###############################################################################
#                                                                             #
#   Copyright 2004 - 2007 Jakob Hull Havgaard, hull@genome.ku.dk              #
#                                                                             #
#   This file is part of Foldalign                                            #
#                                                                             #
#   Foldalign is free software; you can redistribute it and/or modify         #
#   it 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.                                       #
#                                                                             #
#   Foldalign 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 Foldalign; if not, write to the Free Software                  #
#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA #
#                                                                             #
###############################################################################

all: bin/foldalign


#options = -Wall -pedantic -ansi
#options = -Wall -pedantic -ansi -pg
options = -Wall -pedantic -ansi -O3
#options = -Wall -pedantic -ansi -O3 -static 



alignobjects =	src/arguments.cxx \
		src/backtrack.cxx \
		src/cell.cxx \
		src/exception.cxx \
		src/fold.cxx \
		src/helper.cxx \
		src/longCell.cxx \
		src/longCellPtr.cxx \
		src/longCellState.cxx \
		src/longTermMemory.cxx \
		src/mblcell.cxx \
		src/mbllist.cxx \
		src/mem_stack.cxx \
		src/multistacks.cxx \
		src/output.cxx \
		src/que_sll.cxx \
		src/readfile.cxx \
		src/results.cxx \
		src/scorematrix.cxx \
		src/seqs.cxx \
		src/sequenceArg.cxx \
		src/sequence.cxx \
		src/shortTermMemory.cxx \
		src/stack.cxx \
		src/stack_ssl.cxx \
		src/two_link.cxx


cc = g++

bin/foldalign: src/foldalign.cxx $(alignobjects) src/foldalign.h src/empty
	$(cc) $(options) src/foldalign.cxx $(alignobjects) -o bin/foldalign
