pedigrees.h File Reference

Function declarations for pedigrees.c. More...

#include "parent_set_data.h"
#include "property_data.h"
#include <scip/scip.h>

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Functions
SCIP_RETCODE	PD_addPedigreeParameters (SCIP *scip)
	Makes SCIP recognise parameters related to pedigree reconstruction. More...
SCIP_RETCODE	PD_addPedigreeSpecificConstraints (SCIP *scip, ParentSetData *psd)
	Adds any constraints and variables needed for pedigree based constraints. More...
SCIP_RETCODE	PD_assignPedigreeVariables (SCIP *scip, SCIP_SOL *sol, ParentSetData *psd, SCIP_Bool *possible)
	Tries to find values for any pedigree specific variables in a given primal solution. More...
SCIP_Bool *	PD_getCurrentPedigreeVarValues (SCIP *scip)
	Gets the values of the pedigree specific variables in the current solution. More...
SCIP_Bool	PD_inPedigreeMode (SCIP *scip)
	Determines whether the program is being run for learning pedigrees. More...
SCIP_RETCODE	PD_printSolutionPedigreeFormat (SCIP *scip, ParentSetData *psd, SCIP_Real **Scores, SCIP_Bool **selected, SCIP_Real total_score, FILE *stream, SCIP_Bool *pedvars)
	Prints the solution as a pedigree. More...

Detailed Description

Function declarations for pedigrees.c.

Function Documentation

PD_addPedigreeParameters()

SCIP_RETCODE PD_addPedigreeParameters

(

SCIP *

scip

)

Makes SCIP recognise parameters related to pedigree reconstruction.

Parameters

scip	The SCIP instance to which to add the parameters.

Returns

SCIP_OKAY if the operation succeeded or an appropriate error code otherwise.

References UT_addBoolParam(), UT_addIntParam(), UT_addRealParam(), and UT_addStringParam().

Referenced by BN_addParameters().

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PD_addPedigreeSpecificConstraints()

SCIP_RETCODE PD_addPedigreeSpecificConstraints	(	SCIP *	scip,
		ParentSetData *	psd
	)

Adds any constraints and variables needed for pedigree based constraints.

Parameters

scip	The SCIP instance in which to add the constraints.
psd	The parent set data associated with this problem.

Returns

SIP_OKAY if the constraints were added successfully, or an appropriate error code otherwise.

References PedigreeData::ages, MD_getPedigreeData(), MD_setPedigreeData(), PedigreeData::n, ParentSetData::n, PD_addPedigreeConstraints(), PD_addPedigreeVariables(), PE_deallocatePedigreeData(), PedigreeData::sexes, and PedigreeData::SexVars.

Referenced by addAdditionalConstraints().

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PD_assignPedigreeVariables()

SCIP_RETCODE PD_assignPedigreeVariables	(	SCIP *	scip,
		SCIP_SOL *	sol,
		ParentSetData *	psd,
		SCIP_Bool *	possible
	)

Tries to find values for any pedigree specific variables in a given primal solution.

If there is no possible assignment of pedigree variables then the function returns an appropriate error message.

Parameters

scip	The SCIP instance on which the heuristic is running.
sol	The heuristic solution being worked on.
psd	The heursitic data related to this primal heursitic.
possible	Returns whether a valid assignment was possible.

Returns

SCIP_OKAY if a consistent labelling could be found and was made to sol. An appropriate error code otherwise.

References assignSexVariables(), checkSuitableForPedigree(), and usingSexConsistency().

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PD_getCurrentPedigreeVarValues()

SCIP_Bool* PD_getCurrentPedigreeVarValues

(

SCIP *

scip

)

Gets the values of the pedigree specific variables in the current solution.

If no pedigree specific variables are being used, NULL is returned.

Parameters

scip	The SCIP instance for which to find the variable values.

Returns

A list of SCIP_Bools which are TRUE for all variables included in the solution and FALSE otherwise.

References MD_getPedigreeData(), PedigreeData::n, PedigreeData::SexVars, and usingSexConsistency().

Referenced by printSolution().

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PD_inPedigreeMode()

SCIP_Bool PD_inPedigreeMode

(

SCIP *

scip

)

Determines whether the program is being run for learning pedigrees.

Parameters

scip	The SCIP instance that is running.

Returns

TRUE if the program is being used to learn pedigrees. FALSE otherwsie.

Referenced by addAdditionalConstraints(), printSolution(), and usingSexConsistency().

PD_printSolutionPedigreeFormat()

SCIP_RETCODE PD_printSolutionPedigreeFormat	(	SCIP *	scip,
		ParentSetData *	psd,
		SCIP_Real **	Scores,
		SCIP_Bool **	selected,
		SCIP_Real	total_score,
		FILE *	stream,
		SCIP_Bool *	pedvars
	)

Prints the solution as a pedigree.

The pedigree consists of four columns. The first is the individual, thes second is the sex of the individual, the third is its father and the fourth is its mother. If either the father or the mother is not present in the sample, a '-' is printed instead. If sex consistency is enforced, then individuals will not appear as father of one individual and mother of another. The pedigree is sorted such that all individuals are declared on a earlier line than those in which they appear as parents.

Parameters

scip	The SCIP instance to which the solution belongs.
psd	The problem data used by the solution.
Scores	The score data to use for the solution.
selected	Whether each of the variables is selected in the solution.
total_score	The overall score of this solution.
stream	Where to print the solution.
pedvars	Whether each of the pedigree specific variables is selected in the solution.

Returns

SCIP_OKAY if the solution was printed correctly or an appropriate error message otherwise.

References checkSuitableForPedigree(), MD_getPedigreeData(), PedigreeData::n, ParentSetData::nodeNames, ParentSetData::nParents, ParentSetData::nParentSets, ParentSetData::ParentSets, and usingSexConsistency().

Referenced by printToFile().

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