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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnseq_8hpp_source.html below:

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

1 #ifndef OBJECTS_ALNMGR___ALNSEQ__HPP 2 #define OBJECTS_ALNMGR___ALNSEQ__HPP 65 typedef

vector<CRef<CAlnMixSeq> >

TSeqs

;

78

fForceTranslation = 0x02,

90 void

SortByChainScore();

95 void

InitRowsStartIts();

96 void

InitExtraRowsStartIts();

97 void

RowsStartItsContsistencyCheck(

size_t

match_idx);

111 return

(*id1 < *id2);

172 if

( !m_PlusStrandSeqVector ) {

177 return

*m_PlusStrandSeqVector;

182 if

( !m_MinusStrandSeqVector ) {

187 return

*m_MinusStrandSeqVector;

193 bool

positive_strand =

true

)

195 if

(positive_strand) {

196

GetPlusStrandSeqVector().GetSeqData(start, start +

len

, s);

199

GetMinusStrandSeqVector().GetSeqData(

size

- (start +

len

203 if

(s.length() !=

len

) {

204 string

errstr =

"Unable to load data for seq-id=\""

CSeqVector & GetPlusStrandSeqVector(void)

CAlnMixStarts & SetStarts()

CAlnMixSeq * m_AnotherRow

const CAlnMixStarts & GetStarts() const

CRef< CSeqVector > m_PlusStrandSeqVector

CAlnMixSeq & operator=(const CAlnMixSeq &)

list< CAlnMixMatch * > TMatchList

CAlnMixSeq(const CAlnMixSeq &)

forbidden

CSeqVector & GetMinusStrandSeqVector(void)

CRef< CSeqVector > m_MinusStrandSeqVector

unique_ptr< CAlnMixStarts > m_Starts

const CBioseq_Handle * m_BioseqHandle

void GetSeqString(string &s, TSeqPos start, TSeqPos len, bool positive_strand=true)

vector< CRef< CAlnMixSeq > > TSeqs

vector< CRef< CAlnMixSeq > > m_Rows

map< CBioseq_Handle, CRef< CAlnMixSeq > > TBioseqHandleMap

list< CRef< CAlnMixSeq > > m_ExtraRows

map< const CDense_seg *, vector< CRef< CAlnMixSeq > > > m_DsSeq

const TSeqs & Get() const

map< CRef< CSeq_id >, CRef< CAlnMixSeq >, SSeqIds > TSeqIdMap

TBioseqHandleMap m_BioseqHandles

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string AsFastaString(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eStrand_Plus

Plus strand.

@ eStrand_Minus

Minus strand.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

#define NCBI_XALNMGR_EXPORT

const struct ncbi::grid::netcache::search::fields::SIZE size

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