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NCBI C++ ToolKit: src/algo/align/prosplign/nucprot.hpp Source File

(

nuc1,

nuc2,

nuc3)

[nuc1*(8*8)+nuc2*8+nuc3];

(

n1,

n2,

n3)

{

[n1*25+n2*5+n3]; }

(vector<char>& pseq, istream& ifs,

is_nuc,

&

);

void SetAmin(char amin, const CSubstMatrix &matrix)

void Init(const CNSeq &seq, const CSubstMatrix &matrix)

CFastIScore & operator=(const CFastIScore &)

CFastIScore(const CFastIScore &)

int GetScore(int n1, int n2, int n3) const

void CheckUserInterrupt(void) const

CAtomicCounter m_Interrupt

CProSplignInterrupt(void)

bool(* TInterruptFnPtr)(void *callback_data)

void SetInterruptCallback(TInterruptFnPtr prg_callback, void *data)

TInterruptFnPtr m_InterruptFnPtr

Substitution Matrix for Scoring Amino-Acid Alignments.

CConstRef< CTranslationTable > m_trans_table

void SetTranslationTable(const CTranslationTable *trans_table)

const CTranslationTable & GetTranslationTable() const

CSubstMatrix(const string &name, int scaling)

int scaled_subst_matrix[256][256]

int MultScore(int nuc1, int nuc2, int nuc3, char amin) const

int ScaledScore(char amin1, char amin2) const

char GetStartResidue(int state) const

char GetCodonResidue(int state) const

static int SetCodonState(unsigned char ch1, unsigned char ch2, unsigned char ch3)

char TranslateStartTriplet(char n1, char n2, char n3) const

static char NucToChar(int n)

char TranslateTriplet(char n1, char n2, char n3) const

char TranslateStartTriplet(const string &triplet) const

CTranslationTable(int gcode, bool allow_alt_starts)

char nuc2a(int nuc1, int nuc2, int nuc3) const

char TranslateTriplet(const string &triplet) const

const CTrans_table & m_trans_table

static int CharToNuc(char c)

void Set(TValue new_value) THROWS_NONE

Set atomic counter value.

TValue Add(int delta) THROWS_NONE

Atomically add value (=delta), and return new counter value.

TValue Get(void) const THROWS_NONE

Get atomic counter value.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#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.

unsigned int

A callback function used to compare two keys in a database.

void ReadNucFa(CNSeq &seq, const string &fname, string &id)

void FrBackAlign(CBackAlignInfo &bi, CAli &ali)

void ReadFasta(vector< char > &pseq, istream &ifs, bool is_nuc, string &id)

int FindIGapIntrons(const CProSplignInterrupt &interrupt, vector< pair< int, int > > &igi, const PSEQ &pseq, const CNSeq &nseq, int g, int e, int f, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)

int FindFGapIntronNog(const CProSplignInterrupt &interrupt, vector< pair< int, int > > &igi, const PSEQ &pseq, const CNSeq &nseq, bool &left_gap, bool &right_gap, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)

int FrAlign(const CProSplignInterrupt &interrupt, CBackAlignInfo &bi, const PSEQ &pseq, const CNSeq &nseq, int g, int e, int f, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)

void BackAlignNog(CTBackAlignInfo< CBMode > &bi, CAli &ali)

int AlignFNog(const CProSplignInterrupt &interrupt, CTBackAlignInfo< CBMode > &bi, const PSEQ &pseq, const CNSeq &nseq, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)

void ReadProtFa(PSEQ &seq, const string &fname, string &id)

int FrAlignFNog1(const CProSplignInterrupt &interrupt, CBackAlignInfo &bi, const PSEQ &pseq, const CNSeq &nseq, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix, bool left_gap=false, bool right_gap=false)

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

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