Ejemplo n.º 1
0
	//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;
    }
Ejemplo n.º 2
0
//!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;
}
Ejemplo n.º 3
0
//!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;
}