#================ common .o files 

doinit.o : doinit.c defs.h param.h upam.h structs.h uascii.h
	$(CC) $(THR_CC) $(CFLAGS) -c doinit.c

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

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

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

init_rfx.o : initfa.c defs.h param.h upam.h structs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DPRSS -DFASTX initfa.c -o init_rfx.o

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

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

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

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

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

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

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

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

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

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

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

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

#================ miscellaneous

htime.o : htime.c
	$(CC) $(THR_CC) $(CFLAGS) -c htime.c

compacc.o : compacc.c upam.h uascii.h param.h structs.h $(MWH) defs.h
	$(CC) $(THR_CC) $(CFLAGS) -c compacc.c

pssm_asn_subs.o : pssm_asn_subs.c defs.h
	$(CC) $(THR_CC) $(CFLAGS) -c pssm_asn_subs.c

#================ display list of best hits / alignments

showbest.o : $(SHOWBESTC) $(MWH) defs.h param.h structs.h  aln_structs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c $(SHOWBESTC) -o showbest.o

showrss.o : showrss.c $(MWH) defs.h param.h structs.h  aln_structs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c showrss.c

showun.o : mshowbest.c $(MWH) defs.h aln_structs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DSHOWUN mshowbest.c -o showun.o

showrel.o : $(SHOWBESTC) $(MWH) defs.h aln_structs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DSHOWREL $(SHOWBESTC) -o showrel.o

showsum.o : showsum.c $(MWH) defs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c showsum.c

$(SHOWALIGN).o : $(SHOWALIGN).c $(MWHP) defs.h structs.h param.h aln_structs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c $(SHOWALIGN).c -o $(SHOWALIGN).o

$(SHOWALIGN)_u.o : $(SHOWALIGN).c $(MWHP) defs.h structs.h param.h aln_structs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -DSHOWUN -c -o $(SHOWALIGN)_u.o $(SHOWALIGN).c
re_getlib.o : re_getlib.c mw.h mm_file.h
	$(CC) $(THR_CC) $(CFLAGS) -c re_getlib.c

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

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

#================ statistical functions

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

scaleswn.o : scaleswn.c defs.h param.h structs.h $(MWH) alt_parms.h
	$(CC) $(THR_CC) $(CFLAGS) -c scaleswn.c

scaleswtf.o : scaleswt.c defs.h param.h structs.h $(MWH) alt_parms.h
	$(CC) $(THR_CC) $(CFLAGS) -DFASTF -c scaleswt.c -o scaleswtf.o

scaleswts.o : scaleswt.c defs.h param.h structs.h $(MWH) alt_parms.h
	$(CC) $(THR_CC) $(CFLAGS) -c scaleswt.c -o scaleswts.o

tatstats_fs.o : tatstats.c tatstats.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTS tatstats.c -o tatstats_fs.o

tatstats_ff.o : tatstats.c tatstats.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTF tatstats.c -o tatstats_ff.o

tatstats_fm.o : tatstats.c tatstats.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTM tatstats.c -o tatstats_fm.o

last_tat.o : last_tat.c defs.h mm_file.h structs.h param.h
	$(CC) $(THR_CC) $(CFLAGS) -c last_tat.c

#================ drop functions - actual scores/alignments

drop_nfa.o : dropnfa.c dropnfa.h param.h defs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c dropnfa.c -o drop_nfa.o

# drop_ff, _fs, _fm must define FASTF, FASTS, and FASTM to ensure
# that tatstats.h is built appropriately

drop_ff.o : dropff2.c param.h defs.h tatstats.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -DFASTF -c dropff2.c -o drop_ff.o

drop_tff.o : dropff2.c param.h defs.h tatstats.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -DFASTF -DTFAST -c dropff2.c -o drop_tff.o

drop_ff2.o : dropff2.c param.h defs.h tatstats.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTF  dropff2.c -o drop_ff2.o

drop_tff2.o : dropff2.c param.h defs.h tatstats.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTF -DTFAST dropff2.c -o drop_tff.o

