uint64_t
StringExtractor::GetHexWithFixedSize (uint32_t byte_size, bool little_endian, uint64_t fail_value)
{
if (byte_size <= 8 && GetBytesLeft() >= byte_size * 2)
{
uint64_t result = 0;
uint32_t i;
if (little_endian)
{
// Little Endian
uint32_t shift_amount;
for (i = 0, shift_amount = 0;
i < byte_size && IsGood();
++i, shift_amount += 8)
{
result |= ((uint64_t)GetHexU8() << shift_amount);
}
}
else
{
// Big Endian
for (i = 0; i < byte_size && IsGood(); ++i)
{
result <<= 8;
result |= GetHexU8();
}
}
}
m_index = UINT64_MAX;
return fail_value;
}
bool OBConformerSearch::Setup(const OBMol &mol, int numConformers, int numChildren, int mutability, int convergence)
{
// copy some variables
m_mol = mol;
m_numConformers = numConformers;
m_numChildren = numChildren;
m_mutability = mutability;
m_convergence = convergence;
if (m_mol.GetCoordinates() == NULL)
return false;
// Initialize the OBRotorList
m_rotorList.SetFixedBonds(m_fixedBonds);
m_rotorList.Setup(m_mol);
if (!m_rotorList.Size()) { // only one conformer
return false;
}
// create initial population
OBRandom generator;
generator.TimeSeed();
RotorKey rotorKey(m_rotorList.Size() + 1, 0); // indexed from 1
if (IsGood(rotorKey))
m_rotorKeys.push_back(rotorKey);
else {
cout << "Initial conformer does not pass filter!" << endl;
}
int tries = 0;
while (m_rotorKeys.size() < m_numConformers && tries < numConformers * 1000) {
tries++;
// perform random mutation(s)
OBRotorIterator ri;
OBRotor *rotor = m_rotorList.BeginRotor(ri);
for (int i = 1; i < m_rotorList.Size() + 1; ++i, rotor = m_rotorList.NextRotor(ri)) {
if (generator.NextInt() % m_mutability == 0)
rotorKey[i] = generator.NextInt() % rotor->GetResolution().size();
}
// duplicates are always rejected
if (!IsUniqueKey(m_rotorKeys, rotorKey))
continue;
// execute filter(s)
if (!IsGood(rotorKey))
continue;
// add the key
m_rotorKeys.push_back(rotorKey);
}
// print out initial conformers
cout << "Initial conformer count: " << m_rotorKeys.size() << endl;
for (unsigned int i = 0; i < m_rotorKeys.size(); ++i) {
for (unsigned int j = 1; j < m_rotorKeys[i].size(); ++j)
std::cout << m_rotorKeys[i][j] << " ";
std::cout << std::endl;
}
return true;
}
bool NMEA0183L::PreParse( void )
{
wxCharBuffer buf = sentence.Sentence.ToUTF8();
if ( !buf.data() ) // badly formed sentence?
return false;
if ( IsGood() )
{
wxString mnemonic = sentence.Field( 0 );
/*
** See if this is a proprietary field
*/
if ( mnemonic.Left( 1 ) == 'P' )
mnemonic = _T( "P" );
else
mnemonic = mnemonic.Right( 3 );
LastSentenceIDReceived = mnemonic;
return true;
}
else
return false;
}
bool ArrayElementToken::CanConvertTo(Token_Type to) const
{
if (!IsGood())
return false;
else if (to == kTokenType_ArrayElement)
return true;
UInt8 elemType = g_ArrayMap.GetElementType(GetOwningArrayID(), key);
if (elemType == kDataType_Invalid)
return false;
switch (to)
{
case kTokenType_Boolean:
return elemType == kDataType_Form || elemType == kDataType_Numeric;
case kTokenType_String:
return elemType == kDataType_String;
case kTokenType_Number:
return elemType == kDataType_Numeric;
case kTokenType_Array:
return elemType == kDataType_Array;
case kTokenType_Form:
return elemType == kDataType_Form;
}
return false;
}
int
ann_mex_t::annkFRSearch( // approx fixed-radius kNN search
const mxArray* mxQ, // query point
ANNdist sqRad, // squared radius of query ball
int k, // number of near neighbors to return
