void Application::updateCounts(Sequence &S1,Sequence &S2)
{
// First, infer state sequence
int L=S1.getLength();
if(S2.getLength()!=L) throw "unequal sequence lengths";
Array1D<STATE> path(L);
for(int i=0 ; i<L ; ++i)
if(S1[i]==gapSymbol) path[i]=INSERTION_STATE;
else if(S2[i]==gapSymbol) path[i]=DELETION_STATE;
else path[i]=MATCH_STATE;
// Now count state transitions
for(int i=0 ; i<L-1 ; ++i)
++transCounts[path[i]][path[i+1]];
++transCounts[0][path[0]];
++transCounts[path[L-1]][0];
// Make sure there are no ambiguity codes
S1.replaceAll(INVALID_SYMBOL,gapSymbol);
S2.replaceAll(INVALID_SYMBOL,gapSymbol);
// Now count state emissions
for(int i=0 ; i<L ; ++i)
++emitCounts(path[i],S1[i],S2[i]);
}
// XUIElementFactory
Reference< XUIElement > SAL_CALL WWUIElementFactory::createUIElement(
const OUString & rResourceURL,
const Sequence< PropertyValue > & aArgs)
throw (RuntimeException, NoSuchElementException, IllegalArgumentException)
{
::osl::MutexGuard const g( m_aMutex );
if ( !rResourceURL.equalsAsciiL( RTL_CONSTASCII_STRINGPARAM( RESOURCE_NAME ) ) )
throw NoSuchElementException();
Reference< XFrame > xFrame;
Reference< XWindow > xParentWindow;
const PropertyValue * pArgs = aArgs.getConstArray();
const PropertyValue * pEndArgs = aArgs.getConstArray() + aArgs.getLength();
for ( ; pArgs < pEndArgs; ++pArgs )
{
if ( pArgs->Name.equalsAsciiL( RTL_CONSTASCII_STRINGPARAM( "Frame" ) ) )
xFrame.set( pArgs->Value, UNO_QUERY );
else if ( pArgs->Name.equalsAsciiL( RTL_CONSTASCII_STRINGPARAM( "ParentWindow" ) ) )
xParentWindow.set( pArgs->Value, UNO_QUERY );
}
if ( !xFrame.is() )
throw IllegalArgumentException();
if ( !xParentWindow.is() )
throw IllegalArgumentException();
Reference< XUIElement > xElement( new WWUIElement( m_xContext, xFrame, xParentWindow ) );
return xElement;
}
int NmerRateMatrix::countDifferences(const Sequence &seq1,
const Sequence &seq2)
{
int length=seq1.getLength(), diffs=0;
for(int i=0 ; i<length ; ++i)
if(seq1[i]!=seq2[i])
++diffs;
return diffs;
}
Sequence* getSummationSeq(Sequence * seq)
{
Sequence * res = new Sequence(seq->getLength());
res->set(1, seq->get(1));
for(int i = 2; i <= res->getLength(); i++)
{
res->set(i, res->get(i-1) + seq->get(i));
}
return res;
}
Sequence CollationImpl::sort(Sequence data, const DynamicContext* context) const
{
// build a sequence made of strings
Sequence stringSeq = Sequence(data.getLength(), context->getMemoryManager());
for(Sequence::iterator it=data.begin(); it!=data.end(); ++it) {
const XMLCh *str = (*it)->asString(context);
stringSeq.addItem(context->getItemFactory()->createString(str, context).get());
}
stringSeq.sortWithCollation(this, context);
return stringSeq;
}
unsigned convertNmerCode(unsigned rawCode,int seqLength,const Alphabet &alphabet)
{
Sequence S;
S.resize(seqLength);
unsigned base=alphabet.size();
for(int i=seqLength-1 ; i>=0 ; --i) {
unsigned digit=rawCode%base;
Symbol s=(int)digit;
S[i]=s;
rawCode/=base;
}
return S.asInt(alphabet,0,S.getLength());
}
~PrecomputeRes()
{
int n = A->getLength();
A->release();
B->release();
delete [] aSquare;
delete [] bSquare;
for(int i=0; i<=n; i++)
{
for(int j=0; j<3; j++)
delete [] s[i][j];
delete [] s[i];
}
delete [] s;
}
void getContext(PhylogenyNode *node,int &contextCode,int &contextLength)
{
int ID=node->getID();
AlignmentSeq &track=A.getIthTrack(ID);
int contextBegin=column-order;
if(contextBegin<0) contextBegin=0;
contextLength=column-contextBegin;
if(contextLength==0) {contextCode=0;return;}
Sequence context;
track.getSeq().getSubsequence(contextBegin,contextLength,context);
int pos=MultSeqAlignment::rightmostGapPos(context,gapSymbols);
if(pos>=0) {
Sequence temp;
int begin=pos+1, len=contextLength-pos-1;
if(begin<order && len>0)
context.getSubsequence(pos+1,contextLength-pos-1,temp);
context=temp;
contextLength=context.getLength();
}
contextCode=context.asInt(*alphabetMap.getRange());
}
float Application::computePDS(const Sequence &refSeq,const Sequence &altSeq)
{
// Compute raw alignment score
BandedSmithWaterman<float> aligner(AminoAlphabet::global(),refSeq,altSeq,*M,
gapOpen,gapExtend,bandWidth);
Alignment *alignment=aligner.fullAlignment();
double score=alignment->getScore();
delete alignment;
