#	makefile for demo programs
#
#	$Id: makedemo.unx,v 6.94 2008/07/29 19:42:43 ucko Exp $
#
#	Sun with unbundled ANSI compiler [ make CC=acc ]
#	Sun with Gnu C [ make CC=gcc ]
#   Sun with Solaris 2.x OS [ make CC="cc -Xa" OTHERLIBS="-lthread -lm" ]
#	Silicon Graphics [ make OTHERLIBS="-lm -lPW -lsun" ]
#	IBM 3090 with AIX [ make  ]
#	ULTRIX [ make ]
#	Apple AUX [ make SHELL=\usr\bin ]
#	NeXt [ make CFLAGS1="-c -ansi"  ]
#   DEC Alpha under OSF/1  [ make CC=cc ]
#   BeOS [  make OTHERLIBS="" ]
#	
#	Subsequent makes should make ... nocopy instead of make ... all
#	to avoid recopying the include files
#
#	To Make the Motif version of demos add:
#      VIBLIBS="-lXm -lXmu -lXt -lX11" LIB4=-lvibrant VIBFLAG="-I/am/Motif/include -DWIN_MOTIF"
#   to the argument list.  Substitute the path to your Motif includes for
#    /am/Motif/include.
#
#   Motif versions on Solaris 2.x are more complicated because of changes to
#   the socket I/O. You have explicitly include them. Try:
#
# make -f makedemo.unx CC="cc -Xa"
# VIBLIBS="-L/netopt/X11R5/lib -L/netopt/Motif1.2.2/lib -R/netopt/X11R5/lib:/netopt/Motif1.2.2.lib -lXm -lXmu -lXt -lX11 -lsocket -lnsl -lgen"
# LIB4=-lvibrant
# VIBFLAG="-I/netopt/X11R5/include -I/netopt/Motif1.2.2/include -DWIN_MOTIF"
#
#   The build for RedHat Linux 2.XX with X11R6 requires:
#     CC="gcc -ansi"
#     VIBLIBS="-L/usr/X11R6/lib -lXm -lXpm -lXmu -lXp -lXt -lX11 -lXext"
#
#   NOTE: It is now possible to build using shared libraries, which 
#     consumes significantly less disk space.  To date, this has only
#     been tested using Solaris.  To use shared libraries, try:
#       make ... NCBI_LINKINGLIBDIR=../shlib
#            NCBI_OTHERLINKOPTIONS=-R`pwd`/../shlib
#


# default flags for compiling and loading

SUFFIXLCL = $(LCL)
CFLAGS1 = -c -O
LDFLAGS1 = -O
CC = cc
RAN = ls -l
OTHERLIBS = -lm
THREAD_OTHERLIBS = -lthread
THREAD_OTHERLIBS =
THREAD_OBJ = ncbithr.o
THREAD_OBJ =
VIBLIBS = 
VIBFLAG =
VIB =
LIBCOPY = cp -p
SRCCOPY = ./ln-if-absent
BINCOPY = cp -p

SUFFIXENV = unx
ASNDIR = asnstat
LIB1 = -lncbi
LIB2 = -lncbiobj
LIB3 = -lncbicdr
LIB4 = -lvibrant
LIB4 =
LIB5 = -lncbiacc
LIB20 = -lncbidesk
LIB20 =
LIB22 = -lncbimmdb
LIB23 = -lncbitool
LIBCOMPADJ = -lblastcompadj
LIB50 = -lregexp
LIB60 = -lblast
LIB61 = -lblastapi
NCBI_INCDIR = ../include
NCBI_LIBDIR = ../lib
NCBI_LINKINGLIBDIR = $(NCBI_LIBDIR)
# A kludge which tells the linker not to try to use shared libraries
# when linking programs which use main() instead of Nlm_Main()
USES_MAIN_KLUDGE = -L$(NCBI_LIBDIR)
NCBI_OTHERLINKOPTIONS =
CFLAGS = $(CFLAGS1) -I$(NCBI_INCDIR) $(VIBFLAG)
LDFLAGS = $(LDFLAGS1) -I$(NCBI_INCDIR) $(NCBI_OTHERLINKOPTIONS) -L$(NCBI_LINKINGLIBDIR) $(VIBFLAG)
ENTREZLIBS = $(LIB5) $(LIB3)

##
## some things to make
##

# sources needed for versions of demo programs

EXE1 = testcore makeset \
    getmesh indexpub getpub testobj seqtest \
	dosimple asn2ff checksub asndhuff \
	entrcmd errhdr cdscan findspl \
	ncbisort fa2htgs fastacmd formatdb formatrpsdb \
	blastall .WAIT blastpgp testval seedtop \
	makemat copymat impala \
	megablast vecscreen gil2bin blastclust rpsblast \
	asn2xml debruijn asn2idx sortbyquote subfuse \
	test_regexp demo_regexp demo_regexp_grep