mxArray** mxIdx, // nearest neighbor array (modified)
mxArray** mxDst, // dist to near neighbors (modified)
double eps) // error bound
{
index_t j(0);
if ( ! IsGood() )
mexErrMsgIdAndTxt("annmex:annkFRSearch","Class integrity check failed");
// check input point(s)
// dimension of points
if (m_idim != mxGetM(mxQ))
mexErrMsgIdAndTxt("annmex:annkFRSearch","point dimension does not match");
if ( mxGetN(mxQ) != 1 )
mexErrMsgIdAndTxt("annmex:annkFRSearch","FR search can be done for a single point at each time");
if ( k <= 0 )
mexErrMsgIdAndTxt("annmex:annkFRSearch","k must be positive");
if ( k > m_inpoints ) {
// generate warning
mexWarnMsgIdAndTxt("annmex:annkFRSearch","searching for more points than in tree - returning only %d",m_inpoints);
k = m_inpoints;
}
if ( sqRad < 0 )
mexErrMsgIdAndTxt("annmex:annkFRSearch","radius must be positive");
ANNpoint pp = (ANNpoint)mxGetData(mxQ);
ANNidx* tmpidx = new ANNidx[k];
ANNdist* tmpdist = new ANNdist[k];
if ( tmpidx == NULL || tmpdist == NULL )
mexErrMsgIdAndTxt("annmex:annkFRSearch","cannot allocate memory for outputs");
int gotp = m_pTree->annkFRSearch(pp, sqRad, k, tmpidx, tmpdist, eps);
// allocate space for outputs
*mxIdx = mxCreateNumericMatrix(1, min(gotp,k), mxIDX_CLASS, mxREAL);
*mxDst = mxCreateNumericMatrix(1, min(gotp,k), mxDIST_CLASS, mxREAL);
if ( *mxIdx == NULL || *mxDst == NULL )
mexErrMsgIdAndTxt("annmex:annkPriSearch","cannot allocate memory for outputs");
ANNidx * pidx = (ANNidx*)mxGetData(*mxIdx);
ANNdist* pdist= (ANNdist*)mxGetData(*mxDst);
for ( j = 0 ; j < min(gotp,k) ; j++ ) {
pidx[j] = tmpidx[j];
pdist[j] = tmpdist[j];
}
delete [] tmpidx;
delete [] tmpdist;
return gotp; // how many points in range
}
Particle::Particle(int _ft, double _fE, double _fz) {
ftype = _ft;
fE0ph = _fE;
fz0ph = _fz;
SetBetaAndMass();
fIsGood = IsGood();
fwi = 1;
}
const HAL_CONFIG_BLOCK* HAL_CONFIG_BLOCK::Next() const
{
if(IsGood())
{
return (const HAL_CONFIG_BLOCK*)((size_t)Data() + RoundLength( Size ));
}
return NULL;
}
ann_mex_t::~ann_mex_t()
{
// free the tree
if (IsGood() && m_pTree) {
delete m_pTree;
delete [] pa[0];
delete [] pa;
}
// cancel the integrity check
m_clintck = 0;
}
void
ann_mex_t::annkPriSearch( // priority k near neighbor search
const mxArray* mxQ, // query point
int k, // number of near neighbors to return
mxArray** mxIdx, // nearest neighbor array (modified)
mxArray** mxDst, // dist to near neighbors (modified)
double eps) // error bound
{
index_t j(0);
int nqp(0); // number of query points
if ( ! IsGood() )
mexErrMsgIdAndTxt("annmex:annkPriSearch","Class integrity check failed");
// check input point(s)
// dimension of points
if (m_idim != mxGetM(mxQ))
mexErrMsgIdAndTxt("annmex:annkPriSearch","point dimension does not match");
nqp = mxGetN(mxQ);
if (nqp <= 0)
mexErrMsgIdAndTxt("annmex:annkPriSearch","need at least one query point");
if ( k <= 0 )
mexErrMsgIdAndTxt("annmex:annkPriSearch","k must be positive");
if ( k > m_inpoints ) {
// generate warning
mexWarnMsgIdAndTxt("annmex:annkPriSearch","searching for more points than in tree - returning only %d",m_inpoints);
k = m_inpoints;
}
// allocate space for outputs
*mxIdx = mxCreateNumericMatrix(k, nqp, mxIDX_CLASS, mxREAL);
*mxDst = mxCreateNumericMatrix(k, nqp, mxDIST_CLASS, mxREAL);
if ( *mxIdx == NULL || *mxDst == NULL )
mexErrMsgIdAndTxt("annmex:annkPriSearch","cannot allocate memory for outputs");
ANNidx * pidx = (ANNidx*)mxGetData(*mxIdx);
