use default makefile and recovery previous alpha makefile
This commit is contained in:
parent
5e8a7a2520
commit
fe1d5a834e
32 changed files with 2430 additions and 131 deletions
52
src/Misc/makefile
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52
src/Misc/makefile
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@ -0,0 +1,52 @@
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#
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# Makefile for Miscellaneous routines - Alpha version
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#
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# Objects made by this makefile
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#
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LIBS = misc.a
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#
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# Where the wild things are
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#
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SRC = .
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INCLUDES = -I$(SRC)
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#
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# Alpha Version
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#
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CC = cc
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CFLAGS = -g $(INCLUDES)
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ARFLAGS = rv
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#
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# Objects
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#
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OBJS = \
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crash.o \
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date.o \
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filenames.o \
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files.o \
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find.o \
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shell.o \
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strings.o
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#
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# Main dependency
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#
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$(LIBS) : $(OBJS)
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/bin/rm -f $(LIBS) ;\
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$(AR) $(ARFLAGS) $(LIBS) $(OBJS) ;\
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ranlib $(LIBS)
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#
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# Special dependencies
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#
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%.o : $(SRC)/%.c
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$(CC) $(CFLAGS) -c $<
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all : $(LIBS)
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clean :
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/bin/rm -f $(OBJS) $(LIBS)
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@ -16,7 +16,7 @@ INCLUDES = -I$(SRC)
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# Alpha Version
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#
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CC = cc
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CFLAGS = -g $(INCLUDES)
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CFLAGS = -g -std1 -ieee_with_inexact $(INCLUDES)
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ARFLAGS = rv
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#
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43
src/abi/makefile
Normal file
43
src/abi/makefile
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@ -0,0 +1,43 @@
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#
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# Makefile for abi - Alpha version
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#
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#
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# Programs made by this makefile
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#
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PROGS = getABISampleName 2rs
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all: $(PROGS)
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#
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# Where the wild things are
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#
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SRC = .
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#
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# Alpha
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#
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CC = cc
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CFLAGS = -g -I$(SRC)/../ted
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LD = cc
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LDFLAGS = -g
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#
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# Make the programs
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#
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getABISampleName: getABISampleName.o
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$(LD) $(LDFLAGS) -o getABISampleName getABISampleName.o
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2rs: 2rs.o
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$(LD) $(LDFLAGS) -o 2rs 2rs.o
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#
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# Special dependencies
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#
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%.o : $(SRC)/%.c
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$(CC) $(CFLAGS) -c $<
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all: $(PROGS)
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clean:
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/bin/rm -f $(PROGS) *.o *~
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@ -5,8 +5,7 @@
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#
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# Programs made by this makefile
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#
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PROGS = getABISampleName 2rs
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all: $(PROGS)
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PROGS = getABISampleName
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#
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# Where the wild things are
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@ -17,9 +16,9 @@ SRC = .
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# Alpha
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#
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CC = cc
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CFLAGS = -g -I$(SRC)/../ted
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CFLAGS = -g -std1 -ieee_with_inexact -I$(SRC)/../ted
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LD = cc
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LDFLAGS = -g
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LDFLAGS = -g -non_shared
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#
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# Make the programs
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@ -27,8 +26,6 @@ LDFLAGS = -g
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getABISampleName: getABISampleName.o
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$(LD) $(LDFLAGS) -o getABISampleName getABISampleName.o
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2rs: 2rs.o
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$(LD) $(LDFLAGS) -o 2rs 2rs.o
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#
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# Special dependencies
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43
src/alf/makefile
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43
src/alf/makefile
Normal file
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#
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# Makefile for alf - Alpha version
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#
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#
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# Programs made by this makefile
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#
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PROGS = alfsplit
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#
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# Where the wild things are
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#
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SRC = .
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#
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# Alpha
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#
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CC = cc
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CFLAGS = -g -I$(SRC)/../ted
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LD = cc
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LDFLAGS = -g
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#
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# Make the programs
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#
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alfsplit: alfsplit.o
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$(LD) $(LDFLAGS) -o alfsplit alfsplit.o $(LIBS)
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2rs: 2rs.o
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$(LD) $(LDFLAGS) -o 2rs 2rs.o $(LIBS)
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#
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# Special dependencies
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#
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all: $(PROGS)
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clean:
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/bin/rm -f $(PROGS) *.o *~
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%.o : $(SRC)/%.c
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$(CC) $(CFLAGS) -c $<
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@ -16,9 +16,9 @@ SRC = .
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# Alpha
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#
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CC = cc
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CFLAGS = -g -I$(SRC)/../ted
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CFLAGS = -g -std1 -ieee_with_inexact -I$(SRC)/../ted
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LD = cc
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LDFLAGS = -g
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LDFLAGS = -g -non_shared
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#
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580
src/bap/makefile
Normal file
580
src/bap/makefile
Normal file
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# Makefile for staden X programs (Alpha 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 bap sap sip splitp1 splitp2 splitp3 sethelp
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LPROGS= nipl
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XPROGS= xmep xnip 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=$(TEDSRC)
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OSPSRC=$(SRC)/osp-bits
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OSPBIN=$(OSPSRC)
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MISCSRC=$(SRC)/../Misc
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MISCBIN=$(MISCSRC)
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# Use the ted sources compiled for staden executables
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INCLUDES= -I$(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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CC= cc
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CFLAGS= -g $(INCLUDES)
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F77= gfortran
