QRectF KisTransformUtils::handleRect(qreal radius, const QTransform &t, const QRectF &limitingRect, qreal *dOut) {
qreal handlesExtraScale =
scaleFromPerspectiveMatrix(t, limitingRect.center());
const qreal maxD = 0.2 * effectiveSize(limitingRect);
const qreal d = qMin(maxD, radius / handlesExtraScale);
QRectF handleRect(-0.5 * d, -0.5 * d, d, d);
if (dOut) {
*dOut = d;
}
return handleRect;
}
float SizesAttributeParser::length()
{
if (m_isValid)
return effectiveSize();
return effectiveSizeDefaultValue();
}
BWM::BWM(GarbageCollector &gc,BOOM::Vector<TrainingSequence*> &sequences,
SignalType signalType,int consensusOffset,int consensusLength,
float gcContent,float alpha)
: WMM(gc)
{
/*
This constructor performs training of the BWM
*/
// Set some things in the base class
setStrand(FORWARD_STRAND);
setSignalType(signalType);
// Compute background single-nucleotide probabilities
float atContent=1-gcContent;
float AT=atContent/2, GC=gcContent/2;
BOOM::Array1D<float> background(alphabet.getNumElements());
background.setAllTo(0);
Symbol A=alphabet.lookup('A'), T=alphabet.lookup('T');
Symbol C=alphabet.lookup('C'), G=alphabet.lookup('G');
background[A]=AT;
background[T]=AT;
background[C]=GC;
background[G]=GC;
// Allocate the underlying WMM matrix
float pseudocount=0;
int n=sequences.size();
int len=sequences[0]->getLength();
setSizes(consensusLength,consensusOffset,len);
int nAlpha=alphabet.getNumElements();
matrix.resize(len,nAlpha);
matrix.setAllTo(pseudocount);
// Iterate through the training sequences & collect counts
BOOM::FloatArray1D effectiveSize(len);
effectiveSize.setAllTo(0);
for(int i=0 ; i<n ; ++i)
{
TrainingSequence &seq=*sequences[i];
int l=seq.getLength();
if(l!=len) throw BOOM::String("length mismatch in BWM: ")+len+" vs "+l;
for(int pos=0 ; pos<len ; ++pos)
{
Symbol s=seq[pos];
int count=seq.getBoostCount();
matrix[pos][s]+=count;
effectiveSize[pos]+=count;
}
}
// Perform a binomial test at each position to see if frequencies
// are significantly different from the background frequencies
numSignificantPositions=0;
for(int pos=0 ; pos<len ; ++pos)
{
// First, we have to identify the most extreme count
int mostExtremeDiff=0;
Symbol mostExtremeSymbol=0;
int sampleSize=int(effectiveSize[pos]+5/9.0);
for(Symbol s=0 ; s<nAlpha ; ++s)
{
int expected=int(background[s]*sampleSize+5/9.0);
int observed=(int)matrix[pos][s];
int diff=abs(expected-observed);
if(diff>mostExtremeDiff)
{
mostExtremeDiff=diff;
mostExtremeSymbol=s;
}
}
// Apply binomial distribution to get P-value for this count
float p=background[mostExtremeSymbol];
int expected=int(p*sampleSize+5/9.0);
int observed=expected+mostExtremeDiff; // +/- are symmetric, so use +
double P=
BinomialDistribution::rightTailedPValue(observed,sampleSize,p);
// If not significantly different from background, then the observed
// frequencies are probably just a statistical fluctation due to
// small sample size, so use the background probabilities instead
if(P>alpha)
{
effectiveSize[pos]=0;
for(Symbol s=0 ; s<nAlpha ; ++s)
{
matrix[pos][s]=background[s]*sampleSize;
effectiveSize[pos]+=matrix[pos][s];
}
}
else
{
cout<<pos<<" : using OBSERVED frequencies, p="<<P<<endl;
++numSignificantPositions;
}
}
// Normalize counts into probabilities
for(int pos=0 ; pos<len ; ++pos)
for(Symbol s=0 ; s<nAlpha ; ++s)
matrix[pos][s]/=effectiveSize[pos];
// Convert probabilities to log-probabilities
convertToLogs();
}
