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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alntext_8hpp_source.html below:

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

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1 #ifndef OBJTOOLS_ALNTEXT__HPP 2 #define OBJTOOLS_ALNTEXT__HPP 74 CProteinAlignText

(objects::CScope& scope,

const

objects::CSeq_align& seqalign,

const string

& matrix_name =

"BLOSUM62"

);

77 const string

GetDNA

()

const

{

return

m_dna; }

79 const string

GetMatch

()

const

{

return

m_match; }

83 const

objects::CSeq_align& seqalign);

85 static char

TranslateTriplet(

const

objects::CTrans_table&

table

86 const string

& triplet);

97 void

AddDNAText(objects::CSeqVector_CI& genomic_ci,

int

& nuc_prev,

int len

);

98 void

TranslateDNA(

int

phase,

size_t len

bool

is_insertion);

99 void

AddProtText(objects::CSeqVector_CI& protein_ci,

int

& prot_prev,

int len

);

100 void

MatchText(

size_t len

bool

is_match=

false

);

101 char

MatchChar(

size_t i

);

102 void

AddHoleText(

bool

prev_3_prime_splice,

bool

cur_5_prime_splice,

103

objects::CSeqVector_CI& genomic_ci, objects::CSeqVector_CI& protein_ci,

104 int

& nuc_prev,

int

& prot_prev,

105 int

nuc_cur_start,

int

prot_cur_start);

106 void

AddSpliceText(objects::CSeqVector_CI& genomic_ci,

int

& nuc_prev,

char match

);

const char BAD_OR_MISMATCH[]

const char INTRON_OR_GAP[]

Text representation of ProSplign alignment.

SNCBIFullScoreMatrix m_matrix

const string & GetDNA() const

static const char MATCH_CHAR

static const char INTRON_CHAR

static const char SPACE_CHAR

const objects::CTrans_table * m_trans_table

static const char MISMATCH_CHAR

const string & GetMatch() const

const string & GetProtein() const

static const char BAD_PIECE_CHAR

static const char POSIT_CHAR

const string & GetTranslation() const

static const char GAP_CHAR

Include a standard set of the NCBI C++ Toolkit most basic headers.

#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_XALNMGR_EXPORT

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

Defines command line argument related classes.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

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