cpsp::HPThreadingOptions Class Reference

#include <HPThreadingOptions.hh>

---

Detailed Description

Definition at line 34 of file HPThreadingOptions.hh.

Public Types
enum	CORESELECTS { FIRST, ALL_BEST, ALL }
Public Member Functions
bool	countingMode (bool newVal)
bool	countingMode (void)
unsigned int	getContactsInSequence (void)
const CORESELECTS	getCoreSelection () const
HCoreDatabase *	getHCoreDB (void)
std::vector< unsigned int > &	getHSinglets (void)
const std::vector< unsigned int > *const	getHullLevel () const
const biu::LatticeFrame *const	getLattice () const
const int	getMaximalEnergy () const
const unsigned int	getMaximalSolutions () const
const unsigned int	getMaxPCoreDistance () const
unsigned int	getMinEvenOddHs (void)
const int	getMinimalEnergy () const
const bool	getNormalizeStructures (void) const
unsigned int	getNumOfHSinglets (void)
unsigned int	getNumOfPSinglets (void)
std::vector< unsigned int > &	getPSinglets (void)
const std::string *const	getSequence () const
const bool	getUseNoDDS () const
const bool	getUseSymmetryBreaking () const
	HPThreadingOptions ()
	HPThreadingOptions (int argc, char **argv) throw (cpsp::Exception)
void	setCoreSelection (CORESELECTS cs)
void	setHCoreDB (HCoreDatabase *db)
void	setLattice (biu::LatticeFrame *lat)
void	setLatticeFrameSize (const unsigned int newFrameSize)
void	setMaximalEnergy (int val)
void	setMaximalSolutions (unsigned int val)
void	setMinimalEnergy (int val)
void	setNormalizeStructures (const bool val)
unsigned int	setSequence (const std::string &seq) throw (cpsp::Exception)
void	setUseNoDDS (bool val)
void	setUseSymmetryBreaking (bool val)
bool	verboseOut (bool newVal)
bool	verboseOut (void)
virtual	~HPThreadingOptions ()
Private Types
typedef std::map< int, std::vector< unsigned int > >	FeatureMap
enum	SeqFeatures { P_SINGLET, H_SINGLET }
Private Member Functions
void	initAllowedArguments (biu::OptionMap &allowedArgs, std::string &infoText) const
Private Attributes
unsigned int	contactsInSeq
HCoreDatabase *	coreDB
CORESELECTS	coreSelection
std::vector< unsigned int >	hullLvl
const biu::LatticeDescriptor *	latDescr
biu::LatticeFrame *	lattice
int	maxE
unsigned int	maxPCoreDistance
unsigned int	maxSols
int	minE
unsigned int	minEvenOddHs
bool	normalizeStructures
bool	onlyCountingStructures
FeatureMap	seqFeatureMap
std::string *	sequence
bool	useNoDDS
bool	useSymmetryBreaking
bool	verboseOutput

---

Member Typedef Documentation

typedef std::map< int, std::vector <unsigned int> > cpsp::HPThreadingOptions::FeatureMap [private]

Definition at line 80 of file HPThreadingOptions.hh.

---

Member Enumeration Documentation

enum cpsp::HPThreadingOptions::CORESELECTS

constants that define the core selection mode

Enumerator:

FIRST
ALL_BEST
ALL

Definition at line 39 of file HPThreadingOptions.hh.

enum cpsp::HPThreadingOptions::SeqFeatures [private]

sequence features

Enumerator:

P_SINGLET
H_SINGLET

Definition at line 78 of file HPThreadingOptions.hh.

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Constructor & Destructor Documentation

cpsp::HPThreadingOptions::HPThreadingOptions	(	int	argc,
		char **	argv
	)			throw (cpsp::Exception)

construction

Parameters:

	argc	the argument number given by the "main" function
	argv	the string arguments given by the "main" function

Definition at line 50 of file HPThreadingOptions.cc.

cpsp::HPThreadingOptions::HPThreadingOptions

(

)

Definition at line 36 of file HPThreadingOptions.cc.

cpsp::HPThreadingOptions::~HPThreadingOptions

(

)

[virtual]

Definition at line 172 of file HPThreadingOptions.cc.

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Member Function Documentation

bool cpsp::HPThreadingOptions::countingMode

(

bool

newVal

)

[inline]

Definition at line 199 of file HPThreadingOptions.hh.

bool cpsp::HPThreadingOptions::countingMode

(

void

)

[inline]

returns whether or not in counting mode

Definition at line 198 of file HPThreadingOptions.hh.

unsigned int cpsp::HPThreadingOptions::getContactsInSequence

(

void

)

[inline]

Returns the number of sequence internal HH-contacts.