SRC1 = testcore.c makeset.c \
    getmesh.c indexpub.c getpub.c testobj.c seqtest.c dosimple.c asn2ff.c \
    checksub.c asndhuff.c \
    entrcmd.c errhdr.c cdscan.c findspl.c \
    ncbisort.c fa2htgs.c fastacmd.c formatdb.c formatrpsdb.c \
    blast_driver.c blastall.c blastpgp.c testval.c seedtop.c \
    makemat.c copymat.c profiles.c \
	megablast.c vecscreen.c gil2bin.c blastclust.c rpsblast.c \
	asn2xml.c debruijn.c asn2idx.c sortbyquote.c subfuse.c \
	pcretest.c pcredemo.c pcregrep.c

INTERNAL = testgen

## All things to make
##
all : ln-if-absent copy .WAIT nocopy

ln-if-absent:	../make/ln-if-absent
	rm -f ln-if-absent
	ln -s ../make/ln-if-absent .

nocopy : sources $(EXE1) $(VIB)

sources : $(SRC1)

internal: $(INTERNAL)

## To clean out the directory without removing make
##
clean :
	- rm -f *.[acho]

.NO_PARALLEL:	copy

.WAIT:
	echo Waiting...go

## Implicit actions
##

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

## get all the source files
##

$(SRC1) : copy

copy :
	$(SRCCOPY) ../demo/*.* .
	$(SRCCOPY) ../regexp/test/*.* .
	$(SRCCOPY) ../regexp/demo/*.* .
	-$(SRCCOPY) ../internal/*.* .
	-chmod -R ug+rw,o+r .

## make applications
##


# testcore

testcore : testcore.c
	$(CC) -o testcore $(LDFLAGS) testcore.c $(LIB4) $(LIB1) $(VIBLIBS) $(OTHERLIBS)

# getmesh

getmesh : getmesh.c
	$(CC) -o getmesh $(LDFLAGS) getmesh.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)

# indexpub

indexpub : indexpub.c
	$(CC) -o indexpub $(LDFLAGS) indexpub.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)

# makeset

makeset : makeset.c
	$(CC) -o makeset $(LDFLAGS) makeset.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)

# getpub

getpub : getpub.c
	$(CC) -o getpub $(LDFLAGS) getpub.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)

# testobj

testobj : testobj.c
	$(CC) -o testobj $(LDFLAGS) testobj.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)

# dosimple

dosimple : dosimple.c
	$(CC) -o dosimple $(LDFLAGS) dosimple.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)

# seqtest

seqtest : seqtest.c
	$(CC) -o seqtest $(LDFLAGS) seqtest.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)


# checksub

checksub : checksub.c
	$(CC) -o checksub $(LDFLAGS) checksub.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)

# asn2ff

asn2ff : asn2ff.c
	$(CC) -o asn2ff $(LDFLAGS) asn2ff.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)

# fa2htgs

fa2htgs : fa2htgs.c
	$(CC) -o fa2htgs $(LDFLAGS) fa2htgs.c $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)

# cdscan

cdscan : cdscan.c
	$(CC) -o cdscan $(LDFLAGS) cdscan.c $(LIB4) $(ENTREZLIBS) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)

# findspl

findspl : findspl.c
	$(CC) -o findspl $(LDFLAGS) findspl.c $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)

# errhdr

errhdr : errhdr.c
	$(CC) -o errhdr $(LDFLAGS) errhdr.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)



# asndhuff

asndhuff : asndhuff.c
	$(CC) -o asndhuff $(LDFLAGS) asndhuff.c $(LIB4) $(ENTREZLIBS) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
 
# entrcmd

entrcmd : entrcmd.c
	$(CC) -o entrcmd $(LDFLAGS) entrcmd.c $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
 
# ncbisort

ncbisort : sortcmd.c
	$(CC) -o ncbisort $(LDFLAGS) sortcmd.c $(LIB23) $(LIBCOMPADJ) \
		$(LIB1) $(OTHERLIBS)

# testval

testval : testval.c
	$(CC) -o testval $(LDFLAGS) testval.c $(LIB2) $(LIB1) $(OTHERLIBS)

# fastacmd

fastacmd : fastacmd.c
	$(CC) -o fastacmd $(LDFLAGS) fastacmd.c $(LIB23) $(LIBCOMPADJ) \
		$(LIB2) $(LIB1) $(OTHERLIBS)

# formatdb

formatdb : formatdb.c
	$(CC) -o formatdb $(LDFLAGS) formatdb.c $(LIB23) $(LIBCOMPADJ) \
		$(LIB2) $(LIB1) $(OTHERLIBS)

