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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnseq_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/alnmgr/alnseq.cpp Source File

54

m_ContainsAA(

false

),

63

m_ContainsAA(

false

),

109

vector<CRef<CAlnMixSeq> >& ds_seq =

m_DsSeq

[&ds];

130  m_Seqs

.push_back(aln_seq);

138

aln_seq->

m_IsAA

=

false

;

144

aln_seq = it->second;

154  if

(width == 1 && aln_seq->

m_IsAA

!=

true

||

155

width == 3 && aln_seq->

m_IsAA

!=

false

) {

156  string

errstr =

string

(

"CAlnMix::Add(): "

)

159  ") or molecule type("

+

160

(aln_seq->

m_IsAA

?

"AA"

:

"NA"

) +

179  int

row_index = aln_seq->

m_RowIdx

;

180  if

(row_index == -1) {

183

}

else while

(row_index !=

row

) {

198  m_Seqs

.push_back(another_row);

208

ds_seq.push_back(aln_seq);

217  string

errstr =

string

(

"CAlnMix::x_IdentifyAlnMixSeq(): "

)

218

+

"In order to use this functionality " 219  "scope should be provided in CAlnMix constructor."

;

226  if

( !bioseq_handle ) {

227  string

errstr =

string

(

"CAlnMix::x_IdentifyAlnMixSeq(): "

)

228

+

"Seq-id cannot be resolved: " 249  m_Seqs

.push_back(aln_seq);

256

aln_seq->

m_IsAA

=

false

;

260

aln_seq = it->second;

291  if

( !

row

->GetStarts().empty() ) {

292  if

(

row

->m_PositiveStrand) {

293  row

->SetStarts().current =

row

->GetStarts().begin();

295  row

->SetStarts().current =

row

->GetStarts().end();

296  row

->SetStarts().current--;

299  row

->SetStarts().current =

row

->GetStarts().end();

302  string

(

"CAlnMixSequences::InitRowsStartIts():"

) +

303  " Internal error: no starts for row "

+

322  if

( !

row

->GetStarts().empty() ) {

323  if

(

row

->m_PositiveStrand) {

324  row

->SetStarts().current =

row

->GetStarts().begin();

326  row

->SetStarts().current =

row

->GetStarts().end();

327  row

->SetStarts().current--;

330  row

->SetStarts().current =

row

->GetStarts().end();

333  string

(

"CAlnMixSequences::InitExtraRowStartIts():"

) +

334  " Internal error: no starts for row "

+

349

StartItsConsistencyCheck(**row_i,

366

m_PositiveStrand(

true

),

static CRef< CScope > m_Scope

CAlnMixSeq * m_AnotherRow

const CAlnMixStarts & GetStarts() const

const CBioseq_Handle * m_BioseqHandle

void Add(const CDense_seg &ds, TAddFlags flags=0)

vector< CRef< CAlnMixSeq > > TSeqs

vector< CRef< CAlnMixSeq > > m_Rows

void x_IdentifyAlnMixSeq(CRef< CAlnMixSeq > &aln_seq, const CSeq_id &seq_id)

list< CRef< CAlnMixSeq > > m_ExtraRows

void RowsStartItsContsistencyCheck(size_t match_idx)

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

static bool x_CompareScores(const CRef< CAlnMixSeq > &seq1, const CRef< CAlnMixSeq > &seq2)

void InitExtraRowsStartIts()

static bool x_CompareChainScores(const CRef< CAlnMixSeq > &seq1, const CRef< CAlnMixSeq > &seq2)

TBioseqHandleMap m_BioseqHandles

bool IsSetWidths(void) const

const TWidths & GetWidths(void) const

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#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

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

bool IsProtein(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert int to string.

TDim GetDim(void) const

Get the Dim member data.

const TIds & GetIds(void) const

Get the Ids member data.

unsigned int

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

#define row(bind, expected)

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