#
#  Makefile for the AMPS MULTALIGN program AMULT.
#
#  This makefile is for Silicon Graphics
#  It may not be the best combination of flags for maximum speed
#
#  the FFLAGS options should allow compilation on any Unix
#  machine with a fortran compiler.
#
#  There are different FLAGS for some routines because the
#  Sun f77 optimiser croaked when compiling with -O3 on 
#  everything.  I haven't tried this with the latest f77 (24/8/1993).
#  
#  For some reason -i2 gives errors on the R4000.  Change all flags
#  to -i4.  GJB 22/10/1993
#
#  Conservative optimizations for the silicon graphics.
#
FFLAGS= -u -O2 -mips2 
FLAGS2= -u -O2 -mips2 
FLAGS3= -u -O2 -mips2 
FLAGS4= -O2 -mips2 


F77 = f77

amult.sgi: amult.o align2.o almul.o arran.o conser.o dat.o dcgaps.o \
fbloc.o fseqs.o gcheck.o gtest.o konbak.o koncom.o konseq.o master.o \
mast2.o mlook.o mlook2.o mlook3.o mlook4.o multa.o multb.o mzcons.o \
plate.o pretty.o recall.o recd.o recg.o rfreq.o scomp.o setgap.o \
sgap.o wcheck.o wlook.o wmatr.o wnames.o write6.o comchk.o cgaps.o \
info.o extseq.o recp.o recpf.o recpfn.o multc.o multd.o pret2.o konb2.o \
align.o segcom.o \
slook.o bslook.o mlook5.o rlook.o tmult.o retree.o score.o altree.o ampinf.o \
wpatt.o util.o ran2.o retree2.o alook.o
	$(F77) $(FFLAGS) amult.o align2.o almul.o arran.o \
conser.o dat.o dcgaps.o \
fbloc.o fseqs.o gcheck.o gtest.o konbak.o koncom.o konseq.o master.o \
mast2.o mlook.o mlook2.o mlook3.o mlook4.o multa.o multb.o mzcons.o \
plate.o pretty.o recall.o recd.o recg.o rfreq.o scomp.o setgap.o \
sgap.o wcheck.o wlook.o wmatr.o wnames.o write6.o comchk.o \
cgaps.o info.o extseq.o recp.o recpf.o recpfn.o multc.o pret2.o konb2.o \
align.o segcom.o \
slook.o bslook.o mlook5.o rlook.o tmult.o retree.o altree.o score.o ampinf.o \
multd.o wpatt.o util.o ran2.o retree2.o alook.o -o amult.sgi
align2.o: align2.f params.blk matloc.blk gapmis.blk intseq.blk
	$(F77) -c $(FFLAGS) align2.f
almul.o: almul.f params.blk intseq.blk matloc.blk
	$(F77) -c $(FFLAGS) almul.f
amult.o: amult.f params.blk intseq.blk seqcha.blk matloc.blk dayhof.blk \
gapmis.blk conser.blk tester.blk param2.blk probas.blk speedo.blk
	$(F77) -c $(FFLAGS) amult.f
arran.o: arran.f params.blk gapmis.blk seqcha.blk intseq.blk
	$(F77) -c $(FFLAGS) arran.f
conser.o: conser.f params.blk dayhof.blk seqcha.blk intseq.blk conser.blk
	$(F77) -c $(FFLAGS) conser.f
dat.o: dat.f dayhof.blk
	$(F77) -c $(FFLAGS) dat.f
daytb.o: daytb.f
	$(F77) -c $(FFLAGS) daytb.f
dcgaps.o: dcgaps.f params.blk seqcha.blk intseq.blk gapmis.blk param2.blk
	$(F77) -c $(FFLAGS) dcgaps.f
fbloc.o: fbloc.f params.blk seqcha.blk intseq.blk gapmis.blk param2.blk
	$(F77) -c $(FFLAGS) fbloc.f