ANNdist* pdist= (ANNdist*)mxGetData(*mxDst);
ANNpoint pp = (ANNpoint)mxGetData(mxQ);
for ( j = 0 ; j < nqp ; j++ ) {
m_pTree->annkPriSearch(pp, k, pidx, pdist, eps);
pp += m_idim;
pidx += k;
pdist += k;
}
}
int main() {
int nLoop, nFrom, nTo;
int arrnSum[MAX];
arrnSum[0] = 1;
for (nLoop = 1; nLoop < MAX; nLoop++)
arrnSum[nLoop] = IsGood(nLoop) ? arrnSum[nLoop - 1] + 1 : arrnSum[nLoop - 1];
while (scanf("%d %d", &nFrom, &nTo) == 2)
printf("%d\n", arrnSum[nTo] - arrnSum[nFrom - 1]);
return 0;
}
size_t StringExtractor::GetHexBytes(llvm::MutableArrayRef<uint8_t> dest,
uint8_t fail_fill_value) {
size_t bytes_extracted = 0;
while (!dest.empty() && GetBytesLeft() > 0) {
dest[0] = GetHexU8(fail_fill_value);
if (!IsGood())
break;
++bytes_extracted;
dest = dest.drop_front();
}
if (!dest.empty())
::memset(dest.data(), fail_fill_value, dest.size());
return bytes_extracted;
}
//Definition of StartPerforming
//This function starts processing commands in stack
//This function contains an almost never ending loop.
//It shouldn't be called in interrupt, etc..
void StartPerforming(void)
{
bool configured = false;
while(continuePerf && (configured = IsConfigured()))//until it is allowed and machine is configured
{
if(commandStack.first != commandStack.last && IsGood())//There are unprocessed items and no errors
{
if(RedistributeCommandForPerf(&(commandStack.buffer[commandStack.first]), true, false) == COMMAND_PROC_OK)//Distribute item
{
commandStack.lastItem = commandStack.buffer[commandStack.first].ID;
//Item processed successfully - increase counter
commandStack.first = CommandStackIncreaseValue(commandStack.first);
}
}
}
}
peBool proFile::Open(const char* path, peBool bCreate, peBool bDestroyOld)
{
if(!m_fileDef.m_pFileStream)
{
m_fileDef.m_iSize = -1;
if(bDestroyOld)
{
m_fileDef.m_pFileStream = new std::fstream(path, std::ios::binary|std::ios::out|std::ios::in|std::ios::trunc);
}
else
{
m_fileDef.m_pFileStream = new std::fstream(path, std::ios::binary|std::ios::out|std::ios::in);
}
if(m_fileDef.m_pFileStream->is_open())
{
m_fileDef.m_pFileStream->seekg(0, std::ios::end);
m_fileDef.m_iSize = m_fileDef.m_pFileStream->tellg();
m_fileDef.m_pFileStream->seekg(0, std::ios::beg);
}
}
if(!IsGood() && bCreate)
{
Close();
if(bDestroyOld)
{
m_fileDef.m_pFileStream = new std::fstream(path, std::ios::binary|std::ios::out|std::ios::trunc);
}
else
{
m_fileDef.m_pFileStream = new std::fstream(path, std::ios::binary|std::ios::out);
}
m_fileDef.m_pFileStream->write("0", 2);
Close();
if(bDestroyOld)
{
m_fileDef.m_pFileStream = new std::fstream(path, std::ios::binary|std::ios::out|std::ios::trunc);
}
else
{
m_fileDef.m_pFileStream = new std::fstream(path, std::ios::binary|std::ios::out);
}
}
return m_fileDef.m_pFileStream->is_open();
}
size_t
StringExtractor::GetHexBytes (void *dst_void, size_t dst_len, uint8_t fail_fill_value)
{
uint8_t *dst = (uint8_t*)dst_void;
size_t bytes_extracted = 0;
while (bytes_extracted < dst_len && GetBytesLeft ())
{
dst[bytes_extracted] = GetHexU8 (fail_fill_value);
if (IsGood())
++bytes_extracted;
else
break;
}
for (size_t i = bytes_extracted; i < dst_len; ++i)
dst[i] = fail_fill_value;
return bytes_extracted;
}
void OBConformerSearch::NextGeneration()
{
// create next generation population
OBRandom generator;
generator.TimeSeed();
// generate the children
int numConformers = m_rotorKeys.size();
for (int c = 0; c < numConformers; ++c) {
for (int child = 0; child < m_numChildren; ++child) {