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FFLAGS= -g -fdec -std=legacy -C
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#FLIBS= -lfor -lUfor -lots -lFutil
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FLIBS = -lm -lutil
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XLIBS= -lXaw -lXt -lXmu -lXext -lX11
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LFLAGS= $(FLIBS)
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XLFLAGS= $(XLIBS) $(FLIBS)
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LD = gfortran
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XLD = cc
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LDFLAGS = -g -fdec -std=legacy -L/usr/lib -lgfortran
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#
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# Avoid compilation of objects in remote directories
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#
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$(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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$(STADENBIN)/postscript.o\
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$(TEDBIN)/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-aix.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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$(STADENBIN)/seeme-aix.o\
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$(STADENBIN)/xspec.o\
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$(STADENBIN)/subs89.a\
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$(COBJS)
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XCOMMONOBJS2=\
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$(STADENBIN)/seeme-aix.o\
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$(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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$(MEP)\
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$(STADENBIN)/xmepSpec.o\
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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 $(SEQLIB)
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|
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NIPOBJS=\
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$(NIP)\
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$(COMMONOBJS)\
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$(STADENBIN)/pl4010.o
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XNIPOBJS=\
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$(NIP)\
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$(STADENBIN)/xnipSpec.o\
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$(XCOMMONOBJS)\
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$(STADENBIN)/plX.o\
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$(STADENBIN)/textOutput.o
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|
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nip: $(NIPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(NIPOBJS) $(LFLAGS)
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|
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xnip: $(XNIPOBJS)
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$(LD) $(LDFLAGS) -o $@ $(XNIPOBJS) $(XLFLAGS)
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|
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NIPL=\
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$(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) $(LFLAGS)
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|
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|
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|
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PIP=\
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$(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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$(STADENBIN)/pl4010.o
|
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|
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XPIPOBJS=\
|
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$(PIP)\
|
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$(STADENBIN)/xpipSpec.o\
|
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$(XCOMMONOBJS)\
|
||||
$(STADENBIN)/plX.o\
|
||||
$(STADENBIN)/textOutput.o
|
||||
|
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pip: $(PIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(PIPOBJS) $(LFLAGS)
|
||||
|
||||
xpip:$(XPIPOBJS)
|
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$(LD) $(LDFLAGS) -o $@ $(XPIPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
PIPL=\
|
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$(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) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Trace manager objects
|
||||
#
|
||||
STDTEDFILES=\
|
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$(TEDBIN)/seq.o\
|
||||
$(TEDBIN)/seqIOABI.o\
|
||||
$(TEDBIN)/seqIOALF.o\
|
||||
$(TEDBIN)/seqIOSCF.o\
|
||||
$(TEDBIN)/seqIOPlain.o\
|
||||
$(TEDBIN)/opp.o\
|
||||
$(TEDBIN)/fpoint.o\
|
||||
$(TEDBIN)/mach-io.o
|
||||
|
||||
TMANOBJS=\
|
||||
$(STADENBIN)/tman_main.o\
|
||||
$(STADENBIN)/tman_display.o\
|
||||
$(STADENBIN)/tman_traceDisplay.o\
|
||||
$(STADENBIN)/tman_basesDisplay.o\
|
||||
$(STADENBIN)/tman_context.o\
|
||||
$(STADENBIN)/tman_gadgets.o\
|
||||
$(STDTEDFILES)
|
||||
|
||||
OSPOBJS=\
|
||||
$(OSPBIN)/analysis.o\
|
||||
$(OSPBIN)/our_allo.o\
|
||||
$(OSPBIN)/paramIOX.o\
|
||||
$(OSPBIN)/paramIO.o\
|
||||
$(OSPBIN)/get_scores.o\
|
||||
$(OSPBIN)/utils.o\
|
||||
mess.o\
|
||||
$(GNULIB)
|
||||
|
||||
XHACK=\
|
||||
$(STADENBIN)/SmeLine.o
|
||||
|
||||
EDITOR=\
|
||||
$(XHACK)\
|
||||
$(STADENBIN)/xsapConEdit.o\
|
||||
contigEditor.o\
|
||||
edUtils.o\
|
||||
$(STADENBIN)/undo.o\
|
||||
$(STADENBIN)/Sheet.o\
|
||||
$(STADENBIN)/select.o\
|
||||
$(STADENBIN)/extend.o\
|
||||
$(STADENBIN)/searchUtils.o\
|
||||
edMenu.o\
|
||||
oligo.o\
|
||||
oligocom.o\
|
||||
subclone.o\
|
||||
myparams.o\
|
||||
$(STADENBIN)/trans.o\
|
||||
$(MISCBIN)/misc.a
|
||||
|
||||
TAGEDITOR=\
|
||||
$(STADENBIN)/tagEditor.o\
|
||||
$(STADENBIN)/tagdbparse.o\
|
||||
tagU2.o\
|
||||
$(STADENBIN)/tagU1.o
|
||||
|
||||
BAP=\
|
||||
bap.o\
|
||||
dbsysnew.o\
|
||||
dbsyscommon.o\
|
||||
actf.o\
|
||||
dstrand.o\
|
||||
oligo_sel.o\
|
||||
llin.o\
|
||||
guk.o\
|
||||
$(STADENBIN)/asubs89.a\
|
||||
$(STADENBIN)/plot92.a
|
||||
|
||||
BAPOBJS=\
|
||||
$(BAP)\
|
||||
$(COMMONOBJS)\
|
||||
$(STADENBIN)/pl4010.o\
|
||||
$(STADENBIN)/conEdit.o\
|
||||
tagU2.o\
|
||||
$(OSPBIN)/analysis.o\
|
||||
$(OSPBIN)/our_allo.o\
|
||||
$(OSPBIN)/get_scores.o\
|
||||
$(OSPBIN)/utils.o\
|
||||
mess.o\
|
||||
baponly.o\
|
||||
oligocom.o
|
||||
|
||||
XBAPOBJS=\
|
||||
$(BAP)\
|
||||
$(XCOMMONOBJS2)\
|
||||
$(STADENBIN)/plX.o\
|
||||
$(STADENBIN)/textOutput.o\
|
||||
$(EDITOR)\
|
||||
$(TMANOBJS)\
|
||||
$(TAGEDITOR)\
|
||||
$(OSPOBJS)
|
||||
|
||||
bap: $(BAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(BAPOBJS) $(LFLAGS)
|
||||
|
||||
xbap: $(XBAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(XBAPOBJS) $(XLFLAGS)
|
||||
|
||||
SAP=\
|
||||
sap.o\
|
||||
dbsyscommon.o\
|
||||
dbsysold.o\
|
||||
$(STADENBIN)/asubs89.a\
|
||||
$(STADENBIN)/plot92.a
|
||||
|
||||
SAPOBJS=\
|
||||
$(SAP)\
|
||||
$(COMMONOBJS)\
|
||||
$(STADENBIN)/pl4010.o
|
||||
|
||||
XSAPOBJS=\
|
||||
$(SAP)\
|
||||
$(STADENBIN)/xsapSpec.o\
|
||||
$(XCOMMONOBJS)\
|
||||
$(STADENBIN)/plX.o\
|
||||
$(STADENBIN)/textOutput.o
|
||||
|
||||
sap: $(SAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SAPOBJS) $(LFLAGS)
|
||||
|
||||
xsap: $(XSAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(XSAPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SAPF=\
|
||||
$(STADENBIN)/sapf.o\
|
||||
$(STADENBIN)/dbsyscommon.o\
|
||||
$(STADENBIN)/dbsysold.o\
|
||||
$(STADENBIN)/asubs89.a\
|
||||
$(STADENBIN)/plot92.a
|
||||
|
||||
SAPFOBJS=\
|
||||
$(SAPF)\
|
||||
$(STADENBIN)/sapmen.o\
|
||||
$(COMMONOBJS)\
|
||||
$(STADENBIN)/pl4010.o
|
||||
|
||||
sapf: $(SAPFOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SAPFOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
SIP=\
|
||||
$(STADENBIN)/sip.o\
|
||||
$(STADENBIN)/dias89.a\
|
||||
$(STADENBIN)/plot92.a\
|
||||
$(SEQLIB)
|
||||
|
||||
SIPOBJS=\
|
||||
$(SIP)\
|
||||
$(COMMONOBJS)\
|
||||
$(STADENBIN)/pl4010.o
|
||||
|
||||
XSIPOBJS=\
|
||||
$(SIP)\
|
||||
$(STADENBIN)/xsipSpec.o\
|
||||
$(XCOMMONOBJS)\
|
||||
$(STADENBIN)/plX.o\
|
||||
$(STADENBIN)/textOutput.o
|
||||
|
||||
sip: $(SIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SIPOBJS) $(LFLAGS)
|
||||
|
||||
xsip: $(XSIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(XSIPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SIPL=\
|
||||
$(STADENBIN)/sipl.o\
|
||||
$(STADENBIN)/dias89.a\
|
||||
$(SEQLIB)
|
||||
|
||||
SIPLOBJS=\
|
||||
$(SIPL)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
sipl: $(SIPLOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SIPLOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SETHELP=\
|
||||
$(STADENBIN)/sethelp.o
|
||||
|
||||
SETHELPOBJS=\
|
||||
$(SETHELP)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
sethelp: $(SETHELPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SETHELPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SPLITP1=\
|
||||
$(STADENBIN)/splitp1.o
|
||||
SPLITP1OBJS=\
|
||||
$(SPLITP1)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
splitp1: $(SPLITP1OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SPLITP1OBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SPLITP2=\
|
||||
$(STADENBIN)/splitp2.o
|
||||
SPLITP2OBJS=\
|
||||
$(SPLITP2)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
splitp2: $(SPLITP2OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SPLITP2OBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
SPLITP3=\
|
||||
$(STADENBIN)/splitp3.o
|
||||
SPLITP3OBJS=\
|
||||
$(SPLITP3)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
splitp3: $(SPLITP3OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SPLITP3OBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
|
||||
#
|
||||
%.o: $(SRC)/%.f
|
||||
$(F77) $(FFLAGS) -c $<
|
||||
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o: %.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o: $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
||||
|
||||
|
||||
#
|
||||
# The UNIX library (archive) mechanism is fairly weak so the following
|
||||
# procedure is used to generate libraries.
|
||||
# * split the source file up into files which each contain
|
||||
# a single function or subroutine
|
||||
# * compile each of those files
|
||||
# * insert the object files individually into the library
|
||||
# Each library is built by using a temporary directory.
|
||||
# The fortran compilations must be done sequentially in order to
|
||||
# avoid filling up the (small on this machine) /tmp directory
|
||||
# with compiler debugging information.
|
||||
#
|
||||
#%.a: $(SRC)/%.f
|
||||
# BINDIR=`pwd`; \
|
||||
# cd $(SRC); \
|
||||
# SRCDIR=`pwd`; \
|
||||
# TMPDIR=/tmp/staden$$$$; \
|
||||
# if test ! -d $$TMPDIR; \
|
||||
# then mkdir $$TMPDIR; \
|
||||
# fi; \
|
||||
# cd $$TMPDIR; \
|
||||
# rm -f *.f *.o; \
|
||||
# fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
|
||||
# $(F77) $(FFLAGS) -c *.f; \
|
||||
# rm *.f; \
|
||||
# rm -f $$BINDIR/$@; \
|
||||
# ar rcv $$BINDIR/$@ *.o; \
|
||||
# ranlib $$BINDIR/$@; \
|
||||
# rm *.o; \
|
||||
# cd $$BINDIR; \
|
||||
# rm -r $$TMPDIR
|
||||
|
||||
|
||||
#%.a: $(SRC)/%.f
|
||||
# $(F77) $(FFLAGS) -c *.f;
|
||||
# ar rcv $$BINDIR/$@ *.o;
|
||||
|
||||
|
||||
|
||||
all: $(NPROGS) $(XPROGS) $(LPROGS)
|
||||
|
||||
nprogs: $(NPROGS)
|
||||
|
||||
xprogs: $(XPROGS)
|
||||
|
||||
lprogs: $(LPROGS)
|
||||
|
||||
clean:
|
||||
rm -f $(PROGS) *.o *.a *~
|
||||
|
|
@ -3,9 +3,9 @@
|
|||
|
||||
# This makefile generates the following staden programs which
|
||||
# run under xterm (normal, `N') and those which run directly under X.
|
||||
NPROGS= mep nip bap sap sip splitp1 splitp2 splitp3 sethelp
|
||||
LPROGS= nipl
|
||||
XPROGS= xmep xnip xbap xsap xsip
|
||||
NPROGS= mep nip pip bap sap sip splitp1 splitp2 splitp3 sethelp convert_project
|
||||
LPROGS= nipl pip sipl
|
||||
XPROGS= xmep xnip xpip xbap xsap xsip
|
||||
PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
|
||||
|
||||
|
||||
|
|
@ -26,13 +26,13 @@ PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
|
|||
#
|
||||
SRC = .
