC)/%.f
	$(F77) $(FFLAGS) -c $<


#
# The UNIX library (archive) mechanism is fairly weak so the following
# procedure is used to generate libraries.
#   * split the source file up into files which each contain
#     a single function or subroutine
#   * compile each of those files
#   * insert the object files individually into the library
# Each library is built by using a temporary directory.
# The fortran compilations must be done sequentially in order to
# avoid filling up the (small on this machine) /tmp directory
# with compiler debugging information.
#
%.a:	$(SRC)/%.f
	BINDIR=`pwd`; \
	cd $(SRC); \
	SRCDIR=`pwd`; \
	TMPDIR=/tmp/staden$$$$; \
	if test ! -d $$TMPDIR; \
	then mkdir $$TMPDIR; \
	fi; \
	cd $$TMPDIR; \
	rm -f *.f *.o; \
	fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
	$(F77) $(FFLAGS) -c *.f; \
	rm *.f; \
	rm -f $$BINDIR/$@; \
	ar rcv $$BINDIR/$@ *.o; \
	echo ranlib $$BINDIR/$@; \
	rm *.o; \
	cd $$BINDIR; \
	rm -r $$TMPDIR






all: $(PROGS)

nprogs: $(NPROGS)

xprogs: $(XPROGS)

lprogs: $(LPROGS)

clean:
	rm -f $(PROGS) *.a *.o *~