drop_fs.o : dropfs2.c param.h defs.h tatstats.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -DFASTS -c dropfs2.c -o drop_fs.o

drop_tfs.o : dropfs2.c param.h defs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DTFAST -DFASTS dropfs2.c -o drop_tfs.o

drop_fm.o : dropfs2.c param.h defs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DFASTM dropfs2.c -o drop_fm.o

drop_tfm.o : dropfs2.c param.h defs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DTFAST -DFASTM dropfs2.c -o drop_tfm.o

drop_tfa.o : dropnfa.c dropnfa.h upam.h param.h defs.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DTFASTA dropnfa.c -o drop_tfa.o

drop_fx.o : dropfx.c upam.h param.h defs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c dropfx.c -o drop_fx.o

drop_tfx.o : dropfx.c upam.h param.h defs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DTFAST dropfx.c -o drop_tfx.o

drop_fz.o : dropfz2.c upam.h param.h defs.h aamap.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c dropfz2.c -o drop_fz.o

drop_tfz.o : dropfz2.c upam.h param.h defs.h aamap.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DTFAST dropfz2.c -o drop_tfz.o

dropnsw.o : dropnsw.c upam.h param.h structs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c dropnsw.c

dropgsw.o : dropgsw.c dropgsw.h upam.h param.h structs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c dropgsw.c

smith_waterman_altivec.o : smith_waterman_altivec.c smith_waterman_altivec.h dropgsw.h defs.h param.h
	$(CC) $(THR_CC) $(CFLAGS) -c smith_waterman_altivec.c

smith_waterman_sse2.o : smith_waterman_sse2.c smith_waterman_sse2.h dropgsw.h defs.h param.h
	$(CC) $(THR_CC) $(CFLAGS) -c smith_waterman_sse2.c

dropnw.o : dropnw.c upam.h param.h structs.h drop_func.h
	$(CC) $(THR_CC) $(CFLAGS) -c dropnw.c

#================ reading query, libraries

getseq.o : getseq.c defs.h uascii.h structs.h upam.h mm_file.h
	$(CC) $(THR_CC) $(CFLAGS) -c getseq.c

llgetaa.o : llgetaa.c upam.h uascii.h mm_file.h
	$(CC) $(THR_CC) $(CFLAGS) -c -DNOLIB llgetaa.c

lgetlib.o : $(NGETLIB).c altlib.h upam.h uascii.h mm_file.h
	$(CC) $(THR_CC) $(CFLAGS) -c $(NGETLIB).c -o lgetlib.o

lgetaa_m.o : mmgetaa.c altlib.h ncbl2_head.h upam.h uascii.h mm_file.h
	$(CC) $(THR_CC) $(CFLAGS) -c mmgetaa.c -o lgetaa_m.o

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

ncbl2_mlib.o : ncbl2_mlib.c ncbl2_head.h mm_file.h
	$(CC) $(THR_CC) $(CFLAGS) -c ncbl2_mlib.c

mysql_lib.o : mysql_lib.c mm_file.h
	$(CC) $(THR_CC) $(CFLAGS) -c mysql_lib.c

pgsql_lib.o : pgsql_lib.c mm_file.h
	$(CC) $(THR_CC) $(CFLAGS) -c pgsql_lib.c

#================ threading functions

pthr_subs2.o : pthr_subs2.c thr.h pthr_subs.h
	$(CC) $(THR_CC) $(CFLAGS) -c pthr_subs2.c

uthr_subs.o : uthr_subs.c thr.h uthr_subs.h 
	$(CC) $(THR_CC) $(CFLAGS) -c uthr_subs.c

#================ translation

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

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

$(NRAND).o : $(NRAND).c
	$(CC) $(THR_CC) $(CFLAGS) -c $(NRAND).c
#================ pvm/mpi specific functions

hostacc.o : hostacc.c upam.h uascii.h
	$(CC) $(THR_CC) $(CFLAGS) hostacc.c

workacc.o : workacc.c upam.h uascii.h param.h
	$(NCC) $(THR_CC) $(CFLAGS) workacc.c -o workacc.o