A RetroSearch Logo

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Search Query:

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seq_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/cobalt/seq.hpp Source File

Go to the documentation of this file.

Go to the SVN repository for this file.

1 #ifndef ALGO_COBALT___SEQ__HPP 2 #define ALGO_COBALT___SEQ__HPP 72  CSequence

(

const

objects::CSeq_loc& seq, objects::CScope& scope);

77  void

Reset(

const

objects::CSeq_loc& seq, objects::CScope& scope);

82  void

Reset(

int

length);

101  const unsigned char

*

GetSequence

()

const

{

return

&m_Sequence[0]; }

107  unsigned char GetLetter

(

int

pos)

const

{

return

m_Sequence[pos]; }

120  unsigned char

GetPrintableLetter(

int

pos)

const

;

125  int GetLength

()

const

{

return

(

int

)m_Sequence.size(); }

145  void

InsertGaps(

const

vector<Uint4>& gap_locations,

146  bool

consider_gaps =

false

);

156  static void

CompressSequences(vector<CSequence>& seq,

157

vector<int> index_list);

165  static void

CreateMsa(

const

objects::CSeq_align& seq_align,

166

objects::CScope& scope,

167

vector<CSequence>& msa);

Multiple aligner exceptions.

Definitions used by all COBALT aligner components.

Class for representing protein sequences.

CNcbiMatrix< double > TFreqMatrix

Represents the sequence as position-specific amino acid frequencies.

const TFreqMatrix & GetFreqs() const

int GetLength() const

Get the length of the current sequence.

unsigned char GetLetter(int pos) const

Access the sequence letter at a specified position.

TFreqMatrix & GetFreqs()

Access the list of position frequencies associated with a sequence.

const unsigned char * GetSequence() const

Get the raw sequence data in ncbistdaa format.

TFreqMatrix m_Freqs

Position-specific frequency profile corresponding to sequence.

CSequence()

Default constructor: build an empty sequence.

void SetLetter(int pos, unsigned char letter)

Change letter in a given position to a given one.

unsigned char * GetSequence()

Access the raw sequence data, in ncbistdaa format.

vector< unsigned char > m_Sequence

The sequence (ncbistdaa format)

vector< ETranscriptSymbol > TTranscript

static const char kGapChar('-')

The representation of a gap in ASCII format.

#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_COBALT_EXPORT

CSequnceHelper< CObject > CSequence

Definition of SSeqLoc structure.

static Uint4 letter(char c)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4