StochHMM::transitionFuncParam Class Reference

#include <externalFuncs.h>

List of all members.

Public Member Functions
	transitionFuncParam ()
bool	parse (stringList &, tracks &, weights *, StateFuncs *)
	Parse the stringList from model import.
void	setTransFunc (std::string &, transitionFunc *, weight *)
void	setTransTB (tracebackIdentifier, std::string &, combineIdentifier, std::string &)
bool	isTracebackDefined ()
tracebackIdentifier	getTracebackType ()
std::string &	getTracebackName ()
std::string &	getCombineName ()
combineIdentifier	getCombineType ()
std::string &	getTrackName ()
track *	getTrack ()
double	evaluate (const std::string *, size_t, const std::string *, size_t)
void	print ()
	Print the externalFuncts to stdout.
std::string	stringify ()
	prints the string representation of the externFuncs to stdout

Private Attributes
transitionFunc *	transFunc
	Return string representation of the externFuncs definition in the model.
std::string	trackName
track *	transFuncTrack
	What track to pass to the function.
std::string	transFuncName
	Pointer to track function uses.
weight *	transFuncScaling
	< Name of the external function as used in the model
bool	transFuncTraceback
	< weighting information for values
tracebackIdentifier	transFuncTracebackIdentifier
	defines whether a traceback in necessary for the function
std::string	transFuncTracebackString
combineIdentifier	transFuncCombineIdentifier
	Contains name of traceback.
std::string	transFuncCombineString
	< Contains information on how to combine the traceback information

---

Detailed Description

Definition at line 61 of file externalFuncs.h.

---

Constructor & Destructor Documentation

StochHMM::transitionFuncParam::transitionFuncParam

(

)

Create transFuncParam from a stringList parsed from model for given track and applying a weight as defined in the model

Parameters:

lst	stringList from parsing the line in the function
trcks	tracks defined in the model
wts	pointer to weights as defined in the model
funcs	pointer to the state functions defined by user and referenced in the model

Definition at line 39 of file externalFuncs.cpp.

References transFunc.

                                            {
        transFunc=NULL;
    }

---

Member Function Documentation

double StochHMM::transitionFuncParam::evaluate	(	const std::string *	fullSequence,
		size_t	pos,
		const std::string *	partialSequence,
		size_t	length
	)

Definition at line 225 of file externalFuncs.cpp.

References transFunc.

Referenced by StochHMM::trellis::transitionFuncTraceback().

                                                                                                                                 {
        return (*transFunc)(fullSequence, pos, partialSequence,length);
    }

std::string& StochHMM::transitionFuncParam::getCombineName ( )

inline

Return what is suppose to be combined (State/Label/GFF)

Returns:

std::string

Definition at line 93 of file externalFuncs.h.

References transFuncCombineString.

Referenced by StochHMM::state::checkLabels(), and StochHMM::trellis::transitionFuncTraceback().

{return transFuncCombineString;};

combineIdentifier StochHMM::transitionFuncParam::getCombineType ( )

inline

Get the Combine type to apply to the traceback *How the traceback is to be combined (editing of traceback)

Returns:

combineIdentifier

See also:

enum combineIdentifier

Definition at line 99 of file externalFuncs.h.

References transFuncCombineIdentifier.

Referenced by StochHMM::state::checkLabels(), and StochHMM::trellis::transitionFuncTraceback().

{return transFuncCombineIdentifier;};

std::string& StochHMM::transitionFuncParam::getTracebackName ( )

inline

Return where the traceback is to go back to before stopping

Returns:

std::string State/Label/GFF tag to traceback to

Definition at line 89 of file externalFuncs.h.

References transFuncTracebackString.

Referenced by StochHMM::state::checkLabels(), and StochHMM::trellis::transitionFuncTraceback().

{return transFuncTracebackString;};

tracebackIdentifier StochHMM::transitionFuncParam::getTracebackType ( )

inline

Returns what how extensive of a a traceback is required

Returns:

tracbackIdentifier Type of traceback required

See also:

enum tracebackIdentifier

Definition at line 85 of file externalFuncs.h.

References transFuncTracebackIdentifier.

Referenced by StochHMM::state::checkLabels(), and StochHMM::trellis::transitionFuncTraceback().

