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NCBI C++ ToolKit: include/objtools/alnmgr/alnvec.hpp Source File

1 #ifndef OBJECTS_ALNMGR___ALNVEC__HPP 2 #define OBJECTS_ALNMGR___ALNVEC__HPP 70 string

& GetSeqString (

string

buffer

73 string

& GetSeqString (

string

buffer

76 string

& GetSegSeqString(

string

buffer

81 string

& GetAlnSeqString(

string

buffer

89 string

& GetColumnVector(

string

buffer

92 bool

gaps_in_count =

false

)

const

;

101 unsigned int

scrn_width = 0,

117 void

SetGapChar(

TResidue

gap_char);

119 bool

IsSetGapChar()

const

;

123 void

SetEndChar(

TResidue

gap_char);

125 bool

IsSetEndChar()

const

;

132 void

SetGenCode(

int

gen_code,

135 bool

IsSetGenCode()

const

;

136 int

GetGenCode(TNumrow

row

)

const

;

142 const CSeq_id

& consensus_id)

const

;

148

vector<string>* consens =

NULL

)

const

;

151 int

CalculateScore (TNumrow row1, TNumrow row2)

const

;

152 int

CalculatePercentIdentity(

TSeqPos

aln_pos)

const

;

155 static void

TranslateNAToAA(

const string

& na,

string

& aa,

156 int

gen_code = kDefaultGenCode);

160 static int

CalculateScore (

const string

& s1,

const string

& s2,

161 bool

s1_is_prot,

bool

s2_is_prot,

162 int

gen_code1 = kDefaultGenCode,

163 int

gen_code2 = kDefaultGenCode);

166 static unsigned char

FromIupac(

unsigned char

c);

167 static unsigned char

ToIupac (

unsigned char

c);

169 static void

TransposeSequences(vector<string>& segs);

173 void

RetrieveSegmentSequences(

size_t

segment, vector<string>& segs)

const

;

180 void

CreateConsensus(vector<string>& consens)

const

;

214

eUseWholeAlnSeqString

218 void

PopsetStyle (

int

scrn_width = 70,

219

EAlgorithm algorithm = eUseAlnSeqString);

221 void

ClustalStyle(

int

scrn_width = 50,

222

EAlgorithm algorithm = eUseAlnSeqString);

264 string

na_buff, aa_buff;

275

pos : seq_vec.

size

() - pos - 1];

448 case 'A'

return

0x01;

449 case 'C'

return

0x02;

450 case 'M'

return

0x03;

451 case 'G'

return

0x04;

452 case 'R'

return

0x05;

453 case 'S'

return

0x06;

454 case 'V'

return

0x07;

455 case 'T'

return

0x08;

456 case 'W'

return

0x09;

457 case 'Y'

return

0x0a;

458 case 'H'

return

0x0b;

459 case 'K'

return

0x0c;

460 case 'D'

return

0x0d;

461 case 'B'

return

0x0e;

462 case 'N'

return

0x0f;

470 const char

data

"-ACMGRSVTWYHKDBN"

;

471 return

((c < 16) ?

data

[c] : 0);

void CollectNucleotideFrequences(const vector< string > &rows, int col, int base_count[], int numBases)

void CollectProteinFrequences(const vector< string > &rows, int col, int base_count[], int numBases)

TSignedSeqPos GetStop(TNumrow row, TNumseg seg, int offset=0) const

list< TSeqPos > TSeqPosList

int GetWidth(TNumrow row) const

TSegTypeFlags GetSegType(TNumrow row, TNumseg seg, int offset=0) const

TSignedSeqPos GetStart(TNumrow row, TNumseg seg, int offset=0) const

bool IsPositiveStrand(TNumrow row) const

TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

TNumseg GetSeg(TSeqPos aln_pos) const

TDim GetNumRows(void) const

unsigned int TSegTypeFlags

CDense_seg::TNumseg TNumseg

TSeqPos GetAlnStop(void) const

CSeqVector::TResidue TResidue

EAlgorithm

which algorithm to choose

@ eUseAlnSeqString

memory ineficient

TCoding GetNaCoding(void) const

TCoding GetAaCoding(void) const

CSeqVector & x_GetConsensusSeqVector(void) const

CSeq_data::E_Choice TCoding

bool IsSetGenCode() const

bool IsSetEndChar() const

TResidue GetGapChar(TNumrow row) const

string & GetSeqString(string &buffer, TNumrow row, TSeqPos seq_from, TSeqPos seq_to) const

void SetEndChar(TResidue gap_char)

TResidue GetEndChar() const

static void TranslateNAToAA(const string &na, string &aa, int gen_code=kDefaultGenCode)

map< TNumrow, CBioseq_Handle > TBioseqHandleCache

int GetGenCode(TNumrow row) const

void SetGapChar(TResidue gap_char)

bool IsSetGapChar() const

map< TNumrow, CRef< CSeqVector > > TSeqVectorCache

void SetNaCoding(TCoding coding)

CAlnVec & operator=(const CAlnVec &)

CSeqVector & x_GetSeqVector(TNumrow row) const

CScope & GetScope(void) const

void SetAaCoding(TCoding coding)

CSeqVector::TResidue TResidue

void SetGenCode(int gen_code, TNumrow row=-1)

static unsigned char ToIupac(unsigned char c)

TResidue GetResidue(TNumrow row, TSeqPos aln_pos) const

TBioseqHandleCache m_BioseqHandlesCache

vector< int > TResidueCount

static unsigned char FromIupac(unsigned char c)

TSeqVectorCache m_SeqVectorCache

string & GetSegSeqString(string &buffer, TNumrow row, TNumseg seg, TNumseg offset=0) const

objects::CSeqVector::TResidue TResidue

std::ofstream out("events_result.xml")

main entry point for tests

objects::CSeqVectorTypes::TResidue TResidue

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

TResidue GetGapChar(ECaseConversion case_cvt=eCaseConversion_none) const

Return gap symbol corresponding to the selected coding.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

#define NCBI_XALNMGR_EXPORT

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

E_Choice

Choice variants.

static const char * GetResidue(TokenStatBlkPtr stoken)

const struct ncbi::grid::netcache::search::fields::SIZE size

#define row(bind, expected)

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