577 lines
9.1 KiB
Plaintext
577 lines
9.1 KiB
Plaintext
# Makefile for staden X programs (Ultrix mips version)
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# ------------------------------------------------
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# This makefile generates the following staden programs which
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# run under xterm (normal, `N') and those which run directly under X.
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NPROGS= mep nip pip bap sap sip splitp1 splitp2 splitp3 sethelp convert_project
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LPROGS= nipl pip sipl
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XPROGS= xmep xnip xpip xbap xsap xsip
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PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
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#
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# ``Interesting'' suffices that make needs to know about
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#
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.SUFFIXES: .a $(SUFFIXES)
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#
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# Directories
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#
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SRC=.
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STADENSRC=$(SRC)/../staden
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STADENBIN=$(STADENSRC)
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TEDSRC=$(SRC)/../ted
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TEDBIN=$(STADENBIN)
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OSPSRC=$(SRC)/osp-bits
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OSPBIN=$(OSPSRC)
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MISCSRC=$(SRC)/../Misc
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MISCBIN=$(MISCSRC)
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# Use the ted sources compiled for staden executables
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INCLUDES= -I/usr/include/mit -I$(SRC) -I$(STADENSRC) -I$(TEDSRC) -I$(OSPSRC) -I$(MISCSRC)
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#
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# Compilers and flags
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#
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# debug on
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CC= c89
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CFLAGS= -common $(INCLUDES)
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F77= f77
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FFLAGS= -g -C
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LD= c89
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LDFLAGS= -g
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FLIBS= -lfor -lutil -lUfor -li -lots -lm
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XLIBS= -lXaw -lXt -lXmu -lXext -lX11
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LFLAGS= $(FLIBS)
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XLFLAGS= $(FLIBS) $(XLIBS)
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# For stdargs on the Sun
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#GNULIB = /usr/local/lib/gcc-gnulib
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#
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# Avoid compilation of objects in remote directories
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#
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$(STADENBIN)/%.o : $(STADENSRC)/%.f
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$(STADENBIN)/%.o : $(STADENSRC)/%.c
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$(TEDBIN)/%.o : $(TEDSRC)/%.f
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$(TEDBIN)/%.o : $(TEDSRC)/%.c
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#
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# Sequence library handling routines
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#
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SEQLIB=\
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$(STADENBIN)/seqlibsubs.o
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#
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# The C objects, needed by every X program
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#
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CCORE=\
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$(STADENBIN)/postscript.o\
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$(STADENBIN)/Graph.o\
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$(STADENBIN)/plotLog.o\
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$(STADENBIN)/help.o\
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$(STADENBIN)/dialogues.o\
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$(STADENBIN)/userfacecom.o\
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$(STADENBIN)/xmenu.o\
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$(STADENBIN)/locks.o\
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$(STADENBIN)/mcspec.o\
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$(STADENBIN)/helpnmenu.o\
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$(STADENBIN)/FtoC.o
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COBJS=\
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$(STADENBIN)/main.o\
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$(CCORE)
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COBJS2=\
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xbapmain.o\
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$(CCORE)
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#
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# Common objects, needed by every program
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#
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COMMONOBJSB=\
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$(STADENBIN)/fmain.o\
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$(STADENBIN)/seeme-dec.o\
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$(STADENBIN)/nxspec.o\
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$(STADENBIN)/userface.o\
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$(STADENBIN)/userfacecom.o\
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$(STADENBIN)/nxhelpmenu.o\
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$(STADENBIN)/helpnmenu.o\
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$(STADENBIN)/FtoC.o\
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$(STADENBIN)/subs89.a
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COMMONOBJS=\
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$(COMMONOBJSB)\
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$(STADENBIN)/postscript.o
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SCOMMONOBJS=\
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$(COMMONOBJSB)
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XCOMMONOBJS=\
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$(STADENBIN)/seeme-dec.o\
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$(STADENBIN)/xspec.o\
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$(STADENBIN)/subs89.a\
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$(COBJS)
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XCOMMONOBJS2=\
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$(STADENBIN)/seeme-dec.o\
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$(STADENBIN)/xspec.o\
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$(STADENBIN)/subs89.a\
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$(COBJS2)
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#
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# Building the programs
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# This should be just a linking phase because all of the object
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# files and library files are generated using implicit rules.
