#
# makefile for fasta3, fasta3_t.  Use makefile.pvm for pvcompxx.

# MSDOS Borland C commands
#CC= bcc -mm -w-rvl -w-pro -3 -O
CC= bcc32 -WC -w-rvl -w-pro -3 -O
#CFLAGS= -IC:\bc5\include -DFAR_PTR -DALLOCN0 -DMSDOS 
CFLAGS=-IC:\bc5\include -DBIGMEM -DALLOCN0 -DMSDOS
#CL= bcc -mm
CL= bcc32 -WC
LFLAGS= -LC:\bc5\lib
NRAND= nrand
HZ=100


XDIR = /seqprg/slib/bin

SPROGS = fasta34.exe ssearch34.exe fastx34.exe tfastx34.exe fasty34.exe tfasty34.exe fasts34.exe tfasts34.exe prss34.exe prfx34.exe

PROGS = $(SPROGS)

all : $(PROGS)

sall: $(SPROGS)

clean-up:
	del *.obj $(PROGS)

install:
	cp $(PROGS) $(XDIR)

fasta34.exe : comp_lib.obj compacc.obj showbest.obj showalig.obj htime.obj apam.obj doinit.obj init_fa.obj scaleswn.obj karlin.obj drop_nfa.obj getseq.obj lgetlib.obj regetlib.obj ncbl2_lib.obj c_dispn.obj lib_sel.obj url_subs.obj nrand.obj getopt.obj
	$(CL) $(LFLAGS) -efasta34.exe comp_lib.obj showalig.obj init_fa.obj drop_nfa.obj getseq.obj  @fasta3.rsp -lm

fastx34.exe : comp_lib.obj compacc.obj showbest.obj showalig.obj htime.obj apam.obj doinit.obj init_fx.obj scaleswn.obj karlin.obj drop_fx.obj getseq.obj lgetlib.obj regetlib.obj ncbl2_lib.obj c_dispn.obj lib_sel.obj faatran.obj url_subs.obj nrand.obj getopt.obj
	$(CL) $(LFLAGS) -efastx34.exe comp_lib.obj showalig.obj init_fx.obj drop_fx.obj faatran.obj getseq.obj  @fasta3.rsp -lm

fasty34.exe : comp_lib.obj compacc.obj showbest.obj showalig.obj htime.obj apam.obj doinit.obj init_fy.obj scaleswn.obj karlin.obj drop_fz.obj getseq.obj lgetlib.obj regetlib.obj ncbl2_lib.obj c_dispn.obj lib_sel.obj faatran.obj url_subs.obj nrand.obj
	$(CL) $(LFLAGS) -efasty34.exe comp_lib.obj showalig.obj init_fy.obj drop_fz.obj faatran.obj getseq.obj  @fasta3.rsp -lm

tfastx34.exe : comp_lib.obj compacc.obj showbest.obj showalig.obj htime.obj apam.obj doinit.obj init_tfx.obj getseq.obj lgetlib.obj regetlib.obj ncbl2_lib.obj scaleswn.obj karlin.obj tdropfx.obj c_dispn.obj lib_sel.obj faatran.obj url_subs.obj nrand.obj
	$(CL) $(LFLAGS) -etfastx34.exe comp_lib.obj showalig.obj init_tfx.obj tdropfx.obj faatran.obj getseq.obj @fasta3.rsp -lm

tfasty34.exe : comp_lib.obj compacc.obj showbest.obj showalig.obj htime.obj apam.obj doinit.obj init_tfy.obj getseq.obj lgetlib.obj regetlib.obj ncbl2_lib.obj scaleswn.obj karlin.obj tdropfz.obj c_dispn.obj lib_sel.obj faatran.obj url_subs.obj nrand.obj
	$(CL) $(LFLAGS) -etfasty34.exe comp_lib.obj showalig.obj init_tfy.obj tdropfz.obj faatran.obj getseq.obj @fasta3.rsp -lm

ssearch34.exe : comp_lib.obj compacc.obj showbest.obj showalig.obj htime.obj apam.obj doinit.obj init_sw.obj scaleswn.obj karlin.obj dropgsw.obj getseq.obj lgetlib.obj regetlib.obj ncbl2_lib.obj c_dispn.obj lib_sel.obj url_subs.obj nrand.obj pssm_asn_subs.obj
	$(CL) $(LFLAGS) -essearch34.exe comp_lib.obj showalig.obj init_sw.obj dropgsw.obj getseq.obj pssm_asn_subs.obj @fasta3.rsp -lm

