# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack import *


class Poamsa(MakefilePackage):
    """POA is Partial Order Alignment, a fast program for multiple sequence
       alignment in bioinformatics. Its advantages are speed, scalability,
       sensitivity, and the superior ability to handle branching / indels
       in the alignment."""

    homepage = "https://sourceforge.net/projects/poamsa"
    url      = "https://downloads.sourceforge.net/project/poamsa/poamsa/2.0/poaV2.tar.gz"

    version('2.0', sha256='d98d8251af558f442d909a6527694825ef6f79881b7636cad4925792559092c2')

    def url_for_version(self, version):
        url = "https://downloads.sourceforge.net/project/poamsa/poamsa/{0}/poaV{1}.tar.gz"
        return url.format(version.dotted, version.up_to(1))

    def build(self, spec, prefix):
        make('poa')

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        mkdirp(prefix.lib)
        install('poa', prefix.bin)
        install('liblpo.a', prefix.lib)

@@ -933,16 +933,210 @@
 to(1))%0A%0A
+    def edit(self, spec, prefix):%0A        filter_file(r'%5E(char %5C*Program_name;)', 'extern %5C%5C1', 'black_flag.h')%0A        filter_file(r'%5E(char %5C*Program_version;)', 'extern %5C%5C1', 'black_flag.h')%0A%0A
     def 

fix build errors for gcc10+ (#28262)