source: trunk/test/gff.cc @ 2482

// $Id: gff.cc 2482 2011-04-24 22:17:19Z peter $

/*
  Copyright (C) 2011 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library 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.

  The yat library 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 yat. If not, see <http://www.gnu.org/licenses/>.
*/

#include "Suite.h"

#include "yat/omic/GFF2.h"
#include "yat/omic/GFF3.h"

#include <fstream>

using namespace theplu::yat;
using namespace omic;

template<typename T>
void avoid_pedantic_warning(T t) {}

void gff2(test::Suite&);
void gff3(test::Suite&);

template<class T>
void test_gff(test::Suite&, GFF&);

int main(int argc, char* argv[])
{
  test::Suite suite(argc, argv);

  gff2(suite);
  gff3(suite);

  return suite.return_value();
}


void test_gff(test::Suite& suite, GFF& gff)
{
  std::string seqid = gff.seqid();
  std::string source = gff.source();
  std::string type = gff.type();
  avoid_pedantic_warning<const std::string&>(gff.start());
  avoid_pedantic_warning<const std::string&>(gff.end());
  avoid_pedantic_warning<const std::string&>(gff.score());
  avoid_pedantic_warning<const std::string&>(gff.strand());
  avoid_pedantic_warning<const std::string&>(gff.phase());
  const std::map<std::string, std::string>& m = gff.attributes();
  avoid_pedantic_warning(m);
}

void gff2(test::Suite& suite)
{
  suite.out() << "testing GFF2\n";
  std::ifstream is(test::filename("data/small.gff2").c_str());
  assert(is);
  GFF2 gff2;
  suite.add(getline(is, gff2));
  test_gff(suite, gff2);
  const std::string& a = gff2.attribute("genotype");
  if (!suite.add(a=="T or C"))
    suite.err() << "incorrect genotype value: `" << a << "'\n"
                << "expected: `T or C'\n";
  is.close();
}

void gff3(test::Suite& suite)
{
  suite.out() << "testing GFF3\n";
  std::ifstream is(test::filename("data/small.gff3").c_str());
  assert(is);
  GFF3 gff3;
  if (!suite.add(getline(is, gff3)))
    suite.err() << "getline failed\n";
  test_gff(suite, gff3);
  const std::string& a = gff3.attribute("genotype");
  if (!suite.add(a=="T"))
    suite.err() << "incorrect genotype value: `" << a << "'\n"
                << "expected: `T'\n";
  is.close();
}