PolyTableBadBehavior.cc

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#include <Sequence/PolySites.hpp>
#include <Sequence/Fasta.hpp>
#include <Sequence/Alignment.hpp>
#include <Sequence/polySiteVector.hpp>
#include <Sequence/PolyTableFunctions.hpp>
#include <boost/test/unit_test.hpp>
#include <cstdio>
#include <cstdlib>
#include <cctype>
#include <iostream>
#include <functional>

BOOST_AUTO_TEST_SUITE(PolyTableBadBehaviorTest)

BOOST_AUTO_TEST_CASE( exception1 )
{
  std::vector<double> pos = {1,2,3,4,5};
  std::vector<std::string> data = {"AAAAA",
                                   "AAGAA",
                                   "CTGAA",
                                   "NAAC"}; //Sequence not same length as pos.size()
  BOOST_REQUIRE_THROW(Sequence::PolySites ps(std::move(pos),std::move(data)), std::runtime_error );
}

// This test became moot in 1.8.9
// BOOST_AUTO_TEST_CASE( badness1 )
// {
//   std::vector<double> pos = {1,2,3,4,5};
//   std::vector<std::string> data = {"AAAAA",
//                                 "AAGAA",
//                                 "CTGAA",
//                                 "NAACT"};

//   Sequence::PolySites ps(std::move(pos),std::move(data)),
//     ps2(Sequence::copyPolyTable(ps));

//   //force the calculation of const_site_iterator's underlying data
//   std::for_each( ps.sbegin(),ps.send(),[]( const Sequence::PolySites::const_site_iterator::value_type & __p ) {} );

//   //Now, remove that haplo with missing data
//   //by skipping PolyTable's iterator functions (this is BAD)
//   ps.second.erase( std::remove_if(ps.second.begin(),
//                                ps.second.end(),
//                                [](const std::string & __s) {
//                                  return __s.find('N') != std::string::npos;
//                                }),
//                 ps.second.end() );

//   /*
//     Crap!
//     The underlying data did not get reset...
//   */
//   BOOST_CHECK_EQUAL( ps.sbegin()->second,"AACN" );

//   //This will reset the data, as it calls PolyTable::begin in a non-const context
//   auto i = ps.begin();
//   BOOST_CHECK_EQUAL( ps.sbegin()->second,"AAC" );
// }

//Moot in 1.8.9
//Do the above, but correctly this time
// BOOST_AUTO_TEST_CASE( badness1_fix1 )
// {
//   std::vector<double> pos = {1,2,3,4,5};
//   std::vector<std::string> data = {"AAAAA",
//                                 "AAGAA",
//                                 "CTGAA",
//                                 "NAACT"};

//   Sequence::PolySites ps(std::move(pos),std::move(data)),
//     ps2(Sequence::copyPolyTable(ps));

//   //force the calculation of const_site_iterator's underlying data
//   std::for_each( ps.sbegin(),ps.send(),[]( const Sequence::PolySites::const_site_iterator::value_type & __p ) {} );

//   //call PolyTable::begin and end
//   ps.second.erase( std::remove_if(ps.begin(),
//                                ps.end(),
//                                [](const std::string & __s) {
//                                  return __s.find('N') != std::string::npos;
//                                }),
//                 ps.end() );
//   BOOST_CHECK_EQUAL( ps.sbegin()->second,"AAC" );
// }

//Moot in 1.8.9
// BOOST_AUTO_TEST_CASE( badness1_fix2 )
// {
//   std::vector<double> pos = {1,2,3,4,5};
//   std::vector<std::string> data = {"AAAAA",
//                                 "AAGAA",
//                                 "CTGAA",
//                                 "NAACT"};

//   Sequence::PolySites ps(std::move(pos),std::move(data)),
//     ps2(Sequence::copyPolyTable(ps));

//   //force the calculation of const_site_iterator's underlying data
//   std::for_each( ps.sbegin(),ps.send(),[]( const Sequence::PolySites::const_site_iterator::value_type & __p ) {} );

//   //uh-oh, remove_if is not using PolyTable's functions!
//   ps.second.erase( std::remove_if(ps.second.begin(),
//                                ps.second.end(),
//                                [](const std::string & __s) {
//                                  return __s.find('N') != std::string::npos;
//                                }),
//                 ps.end() ); //but, we call PolyTable::end here, and the context is non-const, so the next call to sbegin will be fine.
//   BOOST_CHECK_EQUAL( ps.sbegin()->second,"AAC" );
// }

BOOST_AUTO_TEST_CASE( badness2 )
{
  //std::vector<double> pos = {1,2,3,4,5};
  /*
  std::vector<std::string> data = {"AAAAA",
                                   "AAGAA",
                                   "CTGAA",
                                   "NAACT"};
  */
  std::vector<double> pos(1000,1.);
  std::vector<std::string> data(1000,std::string(1000,'A'));
  Sequence::PolySites ps(std::move(pos),std::move(data)),ps2;

  //You now have a table with unequal haplotype lengths
  //This is bad, and is user error.
  ps[0] = std::string("A");

  //Now, your internal data fail the check that all elements
  //are the same length, which may have unintended consequences
  //for later actions.
  BOOST_CHECK_EQUAL(Sequence::Alignment::IsAlignment(std::vector<std::string>(ps.begin(),ps.end())), false);
}
BOOST_AUTO_TEST_SUITE_END()