fseqs.o: fseqs.f params.blk seqcha.blk intseq.blk gapmis.blk
	$(F77) -c $(FFLAGS) fseqs.f
gcheck.o: gcheck.f params.blk intseq.blk seqcha.blk gapmis.blk tester.blk
	$(F77) -c $(FFLAGS) gcheck.f
gtest.o: gtest.f params.blk tester.blk
	$(F77) -c $(FFLAGS) gtest.f
koncom.o: koncom.f params.blk intseq.blk seqcha.blk dayhof.blk
	$(F77) -c $(FFLAGS) koncom.f
konseq.o: konseq.f params.blk intseq.blk seqcha.blk dayhof.blk
	$(F77) -c $(FFLAGS) konseq.f
konbak.o: konbak.f params.blk intseq.blk seqcha.blk dayhof.blk
	$(F77) -c $(FFLAGS) konbak.f
master.o: master.f params.blk intseq.blk seqcha.blk matloc.blk dayhof.blk \
gapmis.blk conser.blk tester.blk param2.blk speedo.blk
	$(F77) -c $(FFLAGS) master.f
mast2.o: mast2.f params.blk intseq.blk seqcha.blk matloc.blk dayhof.blk \
gapmis.blk conser.blk tester.blk param2.blk speedo.blk
	$(F77) -c $(FLAGS2) mast2.f
mlook.o: mlook.f params.blk matloc.blk intseq.blk seqcha.blk dayhof.blk param2.blk
	$(F77) -c $(FFLAGS) mlook.f
alook.o: alook.f params.blk matloc.blk intseq.blk seqcha.blk dayhof.blk param2.blk gapmis.blk
	$(F77) -c $(FFLAGS) alook.f
mlook2.o: mlook2.f params.blk matloc.blk intseq.blk seqcha.blk dayhof.blk \
param2.blk
	$(F77) -c $(FFLAGS) mlook2.f
mlook3.o: mlook3.f params.blk matloc.blk intseq.blk seqcha.blk dayhof.blk \
param2.blk
	$(F77) -c $(FFLAGS) mlook3.f
mlook4.o: mlook4.f params.blk matloc.blk intseq.blk seqcha.blk dayhof.blk \
param2.blk
	$(F77) -c $(FFLAGS) mlook4.f
mlook5.o: mlook5.f params.blk matloc.blk intseq.blk seqcha.blk dayhof.blk \
param2.blk
	$(F77) -c $(FFLAGS) mlook5.f
multa.o: multa.f params.blk intseq.blk seqcha.blk matloc.blk dayhof.blk \
gapmis.blk param2.blk
	$(F77) -c $(FFLAGS) multa.f
multb.o: multb.f params.blk intseq.blk seqcha.blk matloc.blk dayhof.blk \
gapmis.blk param2.blk
	$(F77) -c $(FLAGS2) multb.f
mzcons.o: mzcons.f params.blk dayhof.blk seqcha.blk intseq.blk conser.blk
	$(F77) -c $(FFLAGS) mzcons.f
plate.o: plate.f params.blk intseq.blk tester.blk
	$(F77) -c $(FFLAGS) plate.f
pretty.o: pretty.f params.blk seqcha.blk gapmis.blk
	$(F77) -c $(FLAGS2) pretty.f
recall.o: recall.f params.blk matloc.blk intseq.blk
	$(F77) -c $(FFLAGS) recall.f
recd.o: recd.f params.blk matloc.blk intseq.blk gapmis.blk
	$(F77) -c $(FFLAGS) recd.f
recg.o: recg.f params.blk matloc.blk intseq.blk gapmis.blk
	$(F77) -c $(FFLAGS) recg.f
rfreq.o: rfreq.f params.blk dayhof.blk param2.blk probas.blk
	$(F77) -c $(FFLAGS) rfreq.f
scomp.o: scomp.f params.blk intseq.blk
	$(F77) -c $(FFLAGS) scomp.f
setgap.o: setgap.f params.blk param2.blk dayhof.blk
	$(F77) -c $(FFLAGS) setgap.f
sgap.o: sgap.f params.blk intseq.blk gapmis.blk param2.blk
	$(F77) -c $(FFLAGS) sgap.f