Definition at line 212 of file HPThreadingOptions.hh.

const CORESELECTS cpsp::HPThreadingOptions::getCoreSelection

(

void

)

const [inline]

Definition at line 136 of file HPThreadingOptions.hh.

HCoreDatabase* cpsp::HPThreadingOptions::getHCoreDB

(

void

)

[inline]

returns the current H-core database

Definition at line 169 of file HPThreadingOptions.hh.

std::vector<unsigned int>& cpsp::HPThreadingOptions::getHSinglets

(

void

)

[inline]

returns the H-singlet corresponding indices

Definition at line 192 of file HPThreadingOptions.hh.

const std::vector<unsigned int>* const cpsp::HPThreadingOptions::getHullLevel

(

)

const [inline]

Definition at line 152 of file HPThreadingOptions.hh.

const biu::LatticeFrame* const cpsp::HPThreadingOptions::getLattice

(

)

const [inline]

Definition at line 132 of file HPThreadingOptions.hh.

const int cpsp::HPThreadingOptions::getMaximalEnergy

(

)

const [inline]

Definition at line 144 of file HPThreadingOptions.hh.

const unsigned int cpsp::HPThreadingOptions::getMaximalSolutions

(

)

const [inline]

Definition at line 148 of file HPThreadingOptions.hh.

const unsigned int cpsp::HPThreadingOptions::getMaxPCoreDistance

(

)

const [inline]

Definition at line 157 of file HPThreadingOptions.hh.

unsigned int cpsp::HPThreadingOptions::getMinEvenOddHs

(

void

)

[inline]

Returns the minimum of even vs. odd H positions of the sequence.

Definition at line 208 of file HPThreadingOptions.hh.

const int cpsp::HPThreadingOptions::getMinimalEnergy

(

)

const [inline]

Definition at line 140 of file HPThreadingOptions.hh.

const bool cpsp::HPThreadingOptions::getNormalizeStructures

(

void

)

const [inline]

getter for normalizeStructures

Definition at line 219 of file HPThreadingOptions.hh.

unsigned int cpsp::HPThreadingOptions::getNumOfHSinglets

(

void

)

[inline]

returns the number of H-singlet positions in the sequence

Definition at line 180 of file HPThreadingOptions.hh.

unsigned int cpsp::HPThreadingOptions::getNumOfPSinglets

(

void

)

[inline]

returns the number of P-singlet positions in the sequence

Definition at line 174 of file HPThreadingOptions.hh.

std::vector<unsigned int>& cpsp::HPThreadingOptions::getPSinglets

(

void

)

[inline]

returns the P-singlet corresponding indices

Definition at line 186 of file HPThreadingOptions.hh.

const std::string* const cpsp::HPThreadingOptions::getSequence

(

void

)

const [inline]

Definition at line 120 of file HPThreadingOptions.hh.

const bool cpsp::HPThreadingOptions::getUseNoDDS

(

)

const [inline]

Definition at line 128 of file HPThreadingOptions.hh.

const bool cpsp::HPThreadingOptions::getUseSymmetryBreaking

(

)

const [inline]

Definition at line 124 of file HPThreadingOptions.hh.

void cpsp::HPThreadingOptions::initAllowedArguments	(	biu::OptionMap &	allowedArgs,
		std::string &	infoText
	)			const [private]

initialisation of the allowed program arguments and the corresponding additinal informations

Definition at line 272 of file HPThreadingOptions.cc.

void cpsp::HPThreadingOptions::setCoreSelection

(

CORESELECTS

cs

)

[inline]

Definition at line 137 of file HPThreadingOptions.hh.

void cpsp::HPThreadingOptions::setHCoreDB

(

HCoreDatabase *

db

)

[inline]

Definition at line 170 of file HPThreadingOptions.hh.

void cpsp::HPThreadingOptions::setLattice

(

biu::LatticeFrame *

lat

)

[inline]

Definition at line 133 of file HPThreadingOptions.hh.

void cpsp::HPThreadingOptions::setLatticeFrameSize

(

const unsigned int

newFrameSize

)

[inline]

Definition at line 162 of file HPThreadingOptions.hh.

void cpsp::HPThreadingOptions::setMaximalEnergy

(

int

val

)

[inline]

Definition at line 145 of file HPThreadingOptions.hh.

void cpsp::HPThreadingOptions::setMaximalSolutions

(

unsigned int

val

)

