MainWindow::MainWindow( QWidget *parent ):
QMainWindow( parent )
{
this->createParameterInputWindow();
this->createMainWindow();
connect( check_original_fun, SIGNAL( clicked() ), this, SLOT( checkOriginal() ) );
connect( start_evolve, SIGNAL( clicked() ), this, SLOT( startEvolve() ) );
connect(dateback_btn, SIGNAL( clicked() ), this, SLOT( dateBack() ) );
connect( individual_num_input, SIGNAL( valueChanged(int) ), this, SLOT( parameterChange() ) );
connect( generation_num_input, SIGNAL( valueChanged(int) ), this, SLOT( parameterChange() ) );
connect( crossover_rate_input, SIGNAL(valueChanged(double)), this, SLOT( parameterChange() ) );
connect( mutation_rate_input, SIGNAL(valueChanged(double)), this, SLOT( parameterChange() ) );
connect( range_min_input, SIGNAL(valueChanged(double)), this, SLOT(parameterChange()) );
connect( range_max_input, SIGNAL(valueChanged(double)), this, SLOT(parameterChange()) );
connect( min_btn, SIGNAL( clicked() ), this, SLOT( parameterChange() ) );
connect( max_btn, SIGNAL( clicked() ), this, SLOT( parameterChange() ) );
connect(range_min_input, SIGNAL(valueChanged(double)), this, SLOT( originalParaChange()) );
connect(range_max_input, SIGNAL(valueChanged(double)), this, SLOT( originalParaChange()) );
connect(individual_num_input, SIGNAL( valueChanged(int) ), this, SLOT( originalParaChange() ) );
connect( dateback_btn, SIGNAL( clicked() ), this, SLOT( dateBack() ) );
}
void HHGate::setupTau( const Eref& e,
vector< double > parms )
{
if ( checkOriginal( e.id(), "setupTau" ) ) {
if ( parms.size() != 13 ) {
cout << "HHGate::setupTau: Error: parms.size() != 13\n";
return;
}
setupTables( parms, true );
}
}
void HHGate::setTableB( const Eref& e, vector< double > v )
{
if ( checkOriginal( e.id(), "tableB" ) ) {
isDirectTable_ = 1;
if ( A_.size() != v.size() ) {
cout << "Warning: HHGate::setTableB: size should be same as table A: " << v.size() << " != " << A_.size() << ". Ignoring.\n";
return;
}
B_ = v;
}
}
void HHGate::setTableA( const Eref& e, vector< double > v )
{
if ( v.size() < 2 ) {
cout << "Warning: HHGate::setTableA: size must be >= 2 entries on "
<< e.id().path() << endl;
return;
}
if ( checkOriginal( e.id(), "tableA" ) ) {
isDirectTable_ = 1;
A_ = v;
unsigned int xdivs = A_.size() - 1;
invDx_ = static_cast< double >( xdivs ) / ( xmax_ - xmin_ );
}
}
void HHGate::setMinfinity( const Eref& e, vector< double > val )
{
if ( val.size() != 5 ) {
cout << "Error: HHGate::setMinfinity on " << e.id().path() <<
": Number of entries on argument vector should be 5, was " <<
val.size() << endl;
return;
}
if ( checkOriginal( e.id(), "mInfinity" ) ) {
mInfinity_ = val;
updateAlphaBeta();
updateTables();
}
}
void HHGate::setAlpha( const Eref& e, vector< double > val )
{
if ( val.size() != 5 ) {
cout << "Error: HHGate::setAlpha on " << e.id().path() <<
": Number of entries on argument vector should be 5, was " <<
val.size() << endl;
return;
}
if ( checkOriginal( e.id(), "alpha" ) ) {
alpha_ = val;
updateTauMinf();
updateTables();
}
}
void HHGate::setMin( const Eref& e, double val )
{
if ( checkOriginal( e.id(), "min" ) ) {
xmin_ = val;
unsigned int xdivs = A_.size() - 1;
if ( isDirectTable_ && xdivs > 0 ) {
// Stuff here to stretch out table using interpolation.
invDx_ = static_cast< double >( xdivs ) / ( xmax_ - val );
tabFill( A_, xdivs, val, xmax_ );
tabFill( B_, xdivs, val, xmax_ );
} else {
updateTables();
}
}
}
void HHGate::setDivs( const Eref& e, unsigned int val )
{
if ( checkOriginal( e.id(), "divs" ) ) {
if ( isDirectTable_ ) {
invDx_ = static_cast< double >( val ) / ( xmax_ - xmin_ );
tabFill( A_, val, xmin_, xmax_ );
tabFill( B_, val, xmin_, xmax_ );
} else {
/// Stuff here to redo sizes.
A_.resize( val + 1 );
B_.resize( val + 1 );
invDx_ = static_cast< double >( val ) / ( xmax_ - xmin_ );
updateTables();
}
}
}
void HHGate::setMax( const Eref& e, double val )
{
if ( checkOriginal( e.id(), "max" ) ) {
xmax_ = val;
unsigned int xdivs = A_.size() - 1;
if ( isDirectTable_ && xdivs > 0 ) {
// Set up using direct assignment of table values.
invDx_ = static_cast< double >( xdivs ) / ( val - xmin_ );
tabFill( A_, xdivs, xmin_, val );
tabFill( B_, xdivs, xmin_, val );
} else {
// Set up using functional form. here we just recalculate.
