Generated on Fri Mar 20 12:35:18 2009 for cpsp-2.3.1 by doxygen 1.5.5

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
HCoreDatabasegetHCoreDB (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
HCoreDatabasecoreDB
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

constants that define the core selection mode

Enumerator:
FIRST 
ALL_BEST 
ALL 

Definition at line 39 of file HPThreadingOptions.hh.

sequence features

Enumerator:
P_SINGLET 
H_SINGLET 

Definition at line 78 of file HPThreadingOptions.hh.


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.


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.


Field Documentation

The number of sequence internal HH-contacts.

Definition at line 95 of file HPThreadingOptions.hh.

the H-core database, the cores are coming from

Definition at line 75 of file HPThreadingOptions.hh.

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.

Definition at line 60 of file HPThreadingOptions.hh.

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.

upper and lower energy bound for structure prediction

Definition at line 60 of file HPThreadingOptions.hh.

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

Definition at line 92 of file HPThreadingOptions.hh.

whether or not to print normalized move string representations

Definition at line 104 of file HPThreadingOptions.hh.

tag if counting in mode

Definition at line 86 of file HPThreadingOptions.hh.

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.

turn off dynamic decomposing search

Definition at line 101 of file HPThreadingOptions.hh.

turn on symmetry breaking

Definition at line 98 of file HPThreadingOptions.hh.

tag if verbose output is wanted

Definition at line 89 of file HPThreadingOptions.hh.


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