#
# 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 -ieee_with_inexact $(SWITCHES) $(INCLUDES)
LD= cc
LDFLAGS= -g -non_shared


#
# 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)