__tb_no_sanitize_address__ tb_size_t tb_pool_data_size(tb_cpointer_t data)
{
// check
tb_check_return_val(data, 0);
// done
tb_size_t size = 0;
tb_pool_data_head_t* data_head = tb_null;
do
{
// tbox must be running normally
tb_check_break(tb_state() == TB_STATE_OK);
// get global allocator
tb_allocator_ref_t allocator = tb_allocator();
tb_check_break(allocator);
// have this data address?
tb_check_break(tb_allocator_have(allocator, data));
// the data head
data_head = &(((tb_pool_data_head_t*)data)[-1]);
tb_check_break(data_head->debug.magic == TB_POOL_DATA_MAGIC);
// ok
size = data_head->size;
} while (0);
// ok?
return size;
}
//! When a transitionFunc is to be called it must performs a traceback
//! and get the required sequence to pass to the function
//! \param
double trellis::transitionFuncTraceback(state* st, size_t position,transitionFuncParam* func){
std::vector<int> tracebackPath;
std::vector<std::string> tracebackString;
//How far to traceback
tracebackIdentifier traceback_identifier = func->getTracebackType();
const std::string& tracebackIdentifierName = func->getTracebackName();
//What to combine
combineIdentifier combineIdent = func->getCombineType();
const std::string& combineIdentName = func->getCombineName();
//Deterimine which track to use
track* alphaTrack = func->getTrack();
size_t trackIndex = alphaTrack->getIndex();
if (!alphaTrack->isAlpha()){
std::cerr << "External transition function called on track that isn't discrete (ALPHANUMERIC)\n";
exit(2);
}
const sequence* seq = seqs->getSeq(trackIndex);
int16_t tb_state(st->getIterator());
int16_t starting_state = tb_state;
for(size_t trellisPos = position-1; trellisPos != SIZE_MAX ; --trellisPos){
tracebackPath.push_back(tb_state);
if ((combineIdent == FULL) ||
(combineIdent == STATENAME && combineIdentName.compare(st->getName())==0)||
(combineIdent == STATELABEL && combineIdentName.compare(st->getLabel())==0)||
(combineIdent == STATEGFF && combineIdentName.compare(st->getGFF())==0))
{
tracebackString.push_back(seq->getSymbol(trellisPos));
}
tb_state= (*traceback_table)[trellisPos][tb_state];
state* temp_st = hmm->getState(tb_state);
//Check to see if stop conditions of traceback are met, if so break;
if(traceback_identifier == START_INIT && tb_state == -1) {break;}
else if (traceback_identifier == DIFF_STATE && starting_state != tb_state) { break;}
else if (traceback_identifier == STATE_NAME && tracebackIdentifierName.compare(temp_st->getName())==0){ break;}
else if (traceback_identifier == STATE_LABEL && tracebackIdentifierName.compare(temp_st->getLabel())==0) { break;}
else if (traceback_identifier == STATE_GFF && tracebackIdentifierName.compare(temp_st->getGFF())==0) { break;}
}
size_t length=tracebackPath.size();
std::string CombinedString;
size_t maxSymbolSize = alphaTrack->getAlphaMax();
//For single letter characters
if (maxSymbolSize ==1){
for(std::vector<std::string>::reverse_iterator rit = tracebackString.rbegin(); rit!=tracebackString.rend();++rit){
CombinedString+=(*rit);
}
}
else{ // For kmer words > 1 in length
std::vector<std::string>::reverse_iterator rit = tracebackString.rbegin();
CombinedString+=(*rit);
++rit;
for(; rit!=tracebackString.rend();++rit){
CombinedString+="," + (*rit);
}
}
//Call the transitionFunc and get the score back
double transitionValue = func->evaluate(seqs->getUndigitized(trackIndex), position, &CombinedString, length);
return transitionValue;
}