fasts34.exe : comp_lib.obj compacc.obj showbest.obj showalig.obj htime.obj apam.obj doinit.obj init_fs.obj dropfs2.obj scaleswt.obj karlin.obj tatsta_s.obj last_tat.obj getseq.obj lgetlib.obj regetlib.obj ncbl2_lib.obj c_dispn.obj lib_sel.obj url_subs.obj nrand.obj getopt.obj
	$(CL) $(LFLAGS) -efasts34.exe comp_lib.obj showalig.obj init_fs.obj dropfs2.obj getseq.obj @fasts3.rsp -lm

tfasts34.exe : comp_lib.obj compacc.obj showbest.obj showalig.obj htime.obj apam.obj doinit.obj init_tfs.obj droptfs2.obj scaleswt.obj karlin.obj tatsttfs.obj last_tat.obj getseq.obj lgetlib.obj regetlib.obj ncbl2_lib.obj c_dispn.obj lib_sel.obj url_subs.obj nrand.obj faatran.obj getopt.obj
	$(CL) $(LFLAGS) -etfasts34.exe comp_lib.obj showalig.obj init_tfs.obj droptfs2.obj getseq.obj faatran.obj @tfasts3.rsp -lm

prss34.exe : rcomplib.obj compacc.obj htime.obj apam.obj doinit.obj init_rss.obj scaleswn.obj karlin.obj dropgsw.obj llgetaa.obj showrss.obj lib_sel.obj nrand.obj getopt.obj pssm_asn_subs.obj
	$(CL) $(LFLAGS) -eprss34.exe rcomplib.obj init_rss.obj dropgsw.obj llgetaa.obj nrand.obj @prss3.rsp -lm

prfx34.exe : rcomplib.obj compacc.obj htime.obj apam.obj doinit.obj init_rfx.obj scaleswn.obj karlin.obj drop_fx.obj llgetaa.obj faatran.obj showrss.obj lib_sel.obj nrand.obj getopt.obj
	$(CL) $(LFLAGS) -eprfx34.exe rcomplib.obj init_rfx.obj drop_fx.obj faatran.obj llgetaa.obj  nrand.obj @prss3.rsp -lm

comp_lib.obj : comp_lib.c mw.h structs.h defs.h param.h
	$(CC) $(CFLAGS) -DPGM_DOC -ocomp_lib.obj -c comp_lib.c

rcomplib.obj : comp_lib.c mw.h structs.h defs.h param.h
	$(CC) $(CFLAGS) -DPRSS -orcomplib.obj -c comp_lib.c

htime.obj : htime.c
	$(CC) $(CFLAGS) -c htime.c

hxgetaa.obj : hxgetaa.c altlib.h upam.h uascii.h
	$(CC) $(CFLAGS) -c hxgetaa.c

init_sw.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DSSEARCH -oinit_sw.obj initfa.c

init_ssw.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DOSEARCH -oinit_ssw.obj initfa.c

init_rss.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DPRSS -oinit_rss.obj initfa.c

init_rfx.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DPRFX -oinit_rfx.obj initfa.c

init_fa.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTA -oinit_fa.obj initfa.c

init_ff.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTF -oinit_ff.obj initfa.c

init_tf.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTF -DTFAST -oinit_tf.obj initfa.c

init_fs.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTS -oinit_fs.obj initfa.c

init_fm.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTM -oinit_fm.obj initfa.c

init_tfs.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTS -DTFAST  -oinit_tfs.obj initfa.c

init_tfm.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTM -DTFAST  -oinit_tfm.obj initfa.c

init_tfa.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTA -DTFAST -oinit_tfa.obj initfa.c

init_fx.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTX -oinit_fx.obj initfa.c

init_tfx.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTX -DTFAST -oinit_tfx.obj initfa.c

init_fy.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTY -oinit_fy.obj initfa.c

init_tfy.obj : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTY -DTFAST -oinit_tfy.obj initfa.c

doinit.obj : doinit.c defs.h param.h upam.h structs.h
	$(CC) $(CFLAGS) -c doinit.c

compacc.obj : compacc.c upam.h uascii.h param.h structs.h mw.h defs.h
	$(CC) $(CFLAGS) -c compacc.c

showbest.obj : mshowbest.c mw.h defs.h param.h structs.h mm_file.h
	$(CC) $(CFLAGS) -oshowbest.obj -c mshowbest.c

showrss.obj : showrss.c mw.h defs.h param.h structs.h
	$(CC) $(CFLAGS) -c showrss.c

showalig.obj : mshowalign.c mw.h defs.h structs.h param.h
	$(CC) $(CFLAGS) -oshowalig.obj -c mshowalign.c