{return transFuncTracebackIdentifier;};

track* StochHMM::transitionFuncParam::getTrack ( )

inline

Definition at line 105 of file externalFuncs.h.

References transFuncTrack.

Referenced by StochHMM::trellis::transitionFuncTraceback().

{return transFuncTrack;};

std::string& StochHMM::transitionFuncParam::getTrackName ( )

inline

Get track name to pass to the function (as defined in the model)

Returns:

std::string Track Name as defined in the model to be passed to the function

Definition at line 103 of file externalFuncs.h.

References trackName.

Referenced by StochHMM::transition::_processTags().

{return trackName;};

bool StochHMM::transitionFuncParam::isTracebackDefined ( )

inline

Check to see if a traceback is defined as necessary

Returns:

true if a traceback is necessary

false if a traceback is not required

Definition at line 80 of file externalFuncs.h.

References transFuncTraceback.

{return transFuncTraceback;};

bool StochHMM::transitionFuncParam::parse	(	stringList &	lst,
		tracks &	trcks,
		weights *	wts,
		StateFuncs *	funcs
	)

Parse the stringList from model import.

Definition at line 50 of file externalFuncs.cpp.

References StochHMM::stringList::contains(), StochHMM::weights::count(), StochHMM::DIFF_STATE, StochHMM::FULL, StochHMM::tracks::getTrack(), StochHMM::StateFuncs::getTransitionFunction(), StochHMM::stringList::indexOf(), StochHMM::isNumeric(), StochHMM::weight::setAbsolute(), StochHMM::START_INIT, StochHMM::STATE_GFF, StochHMM::STATE_LABEL, StochHMM::STATE_NAME, StochHMM::STATEGFF, StochHMM::STATELABEL, StochHMM::STATENAME, StochHMM::stringToDouble(), trackName, transFunc, transFuncCombineIdentifier, transFuncCombineString, transFuncName, transFuncScaling, transFuncTraceback, transFuncTracebackIdentifier, transFuncTracebackString, and transFuncTrack.

Referenced by StochHMM::transition::_processTags().

                                                                                                  {
        
        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;
    }

void StochHMM::transitionFuncParam::print

(

)

Print the externalFuncts to stdout.

Definition at line 164 of file externalFuncs.cpp.

References stringify().

                                   {
        std::cout<<stringify()<<std::endl;
    }

void StochHMM::transitionFuncParam::setTransFunc	(	std::string &	funcName,
		transitionFunc *	function,
		weight *	scaling
	)

Add function to externFunc

Parameters:

funcName	std::string name given to function (as referenced in model)
function	Pointer to pt2StateFunc*, function to use
scaling	Pointer to weight, how to weight the functions results before applying to emission/transition

Definition at line 204 of file externalFuncs.cpp.

References transFunc, transFuncName, and transFuncScaling.

                                                                                                        {
        transFunc=function;
        transFuncName=funcName;
        transFuncScaling=scaling;
    }

void StochHMM::transitionFuncParam::setTransTB	(	tracebackIdentifier	tbIdent,
		std::string &	tbString,
		combineIdentifier	cbIdent,
		std::string &	cbString
	)

Set all the traceback and combine types for the traceback before calling the function

Parameters:

tbIdent	tracebackIdentifier
tbString	Traceback string to use (State/GFF/Label)
cbIdent	combineIdentifier
cbString	Combine string to use when editing traceback (State/GFF/Label)

Definition at line 215 of file externalFuncs.cpp.

References transFuncCombineIdentifier, transFuncCombineString, transFuncTraceback, transFuncTracebackIdentifier, and transFuncTracebackString.

                                                                                                                                       {
        transFuncTracebackIdentifier=tbIdent;
        transFuncTracebackString=tbString;
        transFuncCombineIdentifier=cbIdent;
        transFuncCombineString=cbString;
        transFuncTraceback=true;
        return;
    }

std::string StochHMM::transitionFuncParam::stringify

(

)

prints the string representation of the externFuncs to stdout

Get string representation of the externalFuncs

Returns:

std::string Representation of externalFuncs

Definition at line 170 of file externalFuncs.cpp.

