void
NoAssociationSimulator::runSimulation()
{
if( m_numSamples == 0 )
{
m_numSamples = numCombinations( m_order, m_snps.size( ) );
}
m_simulatedAuc.resize( m_numSamples, 0.0f );
std::vector<bool> shuffledPhenotypes( m_phenotypes );
for(unsigned int sample = 0; sample < m_numSamples; sample++)
{
shufflePhenotypes( &shuffledPhenotypes );
ColumnData<unsigned char> snps;
for(unsigned int k = 0; k < m_order; k++)
{
unsigned int snpIndex = getRandomInteger( m_snps.size( ) - 1 );
snps.addColumn( m_snps.getColumn( snpIndex ) );
}
RocMdrAnalysis mdrAnalyzer( snps, m_phenotypes );
m_simulatedAuc[ sample ] = mdrAnalyzer.getAuc( );
}
sort( m_simulatedAuc.begin( ), m_simulatedAuc.end( ) );
}
//
// Generates and displays a two-column list of choices for the use
// to choose from. The return value is the string the user has chosen.
//
static string getSettingByList( const RaceAnalyzer::StrSet &data,
const char *prompt )
{
cout << endl;
//
// Determine how many rows there will be in the 2-column display
//
size_t numRows = ( data.size() / 2 ) + ( data.size() % 2 );
//
// Generate the container of row/string data
//
ColumnData columnData = buildColumnData(data, numRows);
//
// Display the multi-column choice list.
//
RaceAnalyzer::StrSet::const_iterator midIter = data.begin();
advance( midIter, numRows-1 );
for_each( columnData.begin(), columnData.end(), DisplayChoice(numRows, *midIter) );
if (data.size() % 2)
cout << endl;
//
// Get (and validate) the user's choice
//
unsigned num;
while(true)
{
string numStr = getSetting(prompt);
if ( ! numStr.size() ) // blank indicates "all"
return numStr;
num = atoi( numStr.c_str() );
if ( num >= 1 && num <= data.size() )
break;
cout << endl
<< " *** Invalid number. Try Again. ***"
<< endl;
}
//
// Return the chosen string from the user's numeric input.
//
RaceAnalyzer::StrSet::const_iterator iter = data.begin();
advance( iter, num-1 );
return *iter;
}
void ColumnDiscretizer::transform(ColumnData<float> &before, ColumnData<unsigned char> *after)
{
for(unsigned int i = 0; i < before.size( ); i++)
{
std::vector<unsigned char> discretizedColumn( before.numberOfRows( ), 0 );
discretizeColumn( before.getColumn( i ), m_numIntervals, &discretizedColumn );
after->addColumn( discretizedColumn );
}
}
//
// Builds a container made up of rows, each of which has multiple
// columns. This is used for multi-column choice lists.
//
static ColumnData buildColumnData( const RaceAnalyzer::StrSet &data, size_t numRows )
{
ColumnData result;
transform( data.begin(),
data.end(),
inserter(result, result.end()),
StrToRowPair(numRows) );
return result;
}
Bool_t IsBlacklisted(Int_t index, ColumnData& blacklist)
{
Double_t val = index;
return std::binary_search(blacklist.begin(), blacklist.end(), val);
}