c_dispn.obj : c_dispn.c defs.h structs.h param.h 
	$(CC) $(CFLAGS) -c c_dispn.c

lib_sel.obj : lib_sel.c defs.h structs.h
	$(CC) $(CFLAGS) -c lib_sel.c

scaleswn.obj : scaleswn.c defs.h mw.h alt_parms.h
	$(CC) $(CFLAGS) -c scaleswn.c

scaleswt.obj : scaleswt.c defs.h mw.h alt_parms.h
	$(CC) $(CFLAGS) -c scaleswt.c

tatsta_s.obj : tatstats.c defs.h mw.h alt_parms.h tatstats.h
	$(CC) $(CFLAGS) -DFASTS -otatsta_s.obj -c tatstats.c

tatsttfs.obj : tatstats.c defs.h mw.h alt_parms.h tatstats.h
	$(CC) $(CFLAGS) -DTFAST -DFASTS -otatsttfs.obj -c tatstats.c

karlin.obj : karlin.c param.h
	$(CC) $(CFLAGS) -c karlin.c

scaleswg.obj : scaleswg.c defs.h mw.h alt_parms.h
	$(CC) $(CFLAGS) -c scaleswg.c

drop_nfa.obj : dropnfa.c param.h defs.h
	$(CC) $(CFLAGS) -odrop_nfa.obj -c dropnfa.c

drop_ff.obj : dropffa.c mw.h param.h defs.h
	$(CC) $(CFLAGS) -odrop_ff.obj -c dropffa.c

drop_tff.obj : dropffa.c mw.h param.h defs.h
	$(CC) $(CFLAGS) -DTFAST -odrop_tff.obj -c dropffa.c

drop_fx.obj : dropfx.c mw.h upam.h param.h defs.h
	$(CC) $(CFLAGS) -DFASTX -odrop_fx.obj -c dropfx.c

dropfs2.obj : dropfs2.c mw.h upam.h param.h defs.h tatstats.h
	$(CC) $(CFLAGS) -DFASTS  -c dropfs2.c

droptfs2.obj : dropfs2.c mw.h upam.h param.h defs.h tatstats.h
	$(CC) $(CFLAGS) -DTFAST -DFASTS -c -odroptfs2.obj dropfs2.c

tdropfx.obj : dropfx.c mw.h upam.h param.h defs.h
	$(CC) $(CFLAGS) -DTFAST -otdropfx.obj -c dropfx.c

drop_fz.obj : dropfz2.c mw.h upam.h param.h defs.h aamap.h
	$(CC) $(CFLAGS) -odrop_fz.obj -c dropfz2.c

tdropfz.obj : dropfz2.c mw.h upam.h param.h defs.h aamap.h
	$(CC) $(CFLAGS) -DTFAST -otdropfz.obj -c dropfz2.c

dropnsw.obj : dropnsw.c mw.h upam.h param.h structs.h
	$(CC) $(CFLAGS) -c dropnsw.c

dropgsw.obj : dropgsw.c mw.h upam.h param.h structs.h
	$(CC) $(CFLAGS) -c dropgsw.c

dropnw.obj : dropnw.c mw.h upam.h param.h structs.h
	$(CC) $(CFLAGS) -c dropnw.c

llgetaa.obj : llgetaa.c altlib.h upam.h uascii.h
	$(CC) $(CFLAGS) -DNOLIB -c llgetaa.c

lgetlib.obj : nmgetlib.c altlib.h upam.h uascii.h
	$(CC) $(CFLAGS) -olgetlib.obj  -c nmgetlib.c

regetlib.obj : re_getlib.c mw.h mm_file.h
	$(CC) $(CFLAGS) -oregetlib.obj -c re_getlib.c

getseq.obj : getseq.c defs.h uascii.h structs.h upam.h 
	$(CC) $(CFLAGS) -c getseq.c

ncbl_lib.obj : ncbl_lib.c ncbl_head.h
	$(CC) $(CFLAGS) -c ncbl_lib.c

ncbl2_lib.obj : ncbl2_mlib.c ncbl2_head.h
	$(CC) $(CFLAGS) -c ncbl2_mlib.c

faatran.obj : faatran.c upam.h uascii.h
	$(CC) $(CFLAGS) -c faatran.c

url_subs.obj : url_subs.c structs.h param.h
	$(CC) $(CFLAGS) -c url_subs.c

nrand48.obj : nrand48.c
	$(CC) $(CFLAGS) -c nrand48.c

nrand.obj : nrand.c
	$(CC) $(CFLAGS) -c nrand.c

getopt.obj : getopt.c
	$(CC) $(CFLAGS) -c getopt.c