if(score<0) score=0;
// Normalize by maximal possible score
float maxScore=0;
int L=refSeq.getLength();
for(int i=0 ; i<L ; ++i) maxScore+=(*M)(refSeq[i],refSeq[i]);
//score-=maxScore;
score/=maxScore;
// Convert from a similarity score to a dissimilarity score
//return -score;
//cout<<1-score<<endl;
return 1-score;
}
bool operator()(const uint & w1, const uint & w2) {
return Seq->rank(w1,Seq->getLength()-1) < Seq->rank(w2,Seq->getLength()-1);
}
int main(int argc, char **argv) {
if(argc!=5) {
cout << "usage: " << argv[0] << " <text> <offsets> <queries> <seq>" << endl;
cout << " seq=1: Wavelet Tree Noptrs RG5" << endl;
cout << " seq=2: Wavelet Tree Noptrs RG10" << endl;
cout << " seq=3: Wavelet Tree Noptrs RG20" << endl;
cout << " seq=4: Wavelet Tree Noptrs RRR16" << endl;
cout << " seq=5: Wavelet Tree Noptrs RRR32" << endl;
cout << " seq=6: Wavelet Tree Noptrs RRR64" << endl;
cout << " seq=7: GMR B=RG20 X=RG20 PS=16" << endl;
return 0;
}
uint seq = transform(string(argv[4]));
ifstream input_seq(argv[1]);
Array * A = new Array(input_seq);
input_seq.close();
SequenceBuilder * sb,*sb1,*sb2,*sb3;
Sequence * S;
switch(seq) {
case 1:
S = new WaveletTreeNoptrs(*A, new BitSequenceBuilderRG(5),new MapperNone());
break;
case 2:
S = new WaveletTreeNoptrs(*A, new BitSequenceBuilderRG(10),new MapperNone());
break;
case 3:
S = new WaveletTreeNoptrs(*A, new BitSequenceBuilderRG(20),new MapperNone());
break;
case 4:
S = new WaveletTreeNoptrs(*A, new BitSequenceBuilderRRR(16),new MapperNone());
break;
case 5:
S = new WaveletTreeNoptrs(*A, new BitSequenceBuilderRRR(32),new MapperNone());
break;
case 6:
S = new WaveletTreeNoptrs(*A, new BitSequenceBuilderRRR(64),new MapperNone());
break;
case 7:
sb = new SequenceBuilderGMRChunk(new BitSequenceBuilderRG(20),new PermutationBuilderMRRR(16, new BitSequenceBuilderRG(20)));
S = new SequenceGMR(*A, 2*A->getMax(), new BitSequenceBuilderRG(20), sb);
break;
case 8:
sb1 = new SequenceBuilderWaveletTree(new BitSequenceBuilderRG(20), new MapperNone());
sb2 = new SequenceBuilderGMRChunk(new BitSequenceBuilderRG(20),new PermutationBuilderMRRR(16, new BitSequenceBuilderRG(20)));
sb3 = new SequenceBuilderGMR(new BitSequenceBuilderRG(20),sb2);
S = new SequenceAlphPart(*A, 10, sb1, sb3);
break;
}
cout << "Sequence size: " << S->getSize() << endl;
ifstream input_offs(argv[2]);
uint of;
vector<uint> offsets;
while((input_offs>>of)) offsets.push_back(of);
offsets.push_back(S->getLength());
input_offs.close();
cout << "Structure size: " << S->getSize()+offsets.size()*sizeof(uint) << endl;
cout << "No of documents: " << offsets.size() << endl;
cout << "No of words: " << A->getMax() << endl;
ifstream input(argv[3]);
vector<vector<uint> > queries;
uint qs;
while((input >> qs)) {
vector<uint> query;
for(uint i=0; i<qs; i++) {
uint tmp;
input >> tmp;
query.push_back(tmp);
}
queries.push_back(query);
}
input.close();
#define ERROUT 0
uint acc = 0;
start_timing();
vector<uint> aux;
for(uint i=0; i<queries.size(); i++) {
aux.clear();
intersect2(queries[i],S,offsets,aux);
#if ERROUT
for(uint j=0; j<aux.size(); j++) {
cerr << " " << aux[j];
acc += aux[j];
}
cerr << endl;
#else
acc += aux.size();
#endif
}
double t=get_timing();
cout << "acc: " << acc << endl;
cout << "Total time: " << t << " ms" << endl;
cout << "Time per query: " << t/queries.size() << " ms" << endl;
delete A;
delete S;
}
Sequence * getTransformed(Sequence *a,
Sequence * b, int begin, int end, PrecomputeRes &precomp)
{
if(begin == end) return 0;
Sequence * res = new Sequence(a->getLength());
for(int i=1; i<=res->getLength(); i++)
res->set(i, a->get(i));
// Point tempPt = precomp.A->get(end) - precomp.A->get(begin-1);
// centroids
Point aCenter = (precomp.A->get(end) - precomp.A->get(begin-1))/(end-begin+1);
Point bCenter = (precomp.B->get(end) - precomp.B->get(begin-1))/(end-begin+1);
//cout<<precomp.B->get(1)[0]<<endl;
/*
for(int i=0; i<a->getLength()+1; i++)
{
for(int j=0; j<3; j++)
{
for(int k=0; k<3; k++)
cout<<precomp.s[i][j][k]<<" ";
cout<<endl;
}
cout<<endl;
}
*/
// a' (transpose) b'
double C[3][3];
for(int u=0; u<3; u++)
for(int v=0; v<3; v++)
{
C[u][v] = precomp.s[end][u][v] - precomp.s[begin-1][u][v]
