//Get all Name in order
bool PWM::_getOrderedPositionNames(stringList& pos, stringList& names){
for(size_t i=0;i<pos.size();i++){
size_t nameHeader=pos[i].find("NAME:");
if (nameHeader == std::string::npos){
continue;
}
size_t nameLineEnding=pos[i].find_first_of("\n",nameHeader);
std::string name = pos[i].substr(nameHeader+5,nameLineEnding-(nameHeader+5));
clear_whitespace(name, " \t\n");
if (names.contains(name)){
std::cerr << "Position with name of: " << name << " is defined twice in the model\n";
return false;
}
else{
names.push_back(name);
}
}
return true;
}
//!Parse the stringList from model import
bool transitionFuncParam::parse(stringList& lst, tracks& trcks, weights* wts, StateFuncs* funcs) {
size_t idx;
//FUNCTION NAME (REQUIRED)
if (lst.contains("FUNCTION")) {
idx=lst.indexOf("FUNCTION");
idx++;
transFuncName = lst[idx];
if (funcs!=NULL) {
transFunc = funcs->getTransitionFunction(transFuncName);
}
}
else {
std::cerr << "Tag was parsed but contains no FUNCTION: . Please check the formatting of the tags\n" << std::endl;
return false;
//errorInfo(sCantParseLine, "Tag was parsed but contains no FUNCTION: . Please check the formatting of the tags\n");
}
//Implement Which track to pass to function
if (lst.contains("TRACK")) {
idx=lst.indexOf("TRACK");
idx++;
trackName=lst[idx];
transFuncTrack = trcks.getTrack(trackName);
}
else {
std::cerr << "Tag was parsed but contains no TRACK: . Please check the formatting of the tags\n" << std::endl;
return false;
//errorInfo(sCantParseLine, "Tag was parsed but contains no TRACK: . Please check the formatting of the tags\n");
}
if (lst.contains("SCALE")) {
idx=lst.indexOf("SCALE");
idx++;
if (isNumeric(lst[idx])) {
transFuncScaling = new(std::nothrow) weight;
if (transFuncScaling==NULL) {
std::cerr << "OUT OF MEMORY\nFile" << __FILE__ << "Line:\t"<< __LINE__ << std::endl;
exit(1);
}
double tempValue;
if (!stringToDouble(lst[idx], tempValue)) {
std::cerr << "Ambiguous Value couldn't be parsed: "<< lst[idx] << std::endl;
return false;
}
transFuncScaling->setAbsolute(tempValue);
}
else {
std::string weightName=lst[idx];
if (wts->count(weightName)) {
transFuncScaling = (*wts)[weightName];
}
}
}
//Process Traceback Commands
//Parse the TO Traceback Labels in the function tag
const std::string tbLabels[]= {"TO_LABEL","TB->LABEL","TO_GFF","TB->GFF","TO_STATE","TB->STATE","TO_START","TB->START","DIFF_STATE"};
const tracebackIdentifier typs[]= {STATE_LABEL,STATE_LABEL,STATE_GFF,STATE_GFF,STATE_NAME,STATE_NAME,START_INIT,START_INIT,DIFF_STATE};
for(int i=0; i<9; i++) {
if (lst.contains(tbLabels[i])) {
transFuncTraceback=true;
idx=lst.indexOf(tbLabels[i]);
transFuncTracebackIdentifier=typs[i];
if (typs[i]!=START_INIT || typs[i]!=DIFF_STATE) {
transFuncTracebackString=lst[idx+1];
}
}
}
// Parse the Combine tags
if (transFuncTraceback) {
//Process Traceback Combining Commands
std::string combineLabels[] = {"COMBINE_LABEL","COMBINE_GFF","COMBINE_STATE", "NO_COMBINE"};
const combineIdentifier comtyps[] = {STATELABEL,STATEGFF,STATENAME,FULL};
bool combineTypeProvided=false;
for(int i=0; i<4; i++) {
if (lst.contains(combineLabels[i])) {
idx=lst.indexOf(combineLabels[i]);
transFuncCombineIdentifier=comtyps[i];
transFuncCombineString=lst[idx+1];
combineTypeProvided=true;
}
}
if (!combineTypeProvided) {
std::cerr << "Transition Function tag with a traceback was called, but no CombineType was provided. If no traceback is needed then please remove traceback command. \n" << std::endl;
return false;
//errorInfo(sTagIncorrect, "Transition Function tag with a traceback was called, but no CombineType was provided. If no traceback is needed then please remove traceback command. \n");
}
}
return true;
}
//!Parse the stringList from model import
bool emissionFuncParam::parse(stringList& lst, tracks& trcks, weights* wts, StateFuncs* funcs) {
size_t idx;
//FUNCTION NAME (REQUIRED)
if (lst.contains("FUNCTION")) {
idx=lst.indexOf("FUNCTION");
idx++;
emissionFuncName = lst[idx];
if (funcs!=NULL) {
emissionFunction = funcs->getEmissionFunction(emissionFuncName);
}
}
else {
std::cerr << "Tag was parsed but contains no FUNCTION: . Please check the formatting of the tags\n" << std::endl;
return false;
//errorInfo(sCantParseLine, "Tag was parsed but contains no FUNCTION: . Please check the formatting of the tags\n");
}
//Implement Which track to pass to function
if (lst.contains("TRACK")) {
idx=lst.indexOf("TRACK");
idx++;
trackName=lst[idx];
emissionFuncTrack = trcks.getTrack(trackName);
trackNumber = emissionFuncTrack->getIndex();
}
else {
std::cerr << "Tag was parsed but contains no TRACK: . Please check the formatting of the tags\n" << std::endl;
return false;
//errorInfo(sCantParseLine, "Tag was parsed but contains no TRACK: . Please check the formatting of the tags\n");
}
if (lst.contains("SCALE")) {
idx=lst.indexOf("SCALE");
idx++;
if (isNumeric(lst[idx])) {
emissionFuncScaling = new(std::nothrow) weight;
if (emissionFuncScaling==NULL) {
std::cerr << "OUT OF MEMORY\nFile" << __FILE__ << "Line:\t"<< __LINE__ << std::endl;
exit(1);
}
double tempValue;
if (!stringToDouble(lst[idx], tempValue)) {
std::cerr << "SCALE value could not be converted to numerical value: "<< lst[idx] << std::endl;
return false;
}
emissionFuncScaling->setAbsolute(tempValue);
}
else {
std::string weightName=lst[idx];
if (wts->count(weightName)) {
emissionFuncScaling = (*wts)[weightName];
}
}
}
return true;
}