|
||||
STADENSRC=$(SRC)/../staden
|
||||
STADENBIN=$(STADENSRC)
|
||||
STADENBIN=$(STADENSRC)/alpha-binaries
|
||||
TEDSRC=$(SRC)/../ted
|
||||
TEDBIN=$(TEDSRC)
|
||||
TEDBIN=$(STADENBIN)
|
||||
OSPSRC=$(SRC)/osp-bits
|
||||
OSPBIN=$(OSPSRC)
|
||||
OSPBIN=$(OSPSRC)/alpha-binaries
|
||||
MISCSRC=$(SRC)/../Misc
|
||||
MISCBIN=$(MISCSRC)
|
||||
MISCBIN=$(MISCSRC)/alpha-binaries
|
||||
# Use the ted sources compiled for staden executables
|
||||
INCLUDES= -I$(SRC) -I$(STADENSRC) -I$(TEDSRC) -I$(OSPSRC) -I$(MISCSRC)
|
||||
|
||||
|
|
@ -41,19 +41,18 @@ INCLUDES= -I$(SRC) -I$(STADENSRC) -I$(TEDSRC) -I$(OSPSRC) -I$(MISCSRC)
|
|||
# Compilers and flags
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(INCLUDES)
|
||||
F77= gfortran
|
||||
FFLAGS= -g -fdec -std=legacy -C
|
||||
CFLAGS= -g -std1 -ieee_with_inexact $(INCLUDES)
|
||||
F77= f77
|
||||
FFLAGS= -g -C
|
||||
|
||||
#FLIBS= -lfor -lUfor -lots -lFutil
|
||||
FLIBS = -lm -lutil
|
||||
FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil -ldnet_stub
|
||||
XLIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
LFLAGS= $(FLIBS)
|
||||
XLFLAGS= $(XLIBS) $(FLIBS)
|
||||
|
||||
LD = gfortran
|
||||
LD = f77
|
||||
XLD = cc
|
||||
LDFLAGS = -g -fdec -std=legacy -L/usr/lib -lgfortran
|
||||
LDFLAGS = -g -non_shared
|
||||
|
||||
#
|
||||
# Avoid compilation of objects in remote directories
|
||||
|
|
@ -76,7 +75,7 @@ SEQLIB=\
|
|||
#
|
||||
CCORE=\
|
||||
$(STADENBIN)/postscript.o\
|
||||
$(TEDBIN)/Graph.o\
|
||||
$(STADENBIN)/Graph.o\
|
||||
$(STADENBIN)/plotLog.o\
|
||||
$(STADENBIN)/help.o\
|
||||
$(STADENBIN)/dialogues.o\
|
||||
|
|
@ -101,7 +100,7 @@ COBJS2=\
|
|||
#
|
||||
COMMONOBJSB=\
|
||||
$(STADENBIN)/fmain.o\
|
||||
$(STADENBIN)/seeme-aix.o\
|
||||
$(STADENBIN)/seeme-dec.o\
|
||||
$(STADENBIN)/nxspec.o\
|
||||
$(STADENBIN)/userface.o\
|
||||
$(STADENBIN)/userfacecom.o\
|
||||
|
|
@ -118,13 +117,13 @@ SCOMMONOBJS=\
|
|||
$(COMMONOBJSB)
|
||||
|
||||
XCOMMONOBJS=\
|
||||
$(STADENBIN)/seeme-aix.o\
|
||||
$(STADENBIN)/seeme-dec.o\
|
||||
$(STADENBIN)/xspec.o\
|
||||
$(STADENBIN)/subs89.a\
|
||||
$(COBJS)
|
||||
|
||||
XCOMMONOBJS2=\
|
||||
$(STADENBIN)/seeme-aix.o\
|
||||
$(STADENBIN)/seeme-dec.o\
|
||||
$(STADENBIN)/xspec.o\
|
||||
$(STADENBIN)/subs89.a\
|
||||
$(COBJS2)
|
||||
|
|
@ -367,7 +366,7 @@ bap: $(BAPOBJS)
|
|||
$(LD) $(LDFLAGS) -o $@ $(BAPOBJS) $(LFLAGS)
|
||||
|
||||
xbap: $(XBAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(XBAPOBJS) $(XLFLAGS)
|
||||
$(XLD) $(LDFLAGS) -o $@ $(XBAPOBJS) $(XLFLAGS)
|
||||
|
||||
SAP=\
|
||||
sap.o\
|
||||
|
|
@ -541,30 +540,28 @@ splitp3: $(SPLITP3OBJS)
|
|||
# avoid filling up the (small on this machine) /tmp directory
|
||||
# with compiler debugging information.
|
||||
#
|
||||
#%.a: $(SRC)/%.f
|
||||
# BINDIR=`pwd`; \
|
||||
# cd $(SRC); \
|
||||
# SRCDIR=`pwd`; \
|
||||
# TMPDIR=/tmp/staden$$$$; \
|
||||
# if test ! -d $$TMPDIR; \
|
||||
# then mkdir $$TMPDIR; \
|
||||
# fi; \
|
||||
# cd $$TMPDIR; \
|
||||
# rm -f *.f *.o; \
|
||||
# fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
|
||||
# $(F77) $(FFLAGS) -c *.f; \
|
||||
# rm *.f; \
|
||||
# rm -f $$BINDIR/$@; \
|
||||
# ar rcv $$BINDIR/$@ *.o; \
|
||||
# ranlib $$BINDIR/$@; \
|
||||
# rm *.o; \
|
||||
# cd $$BINDIR; \
|
||||
# rm -r $$TMPDIR
|
||||
%.a: $(SRC)/%.f
|
||||
BINDIR=`pwd`; \
|
||||
cd $(SRC); \
|
||||
SRCDIR=`pwd`; \
|
||||
TMPDIR=/tmp/staden$$$$; \
|
||||
if test ! -d $$TMPDIR; \
|
||||
then mkdir $$TMPDIR; \
|
||||
fi; \
|
||||
cd $$TMPDIR; \
|
||||
rm -f *.f *.o; \
|
||||
fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
|
||||
$(F77) $(FFLAGS) -c *.f; \
|
||||
rm *.f; \
|
||||
rm -f $$BINDIR/$@; \
|
||||
ar rcv $$BINDIR/$@ *.o; \
|
||||
ranlib $$BINDIR/$@; \
|
||||
rm *.o; \
|
||||
cd $$BINDIR; \
|
||||
rm -r $$TMPDIR
|
||||
|
||||
|
||||
|
||||
#%.a: $(SRC)/%.f
|
||||
# $(F77) $(FFLAGS) -c *.f;
|
||||
# ar rcv $$BINDIR/$@ *.o;
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
45
src/convert/makefile
Normal file
45
src/convert/makefile
Normal file
|
|
@ -0,0 +1,45 @@
|
|||
#
|
||||
# Makefile for convert (Alpha version)
|
||||
#
|
||||
|
||||
SRC = .
|
||||
MISCSRC=$(SRC)/../Misc
|
||||
MISCBIN=$(MISCSRC)
|
||||
|
||||
CC = cc
|
||||
CFLAGS = -g -I$(MISCSRC)
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
LIBS = $(MISCBIN)/misc.a
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = convert
|
||||
|
||||
all : $(PROGS)
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
|
||||
OBJS = \
|
||||
list.o \
|
||||
main.o \
|
||||
dapIO.o \
|
||||
dapDB.o \
|
||||
bapIO.o \
|
||||
bapDB.o \
|
||||
process.o \
|
||||
flat_sd.o
|
||||
|
||||
convert: $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o convert $(OBJS) $(LIBS) $(LDFLAGS)
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
%.o:$(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
clean :
|
||||
/bin/rm -f $(PROGS) $(OBJS) *~
|
||||
|
|
@ -4,12 +4,12 @@
|
|||
|
||||
SRC = .
|
||||
MISCSRC=$(SRC)/../Misc
|
||||
MISCBIN=$(MISCSRC)
|
||||
MISCBIN=$(MISCSRC)/alpha-binaries
|
||||
|
||||
CC = cc
|
||||
CFLAGS = -g -I$(MISCSRC)
|
||||
CFLAGS = -g -std1 -ieee_with_inexact -I$(MISCSRC)
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
LDFLAGS = -g -non_shared
|
||||
LIBS = $(MISCBIN)/misc.a
|
||||
|
||||
#
|
||||
|
|
|
|||
114
src/cop/makefile
Normal file
114
src/cop/makefile
Normal file
|
|
@ -0,0 +1,114 @@
|
|||
#
|
||||
# Makefile for COP (Check Out Project) - Alpha version
|
||||
#
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = cop cop-bap
|
||||
all: $(PROGS)
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
TEDSRC = $(SRC)/../ted
|
||||
MISCSRC = $(SRC)/../Misc
|
||||
MISCBIN = $(MISCSRC)
|
||||
CONVERTSRC = $(SRC)/../convert
|
||||
INCLUDES = -I$(SRC) -I$(TEDSRC) -I$(MISCSRC) -I$(CONVERTSRC)
|
||||
|
||||
#
|
||||
# Alpha
|
||||
#
|
||||
CC = cc
|
||||
CFLAGS = -g $(INCLUDES)
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
LIBFLAGS =
|
||||
|
||||
#
|
||||
# Main and miscellaneous routines
|
||||
#
|
||||
COPOBJ = \
|
||||
cop.o
|
||||
|
||||
COPBAPOBJ = \
|
||||
cop-bap.o
|
||||
|
||||
LIBS = \
|
||||
$(MISCBIN)/misc.a
|
||||
|
||||
#
|
||||
# For reading in xdap database
|
||||
#
|
||||
XDAPIO = \
|
||||
dapIO.o
|
||||
|
||||
XBAPIO = \
|
||||
bapIO.o
|
||||
|
||||
#
|
||||
# For reading in trace files
|
||||
#
|
||||
TRACES = \
|
||||
getSeq.o \
|
||||
seqIOABI.o \
|
||||
seqIOALF.o \
|
||||
seqIOSCF.o \
|
||||
seqIOPlain.o \
|
||||
opp.o \
|
||||
seq.o \
|
||||
fpoint.o\
|
||||
mach-io.o
|
||||
|
||||
#
|
||||
# For aligning sequences
|
||||
#
|
||||
ALIGN = \
|
||||
llin.o
|
||||
|
||||
#
|
||||
# The whole lot
|
||||
#
|
||||
OBJ = \
|
||||
$(COPOBJ) \
|
||||
$(XDAPIO) \
|
||||
$(TRACES) \
|
||||
$(ALIGN)
|
||||
|
||||
OBJBAP = \
|
||||
$(COPBAPOBJ) \
|
||||
$(XBAPIO) \
|
||||
$(TRACES) \
|
||||
$(ALIGN)
|
||||
|
||||
|
||||
#
|
||||
# Cop
|
||||
#
|
||||
cop : $(OBJ)
|
||||
$(LD) $(LDFLAGS) -o cop $(OBJ) $(LIBS) $(LIBFLAGS)
|
||||
|
||||
cop-bap : $(OBJBAP)
|
||||
$(LD) $(LDFLAGS) -o cop-bap $(OBJBAP) $(LIBS) $(LIBFLAGS)
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
clean:
|
||||
/bin/rm -f $(OBJ) $(PROGS) *~
|
||||
|
||||
cop-bap.o: $(SRC)/cop.c
|
||||
$(CC) -DBAP_VERSION $(CFLAGS) -o cop-bap.o -c $(SRC)/cop.c
|
||||
|
||||
%.o: $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
%.o: $(TEDSRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
|
@ -6,14 +6,14 @@
|
|||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = cop cop-bap
|
||||
all: $(PROGS)
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
TEDSRC = $(SRC)/../ted
|
||||
MISCSRC = $(SRC)/../Misc
|
||||
MISCBIN = $(MISCSRC)
|
||||
MISCBIN = $(MISCSRC)/alpha-binaries
|
||||
CONVERTSRC = $(SRC)/../convert
|
||||
INCLUDES = -I$(SRC) -I$(TEDSRC) -I$(MISCSRC) -I$(CONVERTSRC)
|
||||
|
||||
|
|
@ -21,9 +21,9 @@ INCLUDES = -I$(SRC) -I$(TEDSRC) -I$(MISCSRC) -I$(CONVERTSRC)
|
|||
# Alpha
|
||||
#
|
||||
CC = cc
|
||||
CFLAGS = -g $(INCLUDES)
|
||||
CFLAGS = -g -std1 -ieee_with_inexact $(INCLUDES)