bool foundKey = false;
int tries = 0;
while (!foundKey) {
tries++;
if (tries > 1000)
foundKey = true;
RotorKey rotorKey = m_rotorKeys[c]; // copy parent gene
// perform random mutation(s)
OBRotorIterator ri;
OBRotor *rotor = m_rotorList.BeginRotor(ri);
for (int i = 1; i < m_rotorList.Size() + 1; ++i, rotor = m_rotorList.NextRotor(ri)) {
if (generator.NextInt() % m_mutability == 0)
rotorKey[i] = generator.NextInt() % rotor->GetResolution().size(); // permutate gene
}
// duplicates are always rejected
if (!IsUniqueKey(m_rotorKeys, rotorKey))
continue;
// execute the filter(s)
if (!IsGood(rotorKey))
continue;
// add the key
m_rotorKeys.push_back(rotorKey); // append child to population
// set foundKey to generate the next child
foundKey = true;
}
}
}
}
bool NMEA0183::PreParse( void )
{
if ( IsGood() )
{
wxString mnemonic = sentence.Field( 0 );
/*
** See if this is a proprietary field
*/
if ( mnemonic.Left( 1 ) == 'P' )
mnemonic = _T("P");
else
mnemonic = mnemonic.Right( 3 );
LastSentenceIDReceived = mnemonic;
return true;
}
else
return false;
}
static int IsGoodAndVisible(TActor *a)
{
return IsGood(a) && (a->flags & FLAGS_VISIBLE);
}
static int IsBad(TActor *a)
{
return !IsGood(a);
}
static bool IsGoodSchema (const MatrixOfCellPtr * theSchema){
LogicAssert(true == IsGoodPtr(theSchema));
return IsGood (theSchema, IsGoodSchemaSequence);
}
void
ann_mex_t::annkFRSearch( // approx fixed-radius kNN search
const mxArray* mxQ, // query points
const mxArray* mxRad, // radius of query ball (a scalar or array of size N)
int k, // number of near neighbors to return
mxArray** mxIdx, // nearest neighbor array (modified)
mxArray** mxDst, // dist to near neighbors (modified)
mxArray** mxInr, // number of points within r of each point
double eps) // error bound
{
index_t j(0);
if ( ! IsGood() )
mexErrMsgIdAndTxt("annmex:annkFRSearch","Class integrity check failed");
// check input point(s)
// dimension of points
if (m_idim != mxGetM(mxQ))
mexErrMsgIdAndTxt("annmex:annkFRSearch","points dimension does not match");
// number of query point(s)
int nqp = mxGetN(mxQ);
if ( k <= 0 )
mexErrMsgIdAndTxt("annmex:annkFRSearch","k must be positive");
if ( k > m_inpoints ) {
// generate warning
mexWarnMsgIdAndTxt("annmex:annkFRSearch","searching for more points than in tree - returning only %d",m_inpoints);
k = m_inpoints;
}
int rad_array_inc = 1;
if ( mxGetNumberOfElements(mxRad) == 1 )
rad_array_inc = 0;
else if ( mxGetNumberOfElements(mxRad) != nqp )
mexErrMsgIdAndTxt("annmex:annkFRSearch","R must be either a scalar or array of size N");
ANNdist* prad = new ANNdist[mxGetNumberOfElements(mxRad)];
GetArrSq<ANNdist>(mxRad, prad);
// allocate space for outputs
*mxIdx = mxCreateNumericMatrix(k, nqp, mxIDX_CLASS, mxREAL);
*mxDst = mxCreateNumericMatrix(k, nqp, mxDIST_CLASS, mxREAL);
*mxInr = mxCreateNumericMatrix(1, nqp, mxINT32_CLASS, mxREAL);
if ( *mxIdx == NULL || *mxDst == NULL || mxInr == NULL)
mexErrMsgIdAndTxt("annmex:annkPriSearch","cannot allocate memory for outputs");
ANNidx * pidx = (ANNidx*)mxGetData(*mxIdx);
ANNdist* pdist= (ANNdist*)mxGetData(*mxDst);
int * pinr = (int*)mxGetData(*mxInr);
ANNpoint pp = (ANNpoint)mxGetData(mxQ);
for ( j = 0 ; j < nqp ; j++ ) {
*pinr = m_pTree->annkFRSearch(pp, prad[rad_array_inc*j], k, pidx, pdist, eps);
pp += m_idim;
pidx += k;
pdist += k;
pinr ++;
}
delete [] prad;
}
explicit operator bool() const noexcept {
return IsGood();
}