References StochHMM::double_to_string(), StochHMM::weight::getAbsolute(), StochHMM::weight::getName(), StochHMM::weight::isAbsolute(), StochHMM::START_INIT, StochHMM::STATE_GFF, StochHMM::STATE_LABEL, StochHMM::STATE_NAME, StochHMM::STATEGFF, StochHMM::STATELABEL, StochHMM::STATENAME, trackName, transFuncCombineIdentifier, transFuncCombineString, transFuncName, transFuncScaling, transFuncTraceback, transFuncTracebackIdentifier, and transFuncTracebackString.

Referenced by print(), and StochHMM::transition::stringify().

                                            {
        std::string exFuncString;
        exFuncString+="[ FUNCTION:\t" + transFuncName + "\t";
        exFuncString+="TRACK:\t" + trackName + "\t";
        if (transFuncTraceback){
            exFuncString+= (transFuncTracebackIdentifier == STATE_NAME)  ? "TO_STATE:\t" + transFuncTracebackString + "\t":
                           (transFuncTracebackIdentifier == STATE_LABEL) ? "TO_LABEL:\t" + transFuncTracebackString + "\t": 
                           (transFuncTracebackIdentifier == STATE_GFF)   ? "TO_GFF:\t" + transFuncTracebackString   + "\t":
                           (transFuncTracebackIdentifier == START_INIT)  ? "TO_START:\t": "DIFF_STATE:\t" ;
            
            exFuncString+=  (transFuncCombineIdentifier == STATENAME) ? "COMBINE_STATE:\t" + transFuncCombineString + "\t":
                            (transFuncCombineIdentifier == STATELABEL) ? "COMBINE_LABEL:\t" + transFuncCombineString + "\t":
                            (transFuncCombineIdentifier == STATEGFF) ? "COMBINE_GFF:\t" + transFuncCombineString :"NO_COMBINE:\t";
        }
        
        if (transFuncScaling!=NULL){
            if (transFuncScaling->isAbsolute()){
                exFuncString+="SCALE:\t" + double_to_string(transFuncScaling->getAbsolute());
            }
            else{
                exFuncString+="SCALE:\t" + transFuncScaling->getName();
            }
        }
        
        exFuncString += " ]";
        
        return exFuncString;
    }

---

Member Data Documentation

std::string StochHMM::transitionFuncParam::trackName

private

Definition at line 114 of file externalFuncs.h.

Referenced by getTrackName(), parse(), and stringify().

transitionFunc* StochHMM::transitionFuncParam::transFunc

private

Return string representation of the externFuncs definition in the model.

Definition at line 113 of file externalFuncs.h.

Referenced by evaluate(), parse(), setTransFunc(), and transitionFuncParam().

combineIdentifier StochHMM::transitionFuncParam::transFuncCombineIdentifier

private

Contains name of traceback.

Definition at line 127 of file externalFuncs.h.

Referenced by getCombineType(), parse(), setTransTB(), and stringify().

std::string StochHMM::transitionFuncParam::transFuncCombineString

private

< Contains information on how to combine the traceback information

Definition at line 128 of file externalFuncs.h.

Referenced by getCombineName(), parse(), setTransTB(), and stringify().

std::string StochHMM::transitionFuncParam::transFuncName

private

Pointer to track function uses.

Definition at line 117 of file externalFuncs.h.

Referenced by parse(), setTransFunc(), and stringify().

weight* StochHMM::transitionFuncParam::transFuncScaling

private

< Name of the external function as used in the model

Definition at line 119 of file externalFuncs.h.

Referenced by parse(), setTransFunc(), and stringify().

bool StochHMM::transitionFuncParam::transFuncTraceback

private

< weighting information for values

Definition at line 122 of file externalFuncs.h.

Referenced by isTracebackDefined(), parse(), setTransTB(), and stringify().

tracebackIdentifier StochHMM::transitionFuncParam::transFuncTracebackIdentifier

private

defines whether a traceback in necessary for the function

What to traceback until

Definition at line 124 of file externalFuncs.h.

Referenced by getTracebackType(), parse(), setTransTB(), and stringify().

std::string StochHMM::transitionFuncParam::transFuncTracebackString

private

Definition at line 125 of file externalFuncs.h.

Referenced by getTracebackName(), parse(), setTransTB(), and stringify().

track* StochHMM::transitionFuncParam::transFuncTrack

private

What track to pass to the function.

Definition at line 115 of file externalFuncs.h.

Referenced by getTrack(), and parse().

---

The documentation for this class was generated from the following files:

• externalFuncs.h
• externalFuncs.cpp