#   FreeContact - program to predict protein residue contacts from a sufficiently large multiple alignment
#   Copyright (C) 2012-2013  Laszlo Kajan <lkajan@rostlab.org> Rost Lab, Technical University of Munich, Germany
#   
#   This program 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 3 of the License, or
#   (at your option) any later version.
#   
#   This program 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 program.  If not, see <http://www.gnu.org/licenses/>.

# BIOXSD comes from configure.ac because of an apparent bug in depfile commands, see configure.ac

if HAVE_XSDCXX
XSDSOURCES = freecontact_input_xsd.cxx freecontact_input_xsd.hxx freecontact_output_xsd.cxx freecontact_output_xsd.hxx $(BIOXSD)_xsd.cxx $(BIOXSD)_xsd.hxx
XMLSOURCES = _write_bioxsd.cpp
endif

man_MANS = freecontact.1
bin_PROGRAMS = freecontact
TESTS = test_freecontact
dist_check_SCRIPTS = test_freecontact
examplesdir = $(docdir)/examples
dist_examples_DATA = demo_1000.aln demo_1000.psicov.50 PF00071_v25_999.fa PF00071_v25_999.xml PF00071_v25_999.evfold.50 PF00071_v25_999.evfold.50.xml
dist_pkgdata_SCRIPTS = a2m2aln
# lkajan: I am not sure where to install these, perhaps [1]? That is not policy, though.
# [1] http://debian-xml-sgml.alioth.debian.org/xml-policy/xml-infrastructure-dirs.html
dist_pkgdata_DATA = $(BIOXSD).xsd freecontact_input.xsd freecontact_output.xsd

AM_CPPFLAGS = $(BOOST_CPPFLAGS) -I$(top_srcdir)/lib -D__sysconfdir__=\"$(sysconfdir)\" -D__pkgdatadir__=\"$(pkgdatadir)\" -Wall
AM_CXXFLAGS = $(OPENMP_CXXFLAGS)
AM_LDFLAGS = $(OPENMP_CXXFLAGS) $(BOOST_LDFLAGS) -Wall

freecontact_SOURCES = $(top_srcdir)/lib/config.h freecontact.cpp fc.h $(top_srcdir)/lib/freecontact.h $(XMLSOURCES)
nodist_freecontact_SOURCES = $(XSDSOURCES)
# lkajan: _xsd.[ch]xx gets built into $(top_builddir)/src
freecontact_CPPFLAGS = -I$(top_srcdir)/lib -I$(top_builddir)/src $(XERCES_CPPFLAGS) $(XSDCXX_CPPFLAGS)
freecontact_LDFLAGS = $(XERCES_LDFLAGS)
freecontact_LDADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(XERCES_LIBS) $(top_builddir)/lib/libfreecontact.la

$(man_MANS) : %.1 : %.cpp
	sed -e 's|__pkgdatadir__|$(pkgdatadir)|g;s|__examplesdir__|$(examplesdir)|g;s|__sysconfdir__|$(sysconfdir)|g;s|__bindir__|$(bindir)|g;s|__PACKAGE_VERSION__|$(PACKAGE_VERSION)|g' "$<" | \
	pod2man --utf8 -c 'User Commands' -r "$(VERSION)" -name $(shell echo "$(basename $@)" | tr '[:lower:]' '[:upper:]') > "$@"

if HAVE_XSDCXX
.SECONDARY: freecontact_input_xsd.cxx freecontact_input_xsd.hxx freecontact_output_xsd.cxx freecontact_output_xsd.hxx
%_xsd.cxx %_xsd.hxx : %.xsd
	$(XSDCXX) cxx-tree --location-map http://bioxsd.org/$(BIOXSD).xsd=$(BIOXSD).xsd \
		--namespace-map http://rostlab.org/freecontact/input=freecontact_input_xsd \
		--namespace-map http://rostlab.org/freecontact/output=freecontact_output_xsd \
		--namespace-map http://bioxsd.org/BioXSD-1.1=BioXSD \
		--generate-serialization --generate-doxygen \
		--generate-polymorphic --polymorphic-type-all \
		--omit-default-attributes \
		--root-element-all \
		--hxx-suffix _xsd.hxx --cxx-suffix _xsd.cxx \
		$<

freecontact_input_xsd.hxx : $(BIOXSD)_xsd.hxx
freecontact_input_xsd.cxx : $(BIOXSD)_xsd.hxx
freecontact_output_xsd.hxx : $(BIOXSD)_xsd.hxx
freecontact_output_xsd.cxx : $(BIOXSD)_xsd.hxx
_write_bioxsd.cpp : freecontact_input_xsd.hxx freecontact_output_xsd.hxx $(BIOXSD)_xsd.hxx
endif

clean-local:
	rm -f $(man_MANS) $(XSDSOURCES)
	rm -f freecontact.static

# statically linked version
STATIC_LAPACK_LIBDIR = /usr/lib/atlas-base
freecontact.static: freecontact
	$(freecontact_LINK) -all-static -L$(STATIC_LAPACK_LIBDIR) $(freecontact_OBJECTS) $(freecontact_LDADD) $(LIBS)

#include $(srcdir)/glassotest.mk