-aCenter[u]*(precomp.B->get(end)[v] - precomp.B->get(begin-1)[v])
-bCenter[v]*(precomp.A->get(end)[u] - precomp.A->get(begin-1)[u])
+(end - begin + 1)*aCenter[u]*bCenter[v];
}
SVDRes svdRes = calcSVD2(C);
double d[3][3];
for(int i=0; i<3; i++)
for(int j=0; j<3; j++)
d[i][j] = 0;
d[0][0] = 1; d[1][1] = 1;
d[2][2] = 1;
if(determinant(C)<0)
d[2][2] = -1;
transpose(svdRes.U);
transpose(svdRes.VT);
double tempMat[3][3];
matrixMul(svdRes.VT, d,tempMat);
double U[3][3];
matrixMul(tempMat, svdRes.U,U);
for(int i= begin; i<=end; i++)
{
res->set(i, mul(a->get(i)-aCenter, U)+bCenter);
}
return res;
}
/*** Evaluate this object ***/
Object* SpecialFunction::evaluate()
{
if(args.size() == 0)
throw Excep(getLineNumber(), getColumnNumber(), "Expected argument to special function!");
std::auto_ptr<Object> arg1(args.at(0)->evaluate());
if(id == SPF_INDEX)
{
if(args.size() != 2)
throw Excep(getLineNumber(), getColumnNumber(), "Invalid number of arguments passed to special function!");
std::auto_ptr<Object> arg2(args.at(1)->evaluate());
if(arg2->getType() == OBJ_TEXT)
{
if(arg1->getType() != OBJ_TEXT)
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_TEXT, arg1->getType(), 1);
Text* cast1 = static_cast<Text*>(arg1.get());
Text* cast2 = static_cast<Text*>(arg2.get());
size_t index = cast2->getValue().find(cast1->getValue());
if(index != std::string::npos)
return new Integer(index + 1);
return new Integer(0);
}
if(arg2->getType() == OBJ_SEQUENCE)
{
Sequence* cast = dynamic_cast<Sequence*>(arg2.get());
for(unsigned int i = 0; i < cast->getLength(); i++)
{
std::auto_ptr<Logical> eqOp(static_cast<Logical*>(Equal(arg1->clone(), cast->getObject(i)->clone()).evaluate()));
if(eqOp->getValue() == true)
return new Integer(i + 1);
}
return new Integer(0);
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_TEXT | OBJ_SEQUENCE, arg2->getType(), 2);
}
if(args.size() > 1)
throw Excep(getLineNumber(), getColumnNumber(), "Invalid number of arguments passed to special function!");
if(id == SPF_ABS)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
if(cast->getValue() < 0)
return new Integer(-cast->getValue());
return new Integer(cast->getValue());
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
if(cast->getValue() < 0)
return new Real(-cast->getValue());
return new Real(cast->getValue());
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_SIGN)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
if(cast->getValue() < 0)
return new Integer(-1);
if(cast->getValue() > 0)
return new Integer(1);
return new Integer(0);
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
if(cast->getValue() < 0)
return new Integer(-1);
if(cast->getValue() > 0)
return new Integer(1);
return new Integer(0);
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_SQRT)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
if(cast->getValue() < 0)
throw NegativeValueException(getLineNumber(), getColumnNumber(), cast->getValue(), 1);
double res = sqrt((double) cast->getValue());
if((long) res == res)
return new Integer((long) res);
return new Real(res);
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
if(cast->getValue() < 0)
throw NegativeValueException(getLineNumber(), getColumnNumber(), cast->getValue(), 1);
double res = sqrt((double) cast->getValue());
return new Real(res);
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_ENTIER)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
return new Integer(cast->getValue());
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
return new Integer(floor(cast->getValue()));
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_ROUND)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
return new Integer(cast->getValue());
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
long rounded = cast->getValue() < 0.0 ? ceil(cast->getValue() - 0.5) : floor(cast->getValue() + 0.5);
return new Integer(rounded);
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_RAND)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
if(cast->getValue() < 0)
throw NegativeValueException(getLineNumber(), getColumnNumber(), cast->getValue(), 1);
double f = (double) rand() / RAND_MAX;
return new Real( f * cast->getValue() );
