bool SslReader::parseFile(){
Verbosity::debug("Parsing File.");
if( ! openSsl() ){
return false;
}
Verbosity::debug("Collecting Psms.");
collectPsms();
// for each ms2 file
if( fileMap_.size() > 1 ){
initSpecFileProgress((int)fileMap_.size());
}
map<string, vector<PSM*> >::iterator fileIterator = fileMap_.begin();
for(; fileIterator != fileMap_.end(); ++fileIterator) {
setSpecFileName((fileIterator->first).c_str());
// move from map to psms_
psms_ = fileIterator->second;
// look at first psm for scanKey vs scanName
if( psms_.front()->specKey == -1 ){ // default value
lookUpBy_ = NAME_ID;
} else {
lookUpBy_ = SCAN_NUM_ID;
}
buildTables(UNKNOWN_SCORE_TYPE);
}
return true;
}
bool HuffmanStringProcessor::readHuffBuffer(BitStream* pStream, char* out_pBuffer)
{
if (mTablesBuilt == false)
buildTables();
if (pStream->readFlag()) {
U32 len = pStream->readInt(8);
for (U32 i = 0; i < len; i++) {
S32 index = 0;
while (true) {
if (index >= 0) {
if (pStream->readFlag() == true) {
index = mHuffNodes[index].index1;
} else {
index = mHuffNodes[index].index0;
}
} else {
out_pBuffer[i] = mHuffLeaves[-(index+1)].symbol;
break;
}
}
}
out_pBuffer[len] = '\0';
return true;
} else {
// Uncompressed string...
U32 len = pStream->readInt(8);
pStream->read(len, out_pBuffer);
out_pBuffer[len] = '\0';
return true;
}
}
// The constructor takes the keyword and builds the tables.
BM::BM(const std::string &key) : p(key)
{
alphabetSize = 256;
delta1.resize(alphabetSize);
pSize = key.length();
delta2.resize(pSize+1);
f.resize(pSize+1);
buildTables(key);
}
void IRGenerator::buildBlocks(VirtualFunction& entry)
{
const CIL::Instructions& instructions = entry.getInstructions();
allocateInstructionBlocks(instructions.size());
createBlock(0);
buildGuards(entry);
buildTables(entry);
buildInstructions(instructions);
}
int main(int argc, char** argv) {
char* seqA = argv[1];
char* seqB = argv[2];
int lenA = strlen(seqA);
int lenB = strlen(seqB);
int** countArray = allocate2Darray(lenA, lenB);
int** direction = allocate2Darray(lenA, lenB);
buildTables(seqA, seqB, lenA, lenB, countArray, direction);
traceSequence(seqA, lenA-1, lenB-1, direction);
return 0;
}
MTrigTable::MTrigTable(unsigned short tableSize){
if(!m_initlized){
tableSize*=2;
m_initlized=true;
m_trigTableSize=tableSize;
m_trigTableFactor=m_trigTableSize/(2*PI64);
m_sinTable=new double[m_trigTableSize];
m_tanTable=new double[m_trigTableSize];
//m_useTable=true;
buildTables();
}
}
inline QVector<int> otsu(QVector<int> histogram,
int classes)
{
qreal maxSum = 0.;
QVector<int> thresholds(classes - 1, 0);
QVector<qreal> H = buildTables(histogram);
QVector<int> index(classes + 1);
index[0] = 0;
index[index.size() - 1] = histogram.size() - 1;
for_loop(&maxSum,
&thresholds,
H,
1,
histogram.size() - classes + 1,
1,
histogram.size(), &index);
return thresholds;
}
bool HuffmanStringProcessor::writeHuffBuffer(BitStream* pStream, const char* out_pBuffer, U32 maxLen)
{
if (out_pBuffer == NULL) {
pStream->writeFlag(false);
pStream->writeInt(0, 8);
return true;
}
if (mTablesBuilt == false)
buildTables();
size_t llen = out_pBuffer ? strlen(out_pBuffer) : 0;
TNLAssertV(llen <= 255, ("String \"%s\" TOO long for writeString", out_pBuffer));
U32 len = static_cast<U32>(llen);
if (len > maxLen)
len = maxLen;
U32 numBits = 0;
U32 i;
for (i = 0; i < len; i++)
numBits += mHuffLeaves[(unsigned char)out_pBuffer[i]].numBits;
if (numBits >= (len * 8)) {
pStream->writeFlag(false);
pStream->writeInt(len, 8);
pStream->write(len, out_pBuffer);
} else {
pStream->writeFlag(true);
pStream->writeInt(len, 8);
for (i = 0; i < len; i++) {
HuffLeaf& rLeaf = mHuffLeaves[((unsigned char)out_pBuffer[i])];
pStream->writeBits(rLeaf.numBits, &rLeaf.code);
}
}
return true;
}