# formatrpsdb

formatrpsdb : formatrpsdb.c
	$(CC) -o formatrpsdb $(LDFLAGS) formatrpsdb.c $(LIB61) $(LIB23) \
		$(LIBCOMPADJ) $(LIB60) $(LIB2) $(LIB1) $(OTHERLIBS)

debruijn : debruijn.c
	$(CC) -o debruijn $(LDFLAGS) debruijn.c $(LIB60) $(LIBCOMPADJ) $(LIB1) $(OTHERLIBS)
# blastall

blastall : blastall.c $(THREAD_OBJ)
	$(CC) -o blastall $(LDFLAGS) blastall.c $(THREAD_OBJ) $(LIB61) \
		$(LIB60) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \
		$(OTHERLIBS) $(THREAD_OTHERLIBS)

# blastpgp

blastpgp : blastpgp.c $(THREAD_OBJ)
	$(CC) -o blastpgp $(LDFLAGS) blastpgp.c $(THREAD_OBJ) $(LIB23) \
		$(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS)

# seedtop

seedtop : seedtop.c $(THREAD_OBJ)
	$(CC) -o seedtop $(LDFLAGS) seedtop.c $(THREAD_OBJ) $(LIB23) \
		$(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS)

# makemat

makemat : makemat.c $(THREAD_OBJ)
	$(CC) -o makemat $(LDFLAGS) makemat.c $(THREAD_OBJ) $(LIB23) \
		$(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS)

# copymat

copymat : copymat.c $(THREAD_OBJ)
	$(CC) -o copymat $(LDFLAGS) copymat.c $(THREAD_OBJ) $(LIB60) $(LIB23) \
		$(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS)

# impala

impala : profiles.c $(THREAD_OBJ)
	$(CC) -o impala $(LDFLAGS) profiles.c $(THREAD_OBJ) $(LIB23) \
		$(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS)

# testgen

testgen : testgen.c
	$(CC) -o testgen $(LDFLAGS) testgen.c $(LIB1) $(OTHERLIBS)

#testmem 

testmem : testmem.c
	$(CC) -o testmem $(LDFLAGS) testmem.c $(LIB2) $(LIB1) $(OTHERLIBS)

#packfilt 

packfilt : packfilt.c
	$(CC) -o packfilt $(LDFLAGS) packfilt.c $(LIB2) $(LIB1) $(OTHERLIBS)

# megablast

megablast : megablast.c $(THREAD_OBJ)
	$(CC) -o megablast $(LDFLAGS) megablast.c $(THREAD_OBJ) $(LIB61) \
		$(LIB60) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) \
		$(THREAD_OTHERLIBS)

# vecscreen

vecscreen : vecscreen.c $(THREAD_OBJ)
	$(CC) -o vecscreen $(LDFLAGS) vecscreen.c $(THREAD_OBJ) $(LIB23) \
		$(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS)

# gil2bin

gil2bin : gil2bin.c 
	$(CC) -o gil2bin $(LDFLAGS) gil2bin.c $(LIB23) $(LIBCOMPADJ) \
		$(LIB2) $(LIB1) $(OTHERLIBS) 

# asn2idx

asn2idx : asn2idx.c 
	$(CC) -o asn2idx $(LDFLAGS) asn2idx.c $(LIB23) $(LIBCOMPADJ) $(LIB2) \
		$(LIB1) $(OTHERLIBS) 

# sortbyquote

sortbyquote : sortbyquote.c 
	$(CC) -o sortbyquote $(LDFLAGS) sortbyquote.c $(LIB2) $(LIB1) $(OTHERLIBS) 

# subfuse

subfuse : subfuse.c 
	$(CC) -o subfuse $(LDFLAGS) subfuse.c $(LIB2) $(LIB1) $(OTHERLIBS) 

# blastclust

blastclust : blastclust.c $(THREAD_OBJ)
	$(CC) -o blastclust $(LDFLAGS) blastclust.c $(THREAD_OBJ) $(LIB23) \
		$(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS)

# rpsblast

rpsblast : rpsblast.c $(THREAD_OBJ)
	$(CC) -o rpsblast $(LDFLAGS) rpsblast.c $(THREAD_OBJ) $(LIB61) \
		$(LIB60) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) \
		$(THREAD_OTHERLIBS)


# asn2xml

asn2xml : asn2xml.c $(THREAD_OBJ)
	$(CC) -o asn2xml $(LDFLAGS) asn2xml.c $(LIB2) $(LIB1) $(OTHERLIBS)

# regexp demos

test_regexp : pcretest.c
	$(CC) -o test_regexp $(LDFLAGS) pcretest.c $(LIB50)
demo_regexp : pcretest.c
	$(CC) -o demo_regexp $(LDFLAGS) pcredemo.c $(LIB50)
demo_regexp_grep : pcretest.c
	$(CC) -o demo_regexp_grep $(LDFLAGS) pcregrep.c $(LIB50)