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# We use the fortran compiler to do linking.
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#
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GIP=\
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$(STADENBIN)/gip.o
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GIPOBJS=\
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$(GIP)\
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$(SCOMMONOBJS)
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gip: $(GIPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(GIPOBJS) $(LFLAGS)
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MEP=\
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$(STADENBIN)/mep.o\
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$(STADENBIN)/mepsub.o\
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$(STADENBIN)/asubs89.a\
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$(STADENBIN)/plot92.a
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MEPOBJS=\
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$(MEP)\
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$(COMMONOBJS)\
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$(STADENBIN)/pl4010.o
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XMEPOBJS=\
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$(MEP)\
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$(XCOMMONOBJS)\
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$(STADENBIN)/plX.o\
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$(STADENBIN)/textOutput.o
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mep: $(MEPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(MEPOBJS) $(LFLAGS)
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xmep: $(XMEPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(XMEPOBJS) $(XLFLAGS)
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NIP=\
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$(STADENBIN)/nip.o\
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$(STADENBIN)/patternn.a\
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$(STADENBIN)/patternnc.a\
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$(STADENBIN)/anals89.a\
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$(STADENBIN)/asubs89.a\
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$(STADENBIN)/plot92.a $(SEQLIB)
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NIPOBJS=\
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$(NIP)\
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$(COMMONOBJS)\
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$(STADENBIN)/pl4010.o
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XNIPOBJS=\
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$(NIP)\
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$(XCOMMONOBJS)\
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$(STADENBIN)/plX.o\
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$(STADENBIN)/textOutput.o
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nip: $(NIPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(NIPOBJS) $(LFLAGS)
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xnip: $(XNIPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(XNIPOBJS) $(XLFLAGS)
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NIPL=\
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$(STADENBIN)/nipl.o\
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$(STADENBIN)/patternnc.a\
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$(STADENBIN)/anals89.a\
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$(STADENBIN)/asubs89.a\
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$(SEQLIB)
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NIPLOBJS=\
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$(NIPL)\
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$(SCOMMONOBJS)
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nipl: $(NIPLOBJS)
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$(LD) $(LDFLAGS) -o $@ $(NIPLOBJS) $(LFLAGS)
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PIP=\
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$(STADENBIN)/pip.o\
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$(STADENBIN)/analps89.a\
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$(STADENBIN)/patternp.a\
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$(STADENBIN)/patternpc.a\
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$(STADENBIN)/asubs89.a\
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$(STADENBIN)/plot92.a\
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$(SEQLIB)
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PIPOBJS=\
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$(PIP)\
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$(COMMONOBJS)\
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$(STADENBIN)/pl4010.o
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XPIPOBJS=\
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$(PIP)\
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$(XCOMMONOBJS)\
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$(STADENBIN)/plX.o\
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$(STADENBIN)/textOutput.o
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pip: $(PIPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(PIPOBJS) $(LFLAGS)
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xpip:$(XPIPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(XPIPOBJS) $(XLFLAGS)
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PIPL=\
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$(STADENBIN)/pipl.o\
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$(STADENBIN)/patternpc.a\
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$(STADENBIN)/analps89.a\
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$(STADENBIN)/asubs89.a\
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$(SEQLIB)
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PIPLOBJS=\
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$(PIPL)\
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$(SCOMMONOBJS)
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pipl: $(PIPLOBJS)
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$(LD) $(LDFLAGS) -o $@ $(PIPLOBJS) $(LFLAGS)
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#
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# Trace manager objects
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#
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STDTEDFILES=\
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$(TEDBIN)/seq.o\
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$(TEDBIN)/seqIOABI.o\
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$(TEDBIN)/seqIOALF.o\
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$(TEDBIN)/seqIOSCF.o\
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$(TEDBIN)/seqIOPlain.o\
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$(TEDBIN)/opp.o\
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$(TEDBIN)/fpoint.o\
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$(TEDBIN)/mach-io.o
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TMANOBJS=\
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$(STADENBIN)/tman_main.o\
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$(STADENBIN)/tman_display.o\
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$(STADENBIN)/tman_traceDisplay.o\
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$(STADENBIN)/tman_basesDisplay.o\
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$(STADENBIN)/tman_context.o\