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
LDFLAGS = -g -non_shared
|
||||
LIBFLAGS =
|
||||
|
||||
#
|
||||
|
|
|
|||
93
src/expGetSeq/makefile
Normal file
93
src/expGetSeq/makefile
Normal file
|
|
@ -0,0 +1,93 @@
|
|||
#
|
||||
# Makefile for expGetSeq - Alpha version
|
||||
#
|
||||
|
||||
#
|
||||
# Turning on the AUTO_CLIP switch allows ted to automatically
|
||||
# select a left (using the -enzyme option or the .enzyme in the
|
||||
# Xted file) and right cutoff on your sequence (using 2 out of
|
||||
# 5 N's)
|
||||
#
|
||||
# Turning on the SAVE_EDITS switch allows the user to maintain
|
||||
# copies of their edits, i.e. when you open up ted on a file
|
||||
# that you have already edited, the old edits show up in the
|
||||
# ted edit window. The user may also call up any of their
|
||||
# past editing sessions.
|
||||
#
|
||||
# Turning on the DEF_OUT switch makes
|
||||
# trace_name.seq the default output file name
|
||||
#
|
||||
# Turning on the QUAL_CODE switch enables LaDeana's trace quality
|
||||
# clipping code.
|
||||
#
|
||||
# Turning on the QUAL_CHECK switch (at the same time as QUAL_CODE)
|
||||
# enables the overall trace quality check.
|
||||
#
|
||||
#SWITCHES = -DAUTO_CLIP -DDEF_OUT -DSAVE_EDITS -DQUAL_CODE -DQUAL_CHECK
|
||||
SWITCHES = -DAUTO_CLIP -DQUAL_CODE
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = expGetSeq
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
TEDSRC = $(SRC)/../newted
|
||||
INCLUDES = -I/usr/include/mit -I$(SRC) -I$(TEDSRC)
|
||||
|
||||
#
|
||||
# Compiler - debug on
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(SWITCHES) $(INCLUDES)
|
||||
LD= cc
|
||||
LDFLAGS= -g
|
||||
|
||||
|
||||
#
|
||||
# Object files
|
||||
#
|
||||
OBJS=\
|
||||
getMCH.o\
|
||||
seq.o\
|
||||
seqIOPlain.o\
|
||||
seqIOABI.o\
|
||||
seqIOEdit.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
opp.o\
|
||||
fpoint.o\
|
||||
match.o\
|
||||
mach-io.o\
|
||||
seqRead.o\
|
||||
traceType.o
|
||||
|
||||
|
||||
#
|
||||
# Linking
|
||||
#
|
||||
expGetSeq: $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(OBJS) $(LIBS)
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o : %.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o : $(TEDSRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
clean:
|
||||
rm -f $(PROGS) $(OBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
|
|
@ -42,9 +42,9 @@ INCLUDES = -I/usr/include/mit -I$(SRC) -I$(TEDSRC)
|
|||
# Compiler - debug on
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(SWITCHES) $(INCLUDES)
|
||||
CFLAGS= -g -ieee_with_inexact $(SWITCHES) $(INCLUDES)
|
||||
LD= cc
|
||||
LDFLAGS= -g
|
||||
LDFLAGS= -g -non_shared
|
||||
|
||||
|
||||
#
|
||||
|
|
|
|||
35
src/frog/makefile
Normal file
35
src/frog/makefile
Normal file
|
|
@ -0,0 +1,35 @@
|
|||
CC = cc
|
||||
CFLAGS = -g
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
LIBFLAGS =
|
||||
|
||||
SRC = .
|
||||
PROGS = frog toad
|
||||
all: $(PROGS)
|
||||
|
||||
FROGOBJ =\
|
||||
frog.o\
|
||||
mach-io.o
|
||||
|
||||
frog : $(FROGOBJ)
|
||||
$(LD) $(LDFLAGS) -o frog $(FROGOBJ) $(LIBFLAGS)
|
||||
|
||||
|
||||
TOADOBJ =\
|
||||
toad.o\
|
||||
scfIO.o\
|
||||
mach-io.o
|
||||
|
||||
toad : $(TOADOBJ)
|
||||
$(LD) $(LDFLAGS) -o toad $(TOADOBJ) $(LIBFLAGS)
|
||||
|
||||
|
||||
#
|
||||
# Specials
|
||||
#
|
||||
%.o:$(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
clean:
|
||||
/bin/rm -f $(PROGS) $(FROGOBJ)
|
||||
|
|
@ -1,7 +1,7 @@
|
|||
CC = cc
|
||||
CFLAGS = -g
|
||||
CFLAGS = -g -std1 -ieee_with_inexact
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
LDFLAGS = -g -non_shared
|
||||
LIBFLAGS =
|
||||
|
||||
SRC = .
|
||||
|
|
|
|||
86
src/getMCH/makefile
Normal file
86
src/getMCH/makefile
Normal file
|
|
@ -0,0 +1,86 @@
|
|||
#
|
||||
# Makefile for getMCH - Alpha version
|
||||
#
|
||||
|
||||
#
|
||||
#Turning on the AUTO_CLIP switch allows ted to automatically
|
||||
#select a left (using the -enzyme option or the .enzyme in the
|
||||
#Xted file) and right cutoff on your sequence (using 2 out of
|
||||
#5 N's)
|
||||
#
|
||||
# Turning on the SAVE_EDITS switch allows the user to maintain
|
||||
# copies of their edits, i.e. when you open up ted on a file
|
||||
# that you have already edited, the old edits show up in the
|
||||
# ted edit window. The user may also call up any of their
|
||||
# past editing sessions.
|
||||
#
|
||||
#Turning on the DEF_OUT switch makes
|
||||
# trace_name.seq the default output file name
|
||||
#
|
||||
#SWITCHES = -DAUTO_CLIP -DDEF_OUT -DSAVE_EDITS
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = getMCH trace2seq
|
||||
all: $(PROGS)
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
TEDSRC = $(SRC)/../ted
|
||||
INCLUDES = -I$(SRC) -I$(TEDSRC)
|
||||
|
||||
#
|
||||
# Compiler - debug on
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(SWITCHES) $(INCLUDES)
|
||||
LD= cc
|
||||
LDFLAGS= -g
|
||||
LIBFLAGS =
|
||||
|
||||
|
||||
#
|
||||
# Object files
|
||||
#
|
||||
OBJS=\
|
||||
getMCH.o\
|
||||
seq.o\
|
||||
seqIOPlain.o\
|
||||
seqIOABI.o\
|
||||
seqIOEdit.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
seqOutput.o\
|
||||
opp.o\
|
||||
fpoint.o\
|
||||
match.o\
|
||||
mach-io.o
|
||||
|
||||
|
||||
#
|
||||
# Linking
|
||||
#
|
||||
trace2seq getMCH: $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(OBJS) $(LIBS) $(LIBFLAGS)
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o : %.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o : $(TEDSRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
clean:
|
||||
rm -f $(PROGS) $(OBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
|
|
@ -23,7 +23,7 @@
|
|||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = getMCH trace2seq
|
||||
all: $(PROGS)
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
|
|
@ -35,9 +35,9 @@ INCLUDES = -I$(SRC) -I$(TEDSRC)
|
|||
# Compiler - debug on
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(SWITCHES) $(INCLUDES)
|
||||
CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) $(INCLUDES)
|
||||
LD= cc
|
||||
LDFLAGS= -g
|
||||
LDFLAGS= -g -non_shared
|
||||
LIBFLAGS =
|
||||
|
||||
|
||||
|
|
|
|||
172
src/indexseqlibs/makefile
Normal file
172
src/indexseqlibs/makefile
Normal file
|
|
@ -0,0 +1,172 @@
|
|||
#
|
||||
# indexseqlibs - Alpha version
|
||||
#
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
#
|
||||
# Programs need making
|
||||
#
|
||||
PROGS = \
|
||||
addnl \
|
||||
genbentryname1 \
|
||||
entryname2 \
|
||||
access4 \
|
||||
access2 \
|
||||
genbaccess1 \
|
||||
title2 \
|
||||
genbtitle1 \
|
||||
emblentryname1 \
|
||||
emblaccess1 \
|
||||
embltitle1 \
|
||||
pirentryname1 \
|
||||
piraccess1 \
|
||||
piraccess2 \
|
||||
pirtitle1 \
|
||||
pirtitle2 \
|
||||
excludewords \
|
||||
emblfreetext \
|
||||
genbfreetext \
|
||||
pirfreetext \
|
||||
freetext2 \
|
||||
freetext4 \
|
||||
emblauthor \
|
||||
genbauthor \
|
||||
pirauthor \
|
||||
hitNtrg \
|
||||
division
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
|
||||
#
|
||||
# Alpha
|
||||
#
|
||||
CC = cc
|
||||
CFLAGS = -g
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
|
||||
#
|
||||
# Shared objects
|
||||
#
|
||||
OBJS = \
|
||||
cdromheader.o \
|
||||
mach-io.o
|
||||
|
||||
#
|
||||
# Dependencies for programs
|
||||
#
|
||||
addnl : addnl.o
|
||||
$(LD) $(LDFLAGS) -o $@ addnl.o
|
||||
|
||||
genbentryname1 : genbentryname1.o
|
||||
$(LD) $(LDFLAGS) -o $@ genbentryname1.o
|
||||
|
||||
entryname2 : entryname2.o $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ entryname2.o $(OBJS)
|
||||
|
||||
access4 : access4.o $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ access4.o $(OBJS)
|
||||
|
||||
access2 : access2.o
|
||||
$(LD) $(LDFLAGS) -o $@ access2.o
|
||||
|
||||
genbaccess1 : genbaccess1.o
|
||||
$(LD) $(LDFLAGS) -o $@ genbaccess1.o
|
||||
|
||||
title2 : title2.o $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ title2.o $(OBJS)
|
||||
|
||||
genbtitle1 : genbtitle1.o
|
||||
$(LD) $(LDFLAGS) -o $@ genbtitle1.o
|
||||
|
||||
emblentryname1 : emblentryname1.o
|
||||
$(LD) $(LDFLAGS) -o $@ emblentryname1.o
|
||||
|
