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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuResidueProfile_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/structure/cd_utils/cuResidueProfile.hpp Source File

35 #ifndef CU_RESIDUE_PROFILE_HPP 36 #define CU_RESIDUE_PROFILE_HPP 49  static unsigned char

getNcbiStdCode(

char

eaa);

50  static char

getEaaCode(

char

stdCode);

51  static const string

getResiduesString();

52  static int

getResiduesStringSize();

57  void

addOccurence(

char

residue,

int row

,

bool

aligned);

58  double

calculateColumnWeight(

char

residue,

bool

countGap,

int

numRows)

const

;

60  double

sumUpColumnWeightsByRow(vector<double>& rowWeights,

bool

countGap,

int

numRows)

const

;

61  double

reweightColumnByRowWeights(

const

vector<double>& rowWeights,

char

& heaviestResidue)

const

;

62  int

getSumCount()

const

;

63  char

getMostFrequentResidue(

int

&

count

)

const

;

65  void

getResiduesByRow(vector<char>& residues,

bool

byNcbiStd=

true

)

const

;

67  unsigned char

getResidueByRow(

int row

);

68  bool

isAligned(

char

residue,

int row

)

const

;

69  bool

isAligned(

int row

);

70  bool

isAllRowsAligned()

const

;

77  double

calcInformationContent();

82  return

(

row

> (

int

)(m_residuesByRow.size()-1)) ? 0 : m_residuesByRow[

row

];

90  static void

useDefaultBackgroundResFreq();

91  double

getBackgroundResFreq(

char

res);

133  typedef

pair<int,int>

Seg

;

137  void

setIndexSequence(

string

& seq);

138  string

getIndexSequence();

141  int

getLenOfLongestSeg();

144  int

getLongUnalignedSegs(

int

length, vector<Seg>& segs);

145  string

subtractLongestSeg(

int

threshold);

147  string

subtractSeg(Seg seg,

string

&

in

);

156  int

getLen(

Seg

seg);

166  void

addOneRow(

BlockModelPair

&

bmp

,

const string

& mSeq,

const string

& sSeq);

167  void

calculateRowWeights();

168  const string

& makeConsensus();

170  const string

getConsensus(

bool

inNcbieaa=

true

) ;

173  int

countColumnsOnMaster(

string

& seq);

177  void

adjustConsensusAndGuide();

184  double

calcInformationContent(

bool

byConsensus=

true

);

197  unsigned int

GetNumUnqualAfterIndex(

int

index)

const

;

198  bool

HasUnqualAfterIndex(

int

index)

const

;

219  void

segsToSet(vector<UnalignedSegReader::Seg>& segs,

set<int>

& cols);

virtual void read(ColumnResidueProfile &crp)=0

unsigned char getResidueByRow(int row)

multimap< char, RowStatusPair > ResidueRowsMap

pair< int, bool > RowStatusPair

ResidueRowsMap::iterator * findRow(int row)

int getIndexByConsensus() const

void setIndexByConsensus(int col)

vector< ResidueRowsMap::iterator * > m_residuesByRow

ResidueRowsMap m_residueRowsMap

int getResidueTypeCount() const

virtual void read(ColumnResidueProfile &crp)

virtual ~MasterColumnCounter()

const vector< CRef< CSeq_id > > getSeqIdsByRow() const

void setInclusionThreshold(double th)

vector< double > m_rowWeights

set< int > m_colsToSkipOnConsensus

UnqualForConsMap::const_iterator UnqualForConsCit

BlockModelPair m_guideAlignment

UnqualForConsMap m_numUnqualAfterConsIndex

set< int > m_colsToSkipOnMaster

map< int, unsigned int > UnqualForConsMap

UnqualForConsMap::iterator UnqualForConsIt

map< ColumnAddress, ColumnResidueProfile > PosProfileMap

vector< CRef< CSeq_id > > m_seqIds

double m_frequencyThreshold

vector< Seg > m_unalignedSegs

container_type::const_iterator const_iterator

container_type::iterator iterator

container_type::iterator iterator

bool operator<(const CEquivRange &A, const CEquivRange &B)

thread_local unique_ptr< FtaMsgPost > bmp

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_CDUTILS_EXPORT

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n th

std::istream & in(std::istream &in_, double &x_)

#define row(bind, expected)

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