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$(STADENBIN)/tman_gadgets.o\
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$(STDTEDFILES)
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OSPOBJS=\
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$(OSPBIN)/analysis.o\
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$(OSPBIN)/our_allo.o\
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$(OSPBIN)/paramIOX.o\
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$(OSPBIN)/paramIO.o\
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$(OSPBIN)/get_scores.o\
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$(OSPBIN)/utils.o\
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mess.o
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XHACK=\
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$(STADENBIN)/SmeLine.o
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EDITOR=\
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$(XHACK)\
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$(STADENBIN)/xsapConEdit.o\
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contigEditor.o\
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edUtils.o\
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$(STADENBIN)/undo.o\
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$(STADENBIN)/Sheet.o\
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$(STADENBIN)/select.o\
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$(STADENBIN)/extend.o\
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$(STADENBIN)/searchUtils.o\
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edMenu.o\
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oligo.o\
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oligocom.o\
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subclone.o\
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myparams.o\
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$(STADENBIN)/trans.o\
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$(MISCBIN)/misc.a
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TAGEDITOR=\
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$(STADENBIN)/tagEditor.o\
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$(STADENBIN)/tagdbparse.o\
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tagU2.o\
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$(STADENBIN)/tagU1.o
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BAP=\
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bap.o\
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dbsysnew.o\
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dbsyscommon.o\
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actf.o\
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dstrand.o\
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oligo_sel.o\
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llin.o\
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guk.o\
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$(STADENBIN)/asubs89.a\
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$(STADENBIN)/plot92.a
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BAPOBJS=\
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$(BAP)\
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$(COMMONOBJS)\
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$(STADENBIN)/pl4010.o\
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$(STADENBIN)/conEdit.o\
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tagU2.o\
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$(OSPBIN)/analysis.o\
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$(OSPBIN)/our_allo.o\
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$(OSPBIN)/get_scores.o\
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$(OSPBIN)/utils.o\
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mess.o\
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baponly.o\
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oligocom.o\
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$(MISCBIN)/misc.a
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XBAPOBJS=\
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$(BAP)\
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$(XCOMMONOBJS2)\
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$(STADENBIN)/plX.o\
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$(STADENBIN)/textOutput.o\
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$(EDITOR)\
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$(TMANOBJS)\
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$(TAGEDITOR)\
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$(OSPOBJS)
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bap: $(BAPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(BAPOBJS) $(LFLAGS)
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xbap: $(XBAPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(XBAPOBJS) $(XLFLAGS)
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convert_project: $(STADENBIN)/cvt.o
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$(CC) $(CFLAGS) -o $@ $(STADENBIN)/cvt.o
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SAP=\
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sap.o\
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dbsyscommon.o\
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dbsysold.o\
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$(STADENBIN)/asubs89.a\
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$(STADENBIN)/plot92.a
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SAPOBJS=\
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$(SAP)\
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$(COMMONOBJS)\
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$(STADENBIN)/pl4010.o
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XSAPOBJS=\
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$(SAP)\
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$(XCOMMONOBJS)\
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$(STADENBIN)/plX.o\
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$(STADENBIN)/textOutput.o
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sap: $(SAPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(SAPOBJS) $(LFLAGS)
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xsap: $(XSAPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(XSAPOBJS) $(XLFLAGS)
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SAPF=\
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$(STADENBIN)/sapf.o\
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$(STADENBIN)/dbsyscommon.o\
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$(STADENBIN)/dbsysold.o\
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$(STADENBIN)/asubs89.a\
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$(STADENBIN)/plot92.a
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SAPFOBJS=\
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$(SAPF)\
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$(STADENBIN)/sapmen.o\
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$(COMMONOBJS)\
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$(STADENBIN)/pl4010.o
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sapf: $(SAPFOBJS)
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$(LD) $(LDFLAGS) -o $@ $(SAPFOBJS) $(LFLAGS)
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SIP=\
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$(STADENBIN)/sip.o\
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$(STADENBIN)/dias89.a\