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
if(cast->getValue() < 0)
throw NegativeValueException(getLineNumber(), getColumnNumber(), cast->getValue(), 1);
double f = (double) rand() / RAND_MAX;
return new Real( f * cast->getValue() );
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_INTRAND)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
if(cast->getValue() < 0)
throw NegativeValueException(getLineNumber(), getColumnNumber(), cast->getValue(), 1);
return new Integer( rand() % cast->getValue() + 1 );
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
if(cast->getValue() < 0)
throw NegativeValueException(getLineNumber(), getColumnNumber(), cast->getValue(), 1);
return new Integer( rand() % (long) cast->getValue() + 1 );
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_ISEMPTY)
{
return new Logical(arg1->getType() == OBJ_EMPTY);
}
if(id == SPF_ISLOG)
{
return new Logical(arg1->getType() == OBJ_LOGICAL);
}
if(id == SPF_ISINT)
{
return new Logical(arg1->getType() == OBJ_INTEGER);
}
if(id == SPF_ISREAL)
{
return new Logical(arg1->getType() == OBJ_REAL);
}
if(id == SPF_ISTEXT)
{
return new Logical(arg1->getType() == OBJ_TEXT);
}
if(id == SPF_ISSEQ)
{
return new Logical(arg1->getType() == OBJ_SEQUENCE);
}
if(id == SPF_ISPROC)
{
return new Logical(arg1->getType() == OBJ_PROCEDURE);
}
if(id == SPF_ISFUN)
{
return new Logical(arg1->getType() == OBJ_FUNCTION || arg1->getType() == OBJ_SPFUNCTION);
}
if(id == SPF_SIN)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
return new Real(sin((double) cast->getValue()));
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
return new Real(sin(cast->getValue()));
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_COS)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
return new Real(cos((double) cast->getValue()));
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
return new Real(cos(cast->getValue()));
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_TG)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
return new Real(tan((double) cast->getValue()));
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
return new Real(tan(cast->getValue()));
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_ARCSIN)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
if(errno == EDOM)
throw new Excep(getLineNumber(), getColumnNumber(), "Invalid value passed to special function!");
return new Real(exp((double) cast->getValue()));
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
if(errno == EDOM)
throw new Excep(getLineNumber(), getColumnNumber(), "Invalid value passed to special function!");
return new Real(exp(cast->getValue()));
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_ARCTG)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
if(errno == EDOM)
throw new Excep(getLineNumber(), getColumnNumber(), "Invalid value passed to special function!");
return new Real(exp((double) cast->getValue()));
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
if(errno == EDOM)
throw new Excep(getLineNumber(), getColumnNumber(), "Invalid value passed to special function!");
return new Real(exp(cast->getValue()));
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_EXP)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
return new Real(exp((double) cast->getValue()));
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
return new Real(exp(cast->getValue()));
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_LN)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
return new Real(log((double) cast->getValue()));
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
return new Real(log(cast->getValue()));
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
if(id == SPF_LG)
{
if(arg1->getType() == OBJ_INTEGER)
{
Integer* cast = static_cast<Integer*>(arg1.get());
return new Real(log10((double) cast->getValue()));
}
if(arg1->getType() == OBJ_REAL)
{
Real* cast = static_cast<Real*>(arg1.get());
return new Real(log10(cast->getValue()));
}
throw InvalidTypeException(getLineNumber(), getColumnNumber(), OBJ_INTEGER | OBJ_REAL, arg1->getType(), 1);
}
throw Excep(getLineNumber(), getColumnNumber(), "Invalid special function!");
}