wcheck.o: wcheck.f params.blk gapmis.blk tester.blk intseq.blk dayhof.blk
	$(F77) -c $(FFLAGS) wcheck.f
wlook.o: wlook.f params.blk dayhof.blk matloc.blk param2.blk
	$(F77) -c $(FLAGS2) wlook.f
wmatr.o: wmatr.f dayhof.blk
	$(F77) -c $(FLAGS2) wmatr.f
wnames.o: wnames.f params.blk gapmis.blk intseq.blk param2.blk
	$(F77) -c $(FFLAGS) wnames.f
write6.o: write6.f params.blk seqcha.blk conser.blk dayhof.blk gapmis.blk \
param2.blk
	$(F77) -c $(FLAGS2) write6.f
comchk.o: comchk.f params.blk param2.blk gapmis.blk
	$(F77) -c $(FFLAGS) comchk.f
cgaps.o: cgaps.f
	$(F77) -c $(FFLAGS) cgaps.f
info.o: info.f params.blk intseq.blk
	$(F77) -c $(FFLAGS) info.f
extseq.o: extseq.f params.blk intseq.blk
	$(F77) -c $(FFLAGS) extseq.f
recp.o: recp.f params.blk matloc.blk intseq.blk dayhof.blk 
	$(F77) -c $(FFLAGS) recp.f
recpf.o: recp.f params.blk matloc.blk intseq.blk dayhof.blk speedo.blk \
param2.blk
	$(F77) -c $(FFLAGS) recpf.f
recpfn.o: recp.f params.blk matloc.blk intseq.blk dayhof.blk speedo.blk \
param2.blk
	$(F77) -c $(FFLAGS) recpfn.f
multc.o: multc.f params.blk intseq.blk seqcha.blk matloc.blk dayhof.blk \
gapmis.blk param2.blk speedo.blk
	$(F77) -c $(FFLAGS) multc.f
multd.o: multd.f params.blk intseq.blk seqcha.blk matloc.blk dayhof.blk \
gapmis.blk param2.blk speedo.blk
	$(F77) -c $(FFLAGS) multd.f
pret2.o: pret2.f params.blk seqcha.blk gapmis.blk param2.blk
	$(F77) -c $(FLAGS2) pret2.f
konb2.o: konb2.f params.blk intseq.blk seqcha.blk dayhof.blk 
	$(F77) -c $(FFLAGS) konb2.f
align.o: align.f params.blk intseq.blk matloc.blk
	$(F77) -c $(FFLAGS) align.f
segcom.o: segcom.f params.blk intseq.blk matloc.blk gapmis.blk
	$(F77) -c $(FFLAGS) segcom.f
slook.o: slook.f params.blk param2.blk matloc.blk gapmis.blk dayhof.blk
	$(F77) -c $(FFLAGS) slook.f
bslook.o: bslook.f params.blk param2.blk matloc.blk gapmis.blk dayhof.blk
	$(F77) -c $(FLAGS2) bslook.f
rlook.o: rlook.f params.blk param2.blk matloc.blk gapmis.blk dayhof.blk
	$(F77) -c $(FFLAGS) rlook.f
tmult.o: tmult.f params.blk intseq.blk seqcha.blk matloc.blk dayhof.blk \
gapmis.blk conser.blk tester.blk param2.blk probas.blk
	$(F77) -c $(FFLAGS) tmult.f
retree.o: retree.f params.blk matloc.blk intseq.blk
	$(F77) -c $(FFLAGS) retree.f
retree2.o: retree2.f params.blk matloc.blk intseq.blk
	$(F77) -c $(FFLAGS) retree2.f
score.o: score.f params.blk dayhof.blk intseq.blk
	$(F77) -c $(FFLAGS) score.f
altree.o: altree.f params.blk intseq.blk matloc.blk
	$(F77) -c $(FFLAGS) altree.f
ampinf.o: ampinf.f params.blk param2.blk
	$(F77) -c $(FFLAGS) ampinf.f
wpatt.o: wpatt.f params.blk seqcha.blk gapmis.blk intseq.blk param2.blk
	$(F77) -c $(FLAGS2) wpatt.f
util.o: util.f
	$(F77) -c $(FLAGS3) util.f
ran2.o: ran2.f
	$(F77) -c $(FLAGS4) ran2.f


