#
# Makefile for ted (trace editor) - SGI fork
#

SHELL=/bin/sh

#
# 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 -ansi -prototypes $(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\
	seqRead.o\
	match.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)