[inline]

Definition at line 149 of file HPThreadingOptions.hh.

void cpsp::HPThreadingOptions::setMinimalEnergy

(

int

val

)

[inline]

Definition at line 141 of file HPThreadingOptions.hh.

void cpsp::HPThreadingOptions::setNormalizeStructures

(

const bool

val

)

[inline]

setter for normalizeStructures

Definition at line 216 of file HPThreadingOptions.hh.

unsigned int cpsp::HPThreadingOptions::setSequence

(

const std::string &

seq

)

throw (cpsp::Exception)

Definition at line 190 of file HPThreadingOptions.cc.

void cpsp::HPThreadingOptions::setUseNoDDS

(

bool

val

)

[inline]

Definition at line 129 of file HPThreadingOptions.hh.

void cpsp::HPThreadingOptions::setUseSymmetryBreaking

(

bool

val

)

[inline]

Definition at line 125 of file HPThreadingOptions.hh.

bool cpsp::HPThreadingOptions::verboseOut

(

bool

newVal

)

[inline]

Definition at line 204 of file HPThreadingOptions.hh.

bool cpsp::HPThreadingOptions::verboseOut

(

void

)

[inline]

returns whether or not in verbose output mode

Definition at line 203 of file HPThreadingOptions.hh.

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Field Documentation

unsigned int cpsp::HPThreadingOptions::contactsInSeq [private]

The number of sequence internal HH-contacts.

Definition at line 95 of file HPThreadingOptions.hh.

HCoreDatabase* cpsp::HPThreadingOptions::coreDB [private]

the H-core database, the cores are coming from

Definition at line 75 of file HPThreadingOptions.hh.

CORESELECTS cpsp::HPThreadingOptions::coreSelection [private]

the core selection mode

Definition at line 57 of file HPThreadingOptions.hh.

std::vector<unsigned int> cpsp::HPThreadingOptions::hullLvl [private]

The hull level for each position of the sequence. The core has hull level 0, all non-core but core-neighbored positions have hull level 1 and so on.

Definition at line 68 of file HPThreadingOptions.hh.

const biu::LatticeDescriptor* cpsp::HPThreadingOptions::latDescr [private]

the descriptor for the underlying lattice model

Definition at line 51 of file HPThreadingOptions.hh.

biu::LatticeFrame* cpsp::HPThreadingOptions::lattice [private]

the underlying lattice model

Definition at line 54 of file HPThreadingOptions.hh.

int cpsp::HPThreadingOptions::maxE [private]

Definition at line 60 of file HPThreadingOptions.hh.

unsigned int cpsp::HPThreadingOptions::maxPCoreDistance [private]

The maximal distance of a P-element of the sequence to an H-element.

Definition at line 72 of file HPThreadingOptions.hh.

unsigned int cpsp::HPThreadingOptions::maxSols [private]

maximal number of structure to generate

Definition at line 63 of file HPThreadingOptions.hh.

int cpsp::HPThreadingOptions::minE [private]

upper and lower energy bound for structure prediction

Definition at line 60 of file HPThreadingOptions.hh.

unsigned int cpsp::HPThreadingOptions::minEvenOddHs [private]

The minimal number of even vs. odd H positions in sequence.

Definition at line 92 of file HPThreadingOptions.hh.

bool cpsp::HPThreadingOptions::normalizeStructures [private]

whether or not to print normalized move string representations

Definition at line 104 of file HPThreadingOptions.hh.

bool cpsp::HPThreadingOptions::onlyCountingStructures [private]

tag if counting in mode

Definition at line 86 of file HPThreadingOptions.hh.

FeatureMap cpsp::HPThreadingOptions::seqFeatureMap [private]

maps the sequence indices to their features

Definition at line 83 of file HPThreadingOptions.hh.

std::string* cpsp::HPThreadingOptions::sequence [private]

the HP-sequence the structures are generated for

Definition at line 48 of file HPThreadingOptions.hh.

bool cpsp::HPThreadingOptions::useNoDDS [private]

turn off dynamic decomposing search

Definition at line 101 of file HPThreadingOptions.hh.

bool cpsp::HPThreadingOptions::useSymmetryBreaking [private]

turn on symmetry breaking

Definition at line 98 of file HPThreadingOptions.hh.

bool cpsp::HPThreadingOptions::verboseOutput [private]

tag if verbose output is wanted

Definition at line 89 of file HPThreadingOptions.hh.

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

• src/cpsp/HPThreadingOptions.hh
• src/cpsp/HPThreadingOptions.cc