||||
emblaccess1 : emblaccess1.o
|
||||
$(LD) $(LDFLAGS) -o $@ emblaccess1.o
|
||||
|
||||
embltitle1 : embltitle1.o
|
||||
$(LD) $(LDFLAGS) -o $@ embltitle1.o
|
||||
|
||||
pirentryname1 : pirentryname1.o
|
||||
$(LD) $(LDFLAGS) -o $@ pirentryname1.o
|
||||
|
||||
piraccess1 : piraccess1.o
|
||||
$(LD) $(LDFLAGS) -o $@ piraccess1.o
|
||||
|
||||
piraccess2 : piraccess2.o
|
||||
$(LD) $(LDFLAGS) -o $@ piraccess2.o
|
||||
|
||||
pirtitle1 : pirtitle1.o
|
||||
$(LD) $(LDFLAGS) -o $@ pirtitle1.o
|
||||
|
||||
pirtitle2 : pirtitle2.o
|
||||
$(LD) $(LDFLAGS) -o $@ pirtitle2.o
|
||||
|
||||
excludewords : excludewords.o
|
||||
$(LD) $(LDFLAGS) -o $@ excludewords.o
|
||||
|
||||
emblfreetext.o: $(SRC)/freetext.c
|
||||
$(CC) $(CFLAGS) -DEMBL -c -o $@ $<
|
||||
emblfreetext : emblfreetext.o
|
||||
$(LD) $(LDFLAGS) -o $@ emblfreetext.o
|
||||
|
||||
genbfreetext.o: $(SRC)/freetext.c
|
||||
$(CC) $(CFLAGS) -DGENBANK -c -o $@ $<
|
||||
genbfreetext : genbfreetext.o
|
||||
$(LD) $(LDFLAGS) -o $@ genbfreetext.o
|
||||
|
||||
pirfreetext.o: $(SRC)/freetext.c
|
||||
$(CC) $(CFLAGS) -DPIR -c -o $@ $<
|
||||
pirfreetext : pirfreetext.o
|
||||
$(LD) $(LDFLAGS) -o $@ pirfreetext.o
|
||||
|
||||
freetext2 : freetext2.o
|
||||
$(LD) $(LDFLAGS) -o $@ freetext2.o
|
||||
|
||||
freetext4 : freetext4.o $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ freetext4.o $(OBJS)
|
||||
|
||||
emblauthor.o : $(SRC)/author.c
|
||||
$(CC) $(CFLAGS) -DEMBL -c -o $@ $<
|
||||
emblauthor : emblauthor.o
|
||||
$(LD) $(LDFLAGS) -o $@ emblauthor.o
|
||||
|
||||
genbauthor.o : $(SRC)/author.c
|
||||
$(CC) $(CFLAGS) -DGENBANK -c -o $@ $<
|
||||
genbauthor : genbauthor.o
|
||||
$(LD) $(LDFLAGS) -o $@ genbauthor.o
|
||||
|
||||
pirauthor.o : $(SRC)/author.c
|
||||
$(CC) $(CFLAGS) -DPIR -c -o $@ $<
|
||||
pirauthor : pirauthor.o
|
||||
$(LD) $(LDFLAGS) -o $@ pirauthor.o
|
||||
|
||||
hitNtrg : hitNtrg.o $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ hitNtrg.o $(OBJS)
|
||||
|
||||
division : division.o $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ division.o $(OBJS)
|
||||
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
||||
|
||||
|
||||
all : $(PROGS)
|
||||
|
||||
clean :
|
||||
/bin/rm -f $(PROGS) *.o *~
|
||||
|
||||
|
||||
|
|
@ -2,7 +2,6 @@
|
|||
# indexseqlibs - Alpha version
|
||||
#
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
#
|
||||
# Programs need making
|
||||
|
|
@ -45,9 +44,9 @@ SRC = .
|
|||
# Alpha
|
||||
#
|
||||
CC = cc
|
||||
CFLAGS = -g
|
||||
CFLAGS = -g -std1 -ieee_with_inexact
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
LDFLAGS = -g -non_shared
|
||||
|
||||
#
|
||||
# Shared objects
|
||||
|
|
|
|||
117
src/newted/makefile
Normal file
117
src/newted/makefile
Normal file
|
|
@ -0,0 +1,117 @@
|
|||
#
|
||||
# Makefile for ted (trace editor) - Alpha fork
|
||||
#
|
||||
|
||||
#
|
||||
# Turning on the AUTO_CLIP switch allows ted to automatically
|
||||
# select a left (using the -enzyme option or the .enzyme in the
|
||||
# Xted file) and right cutoff on your sequence (using 2 out of
|
||||
# 5 N's)
|
||||
#
|
||||
# Turning on the SAVE_EDITS switch allows the user to maintain
|
||||
# copies of their edits, i.e. when you open up ted on a file
|
||||
# that you have already edited, the old edits show up in the
|
||||
# ted edit window. The user may also call up any of their
|
||||
# past editing sessions.
|
||||
#
|
||||
# Turning on the DEF_OUT switch makes
|
||||
# trace_name.seq the default output file name
|
||||
#
|
||||
# Turning on the QUAL_CODE switch enables LaDeana's trace quality
|
||||
# clipping code.
|
||||
#
|
||||
# Turning on the QUAL_CHECK switch (at the same time as QUAL_CODE)
|
||||
# enables the overall trace quality check.
|
||||
#
|
||||
#SWITCHES = -DAUTO_CLIP -DDEF_OUT -DSAVE_EDITS -DQUAL_CODE -DQUAL_CHECK
|
||||
SWITCHES = -DAUTO_CLIP -DQUAL_CODE -DQUAL_CHECK
|
||||
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = ted autoted
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
|
||||
#
|
||||
# Compiler - debug on
|
||||
#
|
||||
CC= cc
|
||||
INCLUDES = -I$(SRC)
|
||||
CFLAGS= -g $(SWITCHES) $(INCLUDES)
|
||||
LIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
#
|
||||
LD= cc
|
||||
LDFLAGS= -g
|
||||
|
||||
#
|
||||
# Object files
|
||||
#
|
||||
TEDOBJS=\
|
||||
ted.o\
|
||||
dialogues.o\
|
||||
seq.o\
|
||||
seqIOPlain.o\
|
||||
seqIOABI.o\
|
||||
help.o\
|
||||
display.o\
|
||||
traceDisplay.o\
|
||||
basesDisplay.o\
|
||||
Graph.o\
|
||||
seqIOEdit.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
seqOutput.o\
|
||||
opp.o\
|
||||
info.o\
|
||||
fpoint.o\
|
||||
mach-io.o\
|
||||
seqRead.o\
|
||||
traceType.o\
|
||||
match.o
|
||||
|
||||
AUTOTEDOBJS=\
|
||||
autoted.o\
|
||||
seq.o\
|
||||
seqIOPlain.o\
|
||||
seqIOABI.o\
|
||||
seqIOEdit.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
seqOutput.o\
|
||||
opp.o\
|
||||
traceType.o\
|
||||
fpoint.o\
|
||||
mach-io.o\
|
||||
match.o\
|
||||
seqRead.o
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Linking
|
||||
#
|
||||
ted: $(TEDOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(TEDOBJS) $(LIBS)
|
||||
autoted: $(AUTOTEDOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(AUTOTEDOBJS) $(LIBS)
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
clean:
|
||||
rm -f ted $(TEDOBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
|
|
@ -42,11 +42,11 @@ SRC = .
|
|||
#
|
||||
CC= cc
|
||||
INCLUDES = -I$(SRC)
|
||||
CFLAGS= -g $(SWITCHES) $(INCLUDES)
|
||||
LIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) $(INCLUDES)
|
||||
LIBS= -lXaw -lXt -lXmu -lXext -lX11 -ldnet_stub
|
||||
#
|
||||
LD= cc
|
||||
LDFLAGS= -g
|
||||
LDFLAGS= -g -non_shared
|
||||
|
||||
#
|
||||
# Object files
|
||||
|
|
|
|||
67
src/scf/makefile
Normal file
67
src/scf/makefile
Normal file
|
|
@ -0,0 +1,67 @@
|
|||
#
|
||||
# getMCH - Alpha version
|
||||
#
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = makeSCF
|
||||
|
||||
#
|
||||
# SWITCHES - see ted makefile
|
||||
#
|
||||
#SWITCHES = -DAUTO_CLIP -DDEF_OUT -DSAVE_EDITS
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
TEDSRC = $(SRC)/../ted
|
||||
|
||||
#
|
||||
# alpha
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(SWITCHES) -I$(TEDSRC)
|
||||
LD= cc
|
||||
LDFLAGS= -g
|
||||
LIBFLAGS =
|
||||
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
%.o : $(TEDSRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
#
|
||||
# Object files
|
||||
#
|
||||
OBJS=\
|
||||
makeSCF.o\
|
||||
writeSCF.o\
|
||||
seq.o\
|
||||
seqIOPlain.o\
|
||||
seqIOABI.o\
|
||||
seqIOEdit.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
seqOutput.o\
|
||||
opp.o\
|
||||
fpoint.o\
|
||||
match.o\
|
||||
mach-io.o
|
||||
|
||||
|
||||
#
|
||||
# Linking
|
||||
#
|
||||
makeSCF: $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(OBJS) $(LIBS) $(LIBFLAGS)
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
all: $(PROGS)
|
||||
|
||||
clean:
|
||||
/bin/rm -f $(OBJS) $(PROGS) *~
|
||||
|
|
@ -22,9 +22,9 @@ TEDSRC = $(SRC)/../ted
|
|||
# alpha
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(SWITCHES) -I$(TEDSRC)
|
||||
CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) -I$(TEDSRC)
|
||||
LD= cc
|
||||
LDFLAGS= -g
|
||||
LDFLAGS= -g -non_shared
|
||||
LIBFLAGS =
|
||||
|
||||
%.o : $(SRC)/%.c
|
||||
|
|
|
|||
603
src/staden/makefile
Normal file
603
src/staden/makefile
Normal file
|
|
@ -0,0 +1,603 @@
|
|||
# Makefile for staden X programs (Alpha OSF/1.2 version)
|
||||
# ------------------------------------------------------
|
||||
|
||||
# This makefile generates the following staden programs which
|
||||
# run under xterm (normal, `N') and those which run directly under X.
|
||||
NPROGS= mep nip pip dap sap sip splitp1 splitp2 splitp3 gip sethelp convert_project rep lip sapf nipf vep
|
||||
LPROGS= nipl pipl sipl
|
||||
XPROGS= xmep xnip xpip xdap xsap xsip
|
||||
PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
|
||||
|
||||
#
|
||||
# ``Interesting'' suffices that make needs to know about
|
||||
#
|
||||
.SUFFIXES: .a $(SUFFIXES)
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC=.