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$(STADENBIN)/plot92.a\
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$(SEQLIB)
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SIPOBJS=\
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$(SIP)\
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$(COMMONOBJS)\
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$(STADENBIN)/pl4010.o
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XSIPOBJS=\
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$(SIP)\
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$(XCOMMONOBJS)\
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$(STADENBIN)/plX.o\
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$(STADENBIN)/textOutput.o
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sip: $(SIPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(SIPOBJS) $(LFLAGS)
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xsip: $(XSIPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(XSIPOBJS) $(XLFLAGS)
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SIPL=\
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$(STADENBIN)/sipl.o\
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$(STADENBIN)/dias89.a\
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$(SEQLIB)
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SIPLOBJS=\
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$(SIPL)\
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$(SCOMMONOBJS)
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sipl: $(SIPLOBJS)
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$(LD) $(LDFLAGS) -o $@ $(SIPLOBJS) $(LFLAGS)
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SETHELP=\
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$(STADENBIN)/sethelp.o
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SETHELPOBJS=\
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$(SETHELP)\
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$(SCOMMONOBJS)
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sethelp: $(SETHELPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(SETHELPOBJS) $(LFLAGS)
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SPLITP1=\
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$(STADENBIN)/splitp1.o
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SPLITP1OBJS=\
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$(SPLITP1)\
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$(SCOMMONOBJS)
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splitp1: $(SPLITP1OBJS)
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$(LD) $(LDFLAGS) -o $@ $(SPLITP1OBJS) $(LFLAGS)
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SPLITP2=\
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$(STADENBIN)/splitp2.o
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SPLITP2OBJS=\
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$(SPLITP2)\
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$(SCOMMONOBJS)
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splitp2: $(SPLITP2OBJS)
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$(LD) $(LDFLAGS) -o $@ $(SPLITP2OBJS) $(LFLAGS)
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SPLITP3=\
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$(STADENBIN)/splitp3.o
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SPLITP3OBJS=\
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$(SPLITP3)\
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$(SCOMMONOBJS)
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splitp3: $(SPLITP3OBJS)
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$(LD) $(LDFLAGS) -o $@ $(SPLITP3OBJS) $(LFLAGS)
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#
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# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
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#
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%.o: $(SRC)/%.f
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$(F77) $(FFLAGS) -c $<
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#
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# Files requiring simple C compilation (thing.c -> thing.o)
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#
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%.o: %.c
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$(CC) $(CFLAGS) -c $<
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%.o: $(SRC)/%.c
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$(CC) $(CFLAGS) -c $<
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#
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# The UNIX library (archive) mechanism is fairly weak so the following
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# procedure is used to generate libraries.
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# * split the source file up into files which each contain
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# a single function or subroutine
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# * compile each of those files
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# * insert the object files individually into the library
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# Each library is built by using a temporary directory.
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# The fortran compilations must be done sequentially in order to
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# avoid filling up the (small on this machine) /tmp directory
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# with compiler debugging information.
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#
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%.a: $(SRC)/%.f
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BINDIR=`pwd`; \
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cd $(SRC); \
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SRCDIR=`pwd`; \
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TMPDIR=/tmp/staden$$$$; \
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if test ! -d $$TMPDIR; \
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then mkdir $$TMPDIR; \
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fi; \
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cd $$TMPDIR; \
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rm -f *.f *.o; \
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fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
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$(F77) $(FFLAGS) -c *.f; \
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rm *.f; \
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rm -f $$BINDIR/$@; \
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ar rcv $$BINDIR/$@ *.o; \
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ranlib $$BINDIR/$@; \
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rm *.o; \
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cd $$BINDIR; \
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rm -r $$TMPDIR
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all: bap xbap
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nprogs: $(NPROGS)
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xprogs: $(XPROGS)
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lprogs: $(LPROGS)
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clean:
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rm -f $(PROGS) *.o *.a *~
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