updateTables();
}
}
}
void HHGate::setupAlpha( const Eref& e,
vector< double > parms )
{
if ( checkOriginal( e.id(), "setupAlpha" ) ) {
if ( parms.size() != 13 ) {
cout << "HHGate::setupAlpha: Error: parms.size() != 13\n";
return;
}
setupTables( parms, false );
alpha_.resize( 5, 0 );
beta_.resize( 5, 0 );
for ( unsigned int i = 0; i < 5; ++i )
alpha_[i] = parms[i];
for ( unsigned int i = 5; i < 10; ++i )
beta_[i - 5] = parms[i];
}
}
void HHChannel2D::destroyGate( const Eref& e, const Qinfo* q,
string gateType )
{
if ( !checkOriginal( e.id() ) ) {
cout << "Warning: HHChannel2D::destroyGate: Not allowed from copied channel:\n" << e.id().path() << "\n";
return;
}
if ( gateType == "X" )
innerDestroyGate( "xGate", &xGate_, e.id() );
else if ( gateType == "Y" )
innerDestroyGate( "yGate", &yGate_, e.id() );
else if ( gateType == "Z" )
innerDestroyGate( "zGate", &zGate_, e.id() );
else
cout << "Warning: HHChannel2D::destroyGate: Unknown gate type '" <<
gateType << "'. Ignored\n";
}
void HHChannel::vCreateGate( const Eref& e,
string gateType )
{
if ( !checkOriginal( e.id() ) ) {
cout << "Warning: HHChannel::createGate: Not allowed from copied channel:\n" << e.id().path() << "\n";
return;
}
if ( gateType == "X" )
innerCreateGate( "xGate", &xGate_, e.id(), Id(e.id().value() + 1) );
else if ( gateType == "Y" )
innerCreateGate( "yGate", &yGate_, e.id(), Id(e.id().value() + 2) );
else if ( gateType == "Z" )
innerCreateGate( "zGate", &zGate_, e.id(), Id(e.id().value() + 3) );
else
cout << "Warning: HHChannel::createGate: Unknown gate type '" <<
gateType << "'. Ignored\n";
}
int processBlatQuery( BlatQuery* blQ, int *idxOrig , float cutoff) {
int i,j;
PslEntry *curr;
int sizes[ arrayMax( blQ->entries ) ];
*idxOrig = -1;
for( i=0; i<arrayMax(blQ->entries); i++ ) {
curr = arrp( blQ->entries, i, PslEntry );
sizes[i]=0;
for( j=0; j < arrayMax( curr->blockSizes ); j++)
sizes[i] += arru( curr->blockSizes, j, int);
sizes[i] -= curr->misMatches;
if( checkOriginal ( blQ, curr ) == 1 )
*idxOrig = i;
}
if( *idxOrig < 0 ) die("Cannot find exact match: %s", blQ->qName);
int sizeOrig = sizes[ *idxOrig ];
for( i=0; i< arrayMax( blQ->entries ); i++ ) {
curr = arrp( blQ->entries, i, PslEntry );
warn( "%s\t%s\t%d\t%d\t[ %d, %d - %f]\t%d\t--\t%d\t%d\t%d", blQ->qName, curr->tName, curr->tStart, curr->tEnd, sizes[i], sizeOrig, ( (float)sizes[i] / (float)sizeOrig ) ,curr->blockCount, curr->misMatches, curr->qNumInsert, curr->tNumInsert);
if( ( (float)sizes[i] / (float)sizeOrig ) > cutoff && (i != *idxOrig) )
return 1;
}
return 0;
}
void HHGate::setupGate( const Eref& e,
vector< double > parms )
{
// The nine arguments are :
// A B C D F size min max isbeta
// If size == 0 then we check that the gate has already been allocated.
// If isbeta is true then we also have to do the conversion to
// HHGate form of alpha, alpha+beta, assuming that the alpha gate
// has already been setup. This uses tweakTables.
// We may need to resize the tables if they don't match here.
if ( !checkOriginal( e.id(), "setupGate" ) )
return;
if ( parms.size() != 9 ) {
cout << "HHGate::setupGate: Error: parms.size() != 9\n";
return;
}
double A = parms[0];
double B = parms[1];
double C = parms[2];
double D = parms[3];
double F = parms[4];
int size = static_cast< int > (parms[5] );
double min = parms[6];
double max = parms[7];
bool isBeta = static_cast< bool >( parms[8] );
vector< double >& ip = ( isBeta ) ? B_ : A_;
if ( size <= 0 ) { // Look up size, min, max from the interpol
size = ip.size() - 1;
if ( size <= 0 ) {
cout << "Error: setupGate has zero size\n";
return;
}
} else {
ip.resize( size + 1 );
}
double dx = ( max - min ) / static_cast< double >( size );
double x = min + dx / 2.0;
for ( int i = 0; i <= size; i++ ) {
if ( fabs ( F ) < SINGULARITY ) {
ip[i] = 0.0;
} else {
double temp2 = C + exp( ( x + D ) / F );
if ( fabs( temp2 ) < SINGULARITY )
ip[i] = ip[i-1];
else
ip[i] = ( A + B * x ) / temp2;
}
}
if ( isBeta ) {
assert( A_.size() > 0 );
// Here we ensure that the tables are the same size
if ( A_.size() != B_.size() ) {
if ( A_.size() > B_.size() ) {
// Note that the tabFill expects to allocate the
// terminating entry, so we put in size - 1.
tabFill( B_, A_.size() - 1, xmin_, xmax_ );
} else {
tabFill( A_, B_.size() - 1, xmin_, xmax_ );
}
}
// Then we do the tweaking to convert to HHChannel form.
tweakTables( 0 );
}
}
void HHGate::setUseInterpolation( const Eref& e, bool val )
{
if ( checkOriginal( e.id(), "useInterpolation" ) )
lookupByInterpolation_ = val;
}