|
||||
TEDSRC=$(SRC)/../ted
|
||||
MISCSRC=$(SRC)/../Misc
|
||||
MISCBIN=$(MISCSRC)
|
||||
INCLUDES= -I$(SRC) -I$(TEDSRC) -I$(MISCSRC)
|
||||
|
||||
#
|
||||
# Compilers and flags
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(INCLUDES)
|
||||
F77= gfortran
|
||||
FFLAGS= -g -fdec -std=legacy -L/usr/lib -lgfortran -C
|
||||
|
||||
FLIBS = -lutil -lm
|
||||
#FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm
|
||||
XLIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
LFLAGS= $(FLIBS)
|
||||
XLFLAGS= $(FLIBS) $(XLIBS)
|
||||
|
||||
LD = gfortran
|
||||
CLD = gfortran
|
||||
#CLD = cc
|
||||
LDFLAGS = -g # Comment out for faster linking when debugging
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Sequence library handling routines
|
||||
#
|
||||
SEQLIB=\
|
||||
seqlibsubs.o
|
||||
|
||||
|
||||
#
|
||||
# The C objects, needed by every X program
|
||||
#
|
||||
CCORE=\
|
||||
postscript.o\
|
||||
Graph.o\
|
||||
plotLog.o\
|
||||
help.o\
|
||||
dialogues.o\
|
||||
userfacecom.o\
|
||||
helpnmenu.o\
|
||||
xmenu.o\
|
||||
FtoC.o\
|
||||
mcspec.o\
|
||||
locks.o
|
||||
|
||||
COBJS=\
|
||||
main.o\
|
||||
$(CCORE)
|
||||
|
||||
XDAPCOBJS=\
|
||||
xdapmain.o\
|
||||
$(CCORE)
|
||||
|
||||
|
||||
#
|
||||
# Common objects, needed by every program
|
||||
#
|
||||
COMMONOBJSB=\
|
||||
fmain.o\
|
||||
seeme-aix.o\
|
||||
nxspec.o\
|
||||
userface.o\
|
||||
userfacecom.o\
|
||||
nxhelpmenu.o\
|
||||
helpnmenu.o\
|
||||
FtoC.o\
|
||||
subs89.a
|
||||
|
||||
COMMONOBJS=\
|
||||
$(COMMONOBJSB)\
|
||||
postscript.o
|
||||
|
||||
SCOMMONOBJS=\
|
||||
$(COMMONOBJSB)
|
||||
|
||||
XCOMMONOBJS=\
|
||||
seeme-aix.o\
|
||||
xspec.o\
|
||||
subs89.a\
|
||||
$(COBJS)
|
||||
|
||||
XDAPCOMMONOBJS=\
|
||||
seeme-aix.o\
|
||||
xspec.o\
|
||||
subs89.a\
|
||||
$(XDAPCOBJS)
|
||||
|
||||
|
||||
#
|
||||
# Building the programs
|
||||
# This should be just a linking phase because all of the object
|
||||
# files and library files are generated using implicit rules.
|
||||
# We use the fortran compiler to do linking.
|
||||
#
|
||||
GIP=\
|
||||
gip.o
|
||||
|
||||
GIPOBJS=\
|
||||
$(GIP)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
gip: $(GIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(GIPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
LIP=\
|
||||
lip.o
|
||||
|
||||
LIPOBJS=\
|
||||
$(LIP)\
|
||||
$(SEQLIB)\
|
||||
$(COMMONOBJS)
|
||||
|
||||
lip: $(LIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(LIPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
MEP=\
|
||||
mep.o\
|
||||
mepsub.o\
|
||||
asubs89.a\
|
||||
plot92.a
|
||||
|
||||
MEPOBJS=\
|
||||
$(MEP)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
XMEPOBJS=\
|
||||
$(MEP)\
|
||||
$(XCOMMONOBJS)\
|
||||
plX.o\
|
||||
textOutput.o
|
||||
|
||||
mep: $(MEPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(MEPOBJS) $(LFLAGS)
|
||||
|
||||
xmep: $(XMEPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(XMEPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
NIP=\
|
||||
nip.o\
|
||||
patternn.a\
|
||||
patternnc.a\
|
||||
anals89.a\
|
||||
asubs89.a\
|
||||
plot92.a \
|
||||
$(SEQLIB)
|
||||
|
||||
NIPOBJS=\
|
||||
$(NIP)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
XNIPOBJS=\
|
||||
$(NIP)\
|
||||
$(XCOMMONOBJS)\
|
||||
plX.o\
|
||||
textOutput.o
|
||||
|
||||
nip: $(NIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(NIPOBJS) $(LFLAGS)
|
||||
|
||||
xnip: $(XNIPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(XNIPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
NIPL=\
|
||||
nipl.o\
|
||||
patternnc.a\
|
||||
anals89.a\
|
||||
asubs89.a\
|
||||
$(SEQLIB)
|
||||
|
||||
NIPLOBJS=\
|
||||
$(NIPL)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
nipl: $(NIPLOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(NIPLOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
NIPF=\
|
||||
nipf.o\
|
||||
asubs89.a\
|
||||
plot92.a
|
||||
|
||||
NIPFOBJS=\
|
||||
$(NIPF)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
|
||||
nipf: $(NIPFOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(NIPFOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
PIP=\
|
||||
pip.o\
|
||||
analps89.a\
|
||||
patternp.a\
|
||||
patternpc.a\
|
||||
asubs89.a\
|
||||
plot92.a\
|
||||
$(SEQLIB)
|
||||
|
||||
PIPOBJS=\
|
||||
$(PIP)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
XPIPOBJS=\
|
||||
$(PIP)\
|
||||
$(XCOMMONOBJS)\
|
||||
plX.o\
|
||||
textOutput.o
|
||||
|
||||
pip: $(PIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(PIPOBJS) $(LFLAGS)
|
||||
|
||||
xpip:$(XPIPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(XPIPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
PIPL=\
|
||||
pipl.o\
|
||||
patternpc.a\
|
||||
analps89.a\
|
||||
asubs89.a\
|
||||
$(SEQLIB)
|
||||
|
||||
PIPLOBJS=\
|
||||
$(PIPL)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
pipl: $(PIPLOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(PIPLOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Trace manager objects
|
||||
#
|
||||
STDTEDFILES=\
|
||||
seq.o\
|
||||
seqIOABI.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
seqIOPlain.o\
|
||||
opp.o\
|
||||
fpoint.o\
|
||||
mach-io.o
|
||||
|
||||
TMANOBJS=\
|
||||
tman_main.o\
|
||||
tman_display.o\
|
||||
tman_traceDisplay.o\
|
||||
tman_basesDisplay.o\
|
||||
tman_context.o\
|
||||
tman_gadgets.o\
|
||||
$(STDTEDFILES)
|
||||
|
||||
# Some versions of X11R4 may have a bug in SmeLine.c
|
||||
XHACK=\
|
||||
SmeLine.o
|
||||
|
||||
EDITOR=\
|
||||
$(XHACK)\
|
||||
xsapConEdit.o\
|
||||
contigEditor.o\
|
||||
edUtils.o\
|
||||
undo.o\
|
||||
Sheet.o\
|
||||
select.o\
|
||||
extend.o\
|
||||
searchUtils.o\
|
||||
edMenu.o\
|
||||
trans.o\
|
||||
$(MISCBIN)/misc.a
|
||||
|
||||
TAGEDITOR=\
|
||||
tagEditor.o\
|
||||
tagdbparse.o\
|
||||
tagU2.o\
|
||||
tagU1.o
|
||||
|
||||
DAP=\
|
||||
dap.o\
|
||||
dbsysnew.o\
|
||||
dbsyscommon.o\
|
||||
asubs89.a\
|
||||
plot92.a
|
||||
|
||||
DAPOBJS=\
|
||||
$(DAP)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o\
|
||||
conEdit.o\
|
||||
tagU2.o
|
||||
|
||||
XDAPOBJS=\
|
||||
$(DAP)\
|
||||
$(XDAPCOMMONOBJS)\
|
||||
plX.o\
|
||||
textOutput.o\
|
||||
$(EDITOR)\
|
||||
$(TMANOBJS)\
|
||||
$(TAGEDITOR)
|
||||
|
||||
dap: $(DAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(DAPOBJS) $(LFLAGS)
|
||||
|
||||
xdap: $(XDAPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(XDAPOBJS) $(XLFLAGS)
|
||||
|
||||
convert_project: cvt.o
|
||||
$(CC) $(CFLAGS) -o $@ cvt.o
|
||||
|
||||
SAP=\
|
||||
sap.o\
|
||||
dbsyscommon.o\
|
||||
dbsysold.o\
|
||||
asubs89.a\
|
||||
plot92.a
|
||||
|
||||
SAPOBJS=\
|
||||
$(SAP)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
XSAPOBJS=\
|
||||
$(SAP)\
|
||||
$(XCOMMONOBJS)\
|
||||
plX.o\
|
||||
textOutput.o
|
||||
|
||||
sap: $(SAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SAPOBJS) $(LFLAGS)
|
||||
|
||||
xsap: $(XSAPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(XSAPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SAPF=\
|
||||
sapf.o\
|
||||
dbsyscommon.o\
|
||||
dbsysold.o\
|
||||
asubs89.a\
|
||||
plot92.a
|
||||
|
||||
SAPFOBJS=\
|
||||
$(SAPF)\
|
||||
sapmen.o\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
sapf: $(SAPFOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SAPFOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
SIP=\
|
||||
sip.o\
|
||||
dias89.a\
|
||||
plot92.a\
|
||||
$(SEQLIB)
|
||||
|
||||
SIPOBJS=\
|
||||
$(SIP)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
XSIPOBJS=\
|
||||
$(SIP)\
|
||||
$(XCOMMONOBJS)\
|
||||
plX.o\
|
||||
textOutput.o
|
||||
|
||||
sip: $(SIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SIPOBJS) $(LFLAGS)
|
||||
|
||||
xsip: $(XSIPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(XSIPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SIPL=\
|
||||
sipl.o\
|
||||
dias89.a\
|
||||
$(SEQLIB)
|
||||
|
||||
SIPLOBJS=\
|
||||
$(SIPL)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
sipl: $(SIPLOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SIPLOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SETHELP=\
|
||||
sethelp.o
|
||||
|
||||
SETHELPOBJS=\
|
||||
$(SETHELP)
|
||||
|
||||
sethelp: $(SETHELPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(SETHELPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SPLITP1=\
|
||||
splitp1.o
|
||||
SPLITP1OBJS=\
|
||||
$(SPLITP1)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
splitp1: $(SPLITP1OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SPLITP1OBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SPLITP2=\
|
||||
splitp2.o
|
||||
SPLITP2OBJS=\
|
||||
$(SPLITP2)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
splitp2: $(SPLITP2OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SPLITP2OBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
SPLITP3=\
|
||||
splitp3.o
|
||||
SPLITP3OBJS=\
|
||||
$(SPLITP3)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
splitp3: $(SPLITP3OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SPLITP3OBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
REP=\
|
||||
rep.o\
|
||||
dias89.a\
|
||||
subs89.a
|
||||
|
||||
REPOBJS=\
|
||||
$(REP)\
|
||||
$(COMMONOBJS)
|
||||
|
||||
rep: $(REPOBJS)
|
||||
$(F77) $(LDFLAGS) -o $@ $(REPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
VEP=\
|
||||
vep.o\
|
||||
dias89.a\
|
||||
subs89.a
|
||||
|
||||
|
||||
VEPOBJS=\
|
||||
$(VEP)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
|
||||
vep: $(VEPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(VEPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
#
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o: $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o: $(TEDSRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
