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)