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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnmatch_8hpp_source.html below:

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

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1 #ifndef OBJECTS_ALNMGR___ALNMATCH__HPP 2 #define OBJECTS_ALNMGR___ALNMATCH__HPP 53  typedef int

(*TCalcScoreMethod)(

const string

& s1,

70

fForceTranslation = 0x02,

80

TCalcScoreMethod calc_score = 0);

96  void

SortByChainScore();

141  if

(

this

!= &

match

) {

160

CAlnMixSeq::TMatchList::const_iterator iter)

const 166  return

iter == list.end();

CAlnMixSeq::TMatchList::iterator m_MatchIter1

CAlnMixMatch(const CAlnMixMatch &match)

bool IsGood(const CAlnMixSeq::TMatchList &list, CAlnMixSeq::TMatchList::const_iterator iter) const

CAlnMixMatch & operator=(const CAlnMixMatch &match)

CAlnMixSeq::TMatchList::iterator m_MatchIter2

vector< CRef< CAlnMixMatch > > TMatches

TCalcScoreMethod x_CalculateScore

CAlnMixSequences::TSeqs & m_Seqs

const TMatches & Get() const

Container accessors.

CRef< CAlnMixSequences > m_AlnMixSequences

CAlnMixMatches::TCalcScoreMethod TCalcScoreMethod

list< CAlnMixMatch * > TMatchList

vector< CRef< CAlnMixSeq > > TSeqs

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_XALNMGR_EXPORT

unsigned int

A callback function used to compare two keys in a database.

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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