|
||||
#
|
||||
%.o: $(SRC)/%.f
|
||||
$(F77) $(FFLAGS) -c $<
|
||||
|
||||
|
||||
#
|
||||
# The UNIX library (archive) mechanism is fairly weak so the following
|
||||
# procedure is used to generate libraries.
|
||||
# * split the source file up into files which each contain
|
||||
# a single function or subroutine
|
||||
# * compile each of those files
|
||||
# * insert the object files individually into the library
|
||||
# Each library is built by using a temporary directory.
|
||||
# The fortran compilations must be done sequentially in order to
|
||||
# avoid filling up the (small on this machine) /tmp directory
|
||||
# with compiler debugging information.
|
||||
#
|
||||
%.a: $(SRC)/%.f
|
||||
sh gen_a.sh
|
||||
|
||||
# BINDIR=`pwd`; \
|
||||
# cd $(SRC); \
|
||||
# SRCDIR=`pwd`; \
|
||||
#
|
||||
# TMPDIR=/tmp/staden$$$$; \
|
||||
# if test ! -d $$TMPDIR; \
|
||||
# then mkdir $$TMPDIR; \
|
||||
# fi; \
|
||||
# cd $$TMPDIR; \
|
||||
# rm -f *.f *.o; \
|
||||
#
|
||||
# fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
|
||||
# $(F77) $(FFLAGS) -c *.f; \
|
||||
#
|
||||
## rm *.f; \
|
||||
#
|
||||
# rm -f $@; \
|
||||
# ar rcv $@ *.o; \
|
||||
# ranlib $@; \
|
||||
##rm *.o; \
|
||||
#
|
||||
# cd $$BINDIR; \
|
||||
# rm -r $$TMPDIR
|
||||
|
||||
|
||||
|
||||
#.f.a:
|
||||
# $(F77) $(FFLAGS) -c $<
|
||||
# ar rcv $@ $*.o
|
||||
# ranlib $@
|
||||
# rm $*.o
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
nprogs: $(NPROGS)
|
||||
|
||||
xprogs: $(XPROGS)
|
||||
|
||||
lprogs: $(LPROGS)
|
||||
|
||||
clean:
|
||||
rm -f $(PROGS) *.a *.o *~
|
||||
|
||||
lint:
|
||||
lint -Q -Nn5000 -DNOSTRDUP $(INCLUDES) *.c
|
||||
|
||||
|
||||
|
|
@ -19,27 +19,25 @@ PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
|
|||
SRC=.
|
||||
TEDSRC=$(SRC)/../ted
|
||||
MISCSRC=$(SRC)/../Misc
|
||||
MISCBIN=$(MISCSRC)
|
||||
MISCBIN=$(MISCSRC)/alpha-binaries
|
||||
INCLUDES= -I$(SRC) -I$(TEDSRC) -I$(MISCSRC)
|
||||
|
||||
#
|
||||
# Compilers and flags
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(INCLUDES)
|
||||
F77= gfortran
|
||||
FFLAGS= -g -fdec -std=legacy -L/usr/lib -lgfortran -C
|
||||
CFLAGS= -g -std1 -ieee_with_inexact $(INCLUDES)
|
||||
F77= f77
|
||||
FFLAGS= -g -C
|
||||
|
||||
FLIBS = -lutil -lm
|
||||
#FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm
|
||||
XLIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil
|
||||
XLIBS= -lXaw -lXt -lXmu -lXext -lX11 -ldnet_stub
|
||||
LFLAGS= $(FLIBS)
|
||||
XLFLAGS= $(FLIBS) $(XLIBS)
|
||||
|
||||
LD = gfortran
|
||||
CLD = gfortran
|
||||
#CLD = cc
|
||||
LDFLAGS = -g # Comment out for faster linking when debugging
|
||||
LD = f77
|
||||
CLD = cc
|
||||
LDFLAGS = -g -non_shared # Comment out for faster linking when debugging
|
||||
|
||||
|
||||
|
||||
|
|
@ -80,7 +78,7 @@ XDAPCOBJS=\
|
|||
#
|
||||
COMMONOBJSB=\
|
||||
fmain.o\
|
||||
seeme-aix.o\
|
||||
seeme-dec.o\
|
||||
nxspec.o\
|
||||
userface.o\
|
||||
userfacecom.o\
|
||||
|
|
@ -97,13 +95,13 @@ SCOMMONOBJS=\
|
|||
$(COMMONOBJSB)
|
||||
|
||||
XCOMMONOBJS=\
|
||||
seeme-aix.o\
|
||||
seeme-dec.o\
|
||||
xspec.o\
|
||||
subs89.a\
|
||||
$(COBJS)
|
||||
|
||||
XDAPCOMMONOBJS=\
|
||||
seeme-aix.o\
|
||||
seeme-dec.o\
|
||||
xspec.o\
|
||||
subs89.a\
|
||||
$(XDAPCOBJS)
|
||||
|
|
@ -551,34 +549,25 @@ vep: $(VEPOBJS)
|
|||
# avoid filling up the (small on this machine) /tmp directory
|
||||
# with compiler debugging information.
|
||||
#
|
||||
%.a: $(SRC)/%.f
|
||||
sh gen_a.sh
|
||||
|
||||
# BINDIR=`pwd`; \
|
||||
# cd $(SRC); \
|
||||
# SRCDIR=`pwd`; \
|
||||
#
|
||||
# TMPDIR=/tmp/staden$$$$; \
|
||||
# if test ! -d $$TMPDIR; \
|
||||
# then mkdir $$TMPDIR; \
|
||||
# fi; \
|
||||
# cd $$TMPDIR; \
|
||||
# rm -f *.f *.o; \
|
||||
#
|
||||
# fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
|
||||
# $(F77) $(FFLAGS) -c *.f; \
|
||||
#
|
||||
## rm *.f; \
|
||||
#
|
||||
# rm -f $@; \
|
||||
# ar rcv $@ *.o; \
|
||||
# ranlib $@; \
|
||||
##rm *.o; \
|
||||
#
|
||||
# cd $$BINDIR; \
|
||||
# rm -r $$TMPDIR
|
||||
|
||||
|
||||
%.a: $(SRC)/%.f
|
||||
BINDIR=`pwd`; \
|
||||
cd $(SRC); \
|
||||
SRCDIR=`pwd`; \
|
||||
TMPDIR=/tmp/staden$$$$; \
|
||||
if test ! -d $$TMPDIR; \
|
||||
then mkdir $$TMPDIR; \
|
||||
fi; \
|
||||
cd $$TMPDIR; \
|
||||
rm -f *.f *.o; \
|
||||
fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
|
||||
$(F77) $(FFLAGS) -c *.f; \
|
||||
rm *.f; \
|
||||
rm -f $$BINDIR/$@; \
|
||||
ar rcv $$BINDIR/$@ *.o; \
|
||||
ranlib $$BINDIR/$@; \
|
||||
rm *.o; \
|
||||
cd $$BINDIR; \
|
||||
rm -r $$TMPDIR
|
||||
|
||||
#.f.a:
|
||||
# $(F77) $(FFLAGS) -c $<
|
||||
|
|
|
|||
90
src/ted/makefile
Normal file
90
src/ted/makefile
Normal file
|
|
@ -0,0 +1,90 @@
|
|||
#
|
||||
# Makefile for ted (trace editor) - Alpha fork
|
||||
#
|
||||
|
||||
#
|
||||
#Turning on the AUTO_CLIP switch allows ted to automatically
|
||||
#select a left (using the -enzyme option or the .enzyme in the
|
||||
#Xted file) and right cutoff on your sequence (using 2 out of
|
||||
#5 N's)
