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37 # define ALIGNMENT_CALLBACK __stdcall 39 # define ALIGNMENT_CALLBACK 65 const string& alphabet,
66 const string&
match,
67 const string& missing,
68 const string& beginningGap,
69 const string& middleGap,
70 const string& endGap):
84 const string& alphabet) {
mAlphabet= alphabet;
return*
this; }
91 const string& c) {
mMatch= c;
return*
this; };
98 const string& c) {
mMissing= c;
return*
this; };
112 const string& c) {
mMiddleGap= c;
return*
this; };
119 const string& c) {
mEndGap= c;
return*
this; };
struct SLineInfo SLineInfo
bool ReadAlignmentFile(istream &istr, bool gen_local_ids, bool use_nexus_info, CSequenceInfo &sequence_info, SAlignmentFile &alignmentInfo, ILineErrorListener *pErrorListener=nullptr)
const string & Missing() const
const string & BeginningGap() const
const string & Alphabet() const
const string & MiddleGap() const
CSequenceInfo(const string &alphabet, const string &match, const string &missing, const string &beginningGap, const string &middleGap, const string &endGap)
CSequenceInfo & SetMissing(const string &c)
const string & EndGap() const
const string & Match() const
CSequenceInfo & SetAlphabet(const string &alphabet)
CSequenceInfo & SetBeginningGap(const string &c)
CSequenceInfo & SetEndGap(const string &c)
CSequenceInfo & SetMiddleGap(const string &c)
CSequenceInfo & SetMatch(const string &c)
vector< string > mSequences
size_t NumDeflines() const
size_t NumSequences() const
vector< TLineInfo > mDeflines
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_XOBJREAD_EXPORT
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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