# ======================================================================
# (c) Copyright 1996,1997,1998,1999,2000,2001,2004,2006,2007, 2008
# Whitehead Institute for Biomedical Research, Steve Rozen, 
# Andreas Untergasser and Helen Skaletsky
# All rights reserved.
# 
#   This file is part of primer3, the libprimer3 library, the oligotm 
#   library and the dpal library.
#
#   Primer3 and the libraries above are free software; you can
#   redistribute them and/or modify them under the terms of the GNU
#   General Public License as published by the Free Software Foundation;
#   either version 2 of the License, or (at your option) any later
#   version.
#
#   This software is distributed in the hope that it will be useful,
#   but WITHOUT ANY WARRANTY; without even the implied warranty of
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#   GNU General Public License for more details.
#
#   You should have received a copy of the GNU General Public License
#   along with this file (file gpl-2.0.txt in the source distribution); if
#   not, write to the Free Software Foundation, Inc., 51 Franklin St,
#   Fifth Floor, Boston, MA 02110-1301 USA
# 
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ======================================================================

# ======================================================================
# CITING PRIMER3
# 
# Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for
# general users and for biologist programmers. In: Krawetz S, Misener S
# (eds) Bioinformatics Methods and Protocols: Methods in Molecular
# Biology. Humana Press, Totowa, NJ, pp 365-386.  Source code available
# from https://sourceforge.net/projects/primer3/
# ======================================================================

LDLIBS = -lm
CC      = gcc
O_OPTS  = -O2
CC_OPTS = -g -Wall -D__USE_FIXED_PROTOTYPES__
P_DEFINES =

#CFLAGS  = $(CC_OPTS) $(O_OPTS)
#LDFLAGS = -g

CFLAGS=-isysroot /Developer/SDKs/MacOSX10.5.sdk -arch ppc -arch i386
LDFLAGS=-g -Wl,-syslibroot,/Developer/SDKs/MacOSX10.5.sdk -arch ppc -arch i386

# ======================================================================
# If you have trouble with library skew when moving primer3 executables
# between systems, you might want to set LIBOPTS to -static
LIBOPTS =

PRIMER_EXE      = primer3_core
LIBOLIGOTM      = liboligotm.a
LIBOLIGOTM_DYN  = liboligotm.so.1.2.0
LIBDPAL         = libdpal.a
LIBDPAL_DYN     = libdpal.a.so.1.0.0
LIBPRIMER3      = libprimer3.a
LIBPRIMER3_DYN  = libprimer3.so.1.0.0
LIBRARIES       = $(LIBPRIMER3) $(LIBDPAL) $(LIBOLIGOTM) 
DYNLIBS         = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBOLIGOTM_DYN)
RANLIB          = ranlib

PRIMER_OBJECTS1=primer3_boulder_main.o\
                format_output.o\
                read_boulder.o\
                print_boulder.o

PRIMER_OBJECTS=$(PRIMER_OBJECTS1) $(LIBRARIES)
PRIMER_DYN_OBJECTS=$(PRIMER_OBJECTS1) $(DYNLIBS)
# These are files generated by running ./primer3_core < ../example
example_files=example.for example.rev example.int

EXES=$(PRIMER_EXE) ntdpal oligotm long_seq_tm_test

all: $(EXES) $(LIBRARIES)

clean_src:
	-rm -f *.o $(EXES) *~ $(LIBRARIES) $(DYNLIBS) $(example_files) core

clean: clean_src
	cd ../test/; make clean

$(LIBOLIGOTM): oligotm.o
	ar rv $@ oligotm.o
	$(RANLIB) $@

$(LIBOLIGOTM_LIB): oligotm.o
	gcc -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o

$(LIBDPAL): dpal_primer.o
	ar rv $@ dpal_primer.o
	$(RANLIB) $@

$(LIBDPAL_DYN): dpal_primer.o
	gcc -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o

$(LIBPRIMER3): libprimer3.o p3_seq_lib.o
	ar rv $@ libprimer3.o p3_seq_lib.o
	$(RANLIB) $@

$(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o
	gcc -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o

$(PRIMER_EXE): $(PRIMER_OBJECTS)
	$(CC) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)

libprimer3.o: libprimer3.c libprimer3.h p3_seq_lib.h dpal.h oligotm.h
	$(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ libprimer3.c

ntdpal: ntdpal_main.o dpal.o
	$(CC) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o

oligotm: oligotm_main.c oligotm.h $(LIBOLIGOTM)
	$(CC) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)

long_seq_tm_test: long_seq_tm_test_main.c oligotm.o
	$(CC) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)

read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h p3_seq_lib.h 
	$(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c

print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h 
	$(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c

dpal.o: dpal.c dpal.h
	$(CC) -c $(CFLAGS) -o $@ dpal.c

p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h
	$(CC) -c $(CFLAGS) -o $@ p3_seq_lib.c

dpal_primer.o: dpal.c dpal.h
	$(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c

format_output.o: format_output.c format_output.h libprimer3.h dpal.h p3_seq_lib.h 
	$(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c

#ntdpal_main.o: ntdpal_main.c dpal.h
#	$(CC) -c $(CC_OPTS) -o $@ ntdpal_main.c
# We use CC_OPTS above rather than CFLAGS because
# gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2

ntdpal_main.o: ntdpal_main.c dpal.h
	$(CC) -c $(CFLAGS) -o $@ ntdpal_main.c

oligotm.o: oligotm.c oligotm.h

primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h oligotm.h format_output.h print_boulder.h read_boulder.h
	$(CC) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c

primer_test: test

test: $(PRIMER_EXE) ntdpal
	cd ../test; make test

# ======================================================================
# 
# VALGRIND INSTRUCTIONS.
#
# As far as we know, valgrind is not available for Mac OS Leopard. 
#
# ======================================================================