|
||||
#
|
||||
# Turning on the SAVE_EDITS switch allows the user to maintain
|
||||
# copies of their edits, i.e. when you open up ted on a file
|
||||
# that you have already edited, the old edits show up in the
|
||||
# ted edit window. The user may also call up any of their
|
||||
# past editing sessions.
|
||||
#
|
||||
#Turning on the DEF_OUT switch makes
|
||||
# trace_name.seq the default output file name
|
||||
#
|
||||
#SWITCHES = -DAUTO_CLIP -DDEF_OUT -DSAVE_EDITS
|
||||
SWITCHES = -DAUTO_CLIP
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = ted
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
|
||||
#
|
||||
# Compiler - debug on
|
||||
#
|
||||
CC= gfortran
|
||||
INCLUDES = -I$(SRC)
|
||||
CFLAGS= -g $(SWITCHES) $(INCLUDES)
|
||||
LIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
#-ldnet_stub
|
||||
#
|
||||
LD= gfortran
|
||||
LDFLAGS= -g
|
||||
|
||||
#
|
||||
# Object files
|
||||
#
|
||||
TEDOBJS=\
|
||||
ted.o\
|
||||
dialogues.o\
|
||||
seq.o\
|
||||
seqIOPlain.o\
|
||||
seqIOABI.o\
|
||||
help.o\
|
||||
display.o\
|
||||
traceDisplay.o\
|
||||
basesDisplay.o\
|
||||
Graph.o\
|
||||
seqIOEdit.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
seqOutput.o\
|
||||
opp.o\
|
||||
info.o\
|
||||
fpoint.o\
|
||||
mach-io.o\
|
||||
seqRead.o
|
||||
|
||||
|
||||
#
|
||||
# Linking
|
||||
#
|
||||
ted: $(TEDOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(TEDOBJS) $(LIBS)
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
clean:
|
||||
rm -f ted $(TEDOBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
|
|
@ -33,14 +33,13 @@ SRC = .
|
|||
#
|
||||
# Compiler - debug on
|
||||
#
|
||||
CC= gfortran
|
||||
CC= cc
|
||||
INCLUDES = -I$(SRC)
|
||||
CFLAGS= -g $(SWITCHES) $(INCLUDES)
|
||||
LIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
#-ldnet_stub
|
||||
CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) $(INCLUDES)
|
||||
LIBS= -lXaw -lXt -lXmu -lXext -lX11 -ldnet_stub
|
||||
#
|
||||
LD= gfortran
|
||||
LDFLAGS= -g
|
||||
LD= cc
|
||||
LDFLAGS= -g -non_shared
|
||||
|
||||
#
|
||||
# Object files
|
||||
|
|
|
|||
42
src/update_subclones/makefile
Normal file
42
src/update_subclones/makefile
Normal file
|
|
@ -0,0 +1,42 @@
|
|||
#
|
||||
# Makefile for subclonedb
|
||||
#
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = update_subclones
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
MISCSRC = $(SRC)/../Misc
|
||||
MISCBIN = $(MISCSRC)
|
||||
INCLUDES = -I$(SRC) -I$(MISCSRC)
|
||||
|
||||
#
|
||||
# Alpha
|
||||
#
|
||||
CC = cc
|
||||
CFLAGS = -g $(INCLUDES)
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
|
||||
#
|
||||
# Here they are
|
||||
#
|
||||
|
||||
update_subclones : update_subclones.o $(MISCBIN)/misc.a
|
||||
$(LD) $(LDFLAGS) -o update_subclones update_subclones.o $(MISCBIN)/misc.a
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
all: $(PROGS)
|
||||
|
||||
clean:
|
||||
/bin/rm -f $(PROGS)
|
||||
|
||||
%.o: $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
|
@ -12,16 +12,16 @@ PROGS = update_subclones
|
|||
#
|
||||
SRC = .
|
||||
MISCSRC = $(SRC)/../Misc
|
||||
MISCBIN = $(MISCSRC)
|
||||
MISCBIN = $(MISCSRC)/alpha-binaries
|
||||
INCLUDES = -I$(SRC) -I$(MISCSRC)
|
||||
|
||||
#
|
||||
# Alpha
|
||||
#
|
||||
CC = cc
|
||||
CFLAGS = -g $(INCLUDES)
|
||||
CFLAGS = -g -std1 -ieee_with_inexact $(INCLUDES)
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
LDFLAGS = -g -non_shared
|
||||
|
||||
#
|
||||
# Here they are
|
||||
|
|
|
|||
137
src/vepe/makefile
Normal file
137
src/vepe/makefile
Normal file
|
|
@ -0,0 +1,137 @@
|
|||
# Makefile for vepe - Alpha version
|
||||
# -------------------------------
|
||||
|
||||
PROGS= vepe
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
#
|
||||
# ``Interesting'' suffices that make needs to know about
|
||||
#
|
||||
.SUFFIXES: .a $(SUFFIXES)
|
||||
|
||||
|
||||
#
|
||||
# Directories
|
||||
#
|
||||
SRC = .
|
||||
#STADENSRC=/nfs/rutland/home3/pubseq/inhouse/share/src/staden
|
||||
STADENSRC=$(SRC)/../staden
|
||||
STADENBIN=$(STADENSRC)
|
||||
# Use the ted sources compiled for staden executables
|
||||
INCLUDES= -I$(STADENSRC)
|
||||
|
||||
|
||||
#
|
||||
# Compilers and flags
|
||||
#
|
||||
# debug on
|
||||
CC= cc
|
||||
CFLAGS= -g $(INCLUDES)
|
||||
F77= gfortran
|
||||
FFLAGS= -g
|
||||
LD= gfortran
|
||||
LDFLAGS= -g
|
||||
|
||||
FLAGS = -lutil -lm
|
||||
#FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil
|
||||
XLIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
#LFLAGS= $(FLIBS)
|
||||
XLFLAGS= $(FLIBS) $(XLIBS)
|
||||
|
||||
#
|
||||
# Avoid compilation of objects in remote directories
|
||||
#
|
||||
$(STADENBIN)/%.o : $(STADENSRC)/%.f
|
||||
$(STADENBIN)/%.o : $(STADENSRC)/%.c
|
||||
|
||||
#
|
||||
# Common objects, needed by every program
|
||||
#
|
||||
COMMONOBJS=\
|
||||
$(STADENBIN)/seeme-aix.o\
|
||||
$(STADENBIN)/nxspec.o\
|
||||
$(STADENBIN)/userface.o\
|
||||
$(STADENBIN)/userfacecom.o\
|
||||
$(STADENBIN)/helpnmenu.o\
|
||||
$(STADENBIN)/nxhelpmenu.o\
|
||||
$(STADENBIN)/FtoC.o\
|
||||
$(STADENBIN)/subs89.a\
|
||||
|
||||
|
||||
#
|
||||
# Building the programs
|
||||
# This should be just a linking phase because all of the object
|
||||
# files and library files are generated using implicit rules.
|
||||
# We use the fortran compiler to do linking.
|
||||
#
|
||||
|
||||
#
|
||||
# Vector excision program
|
||||
#
|
||||
|
||||
VEP=\
|
||||
vep.o\
|
||||
$(STADENBIN)/dias89.a\
|
||||
$(STADENBIN)/subs89.a
|
||||
|
||||
|
||||
VEPOBJS=\
|
||||
$(VEP)\
|
||||
$(COMMONOBJS)
|
||||
|
||||
|
||||
vep: $(VEPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(VEPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
VEPE=\
|
||||
vepe.o\
|
||||
$(STADENBIN)/dias89.a\
|
||||
expio.o\
|
||||
expFileIO.o
|
||||
|
||||
|
||||
VEPEOBJS=\
|
||||
$(VEPE)\
|
||||
$(COMMONOBJS)
|
||||
|
||||
|
||||
vepe: $(VEPEOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(VEPEOBJS) $(LFLAGS)
|
||||
|
||||
COBJS = expFileIO.o testc.o
|
||||
FOBJS = expFileIO.o testf.o
|
||||
|
||||
|
||||
testc: $(COBJS)
|
||||
$(CC) $(CFLAGS) -o $@ $(COBJS)
|
||||
|
||||
testf: $(FOBJS)
|
||||
$(F77) $(FFLAGS) -o $@ $(FOBJS)
|
||||
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o: %.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o: $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
#
|
||||
# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
|
||||
#
|
||||
%.o: $(SRC)/%.f
|
||||
$(F77) $(FFLAGS) -c $<
|
||||
|
||||
clean:
|
||||
rm -f $(PROGS) *.o *.a *~
|
||||
|
||||
|
||||
install: clean all
|
||||
|
|
@ -21,7 +21,7 @@ all: $(PROGS)
|
|||
SRC = .
|
||||
#STADENSRC=/nfs/rutland/home3/pubseq/inhouse/share/src/staden
|
||||
STADENSRC=$(SRC)/../staden
|
||||
STADENBIN=$(STADENSRC)
|
||||
STADENBIN=$(STADENSRC)/alpha-binaries
|
||||
# Use the ted sources compiled for staden executables
|
||||
INCLUDES= -I$(STADENSRC)
|
||||
|
||||
|
|
@ -31,14 +31,13 @@ INCLUDES= -I$(STADENSRC)
|
|||
#
|
||||
# debug on
|
||||
CC= cc
|
||||
CFLAGS= -g $(INCLUDES)
|
||||
F77= gfortran
|
||||
CFLAGS= -g -std1 -ieee_with_inexact $(INCLUDES)
|
||||
F77= f77
|
||||
FFLAGS= -g
|
||||
LD= gfortran
|
||||
LDFLAGS= -g
|
||||
LD= f77
|
||||
LDFLAGS= -g -non_shared
|
||||
|
||||
FLAGS = -lutil -lm
|
||||
#FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil
|
||||
FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil
|
||||
XLIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
#LFLAGS= $(FLIBS)
|
||||
XLFLAGS= $(FLIBS) $(XLIBS)
|
||||
|
|
@ -53,7 +52,7 @@ $(STADENBIN)/%.o : $(STADENSRC)/%.c
|
|||
# Common objects, needed by every program
|
||||
#
|
||||
COMMONOBJS=\
|
||||
$(STADENBIN)/seeme-aix.o\
|
||||
$(STADENBIN)/seeme-dec.o\
|
||||
$(STADENBIN)/nxspec.o\
|
||||
$(STADENBIN)/userface.o\
|
||||
$(STADENBIN)/userfacecom.o\
|
||||
|
|
|
|||
Loading…
Reference in a new issue