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NCBI C++ ToolKit: src/app/table2asn/fcs_reader.cpp Source File

vector<CTempString> values;

(!reader.

())

(current.

())

(*current.

() ==

)

(values.size() == 5)

new_cols.

= values[0];

(values[2] !=

)

new_cols.

= values[3][0];

new_cols.

= values[4];

strdata.erase(it->first - removed, it->second);

removed += it->second;

* encoded_str =

;

vector< char >* encoded_vec =

;

encoded_str = &lit.

().SetIupacna().Set();

encoded_str = &lit.

().SetIupacaa().Set();

encoded_vec = &lit.

().SetNcbi2na().Set();

encoded_vec = &lit.

().SetNcbi4na().Set();

encoded_vec = &lit.

().SetNcbi8na().Set();

encoded_vec = &lit.

().SetNcbipna().Set();

encoded_vec = &lit.

().SetNcbi8aa().Set();

encoded_str = &lit.

().SetNcbieaa().Set();

encoded_vec = &lit.

().SetNcbipaa().Set();

encoded_vec = &lit.

().SetNcbistdaa().Set();

decoded.erase(start, stop-start+1);

(CDelta_ext::Tdata::iterator it =

.begin(); it !=

.end();)

CDelta_ext::Tdata::iterator removable = it++;

local_removed = 0;

start = it_locs->first;

(start < current_abs+orig_lit_len-local_removed &&

current_abs < start+it_locs->second)

local_start =

(start-current_abs, 0);

local_end = start+it_locs->second-local_removed-current_abs-1;

local_removed += (local_end-local_start+1);

.erase(removable);

current_abs += orig_lit_len;

(delta_seq.

())

(

.mode ==

)

(

.mode ==

)

feat->

().SetInt().SetFrom(it_loc->first + 1);

feat->

().SetInt().SetTo(it_loc->first + it_loc->second);

feat->

().SetImp().SetKey(

);

feat->

(

);

set_annot->

().SetFtable().push_back(feat);

CSeq_entry::TSet::TSeq_set::iterator it = entry.

().

().begin();

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

TSeqPos GetLength(void) const

bool IsSetLength(void) const

bool xCheckLen(const objects::CBioseq &inst) const

void xTrimData(objects::CSeq_inst &inst, const Tlocs &col) const

void PostProcess(objects::CSeq_entry &entry)

void LoadFile(ILineReader &linereader)

void xTrimLiteral(objects::CSeq_literal &lit, int start, int end) const

void xTrimExt(objects::CSeq_inst &inst, const Tlocs &col) const

CForeignContaminationScreenReportReader(const CTable2AsnContext &context)

const CTable2AsnContext & m_context

bool AnnotateOrRemove(objects::CSeq_entry &entry) const

~CForeignContaminationScreenReportReader()

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

void GetLabel(string *label, ELabelType type) const

namespace ncbi::objects::

TSeqPos m_minimal_sequence_length

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

Abstract base class for lightweight line-by-line reading.

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

Operators to edit gaps in sequences.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const TPrim & Get(void) const

CTempString GetCurrentLine(void) const

virtual bool AtEOF(void) const =0

Indicates (negatively) whether there is any more input.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

void clear(void)

Clears the string.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

const_iterator begin() const

Return an iterator to the string's starting position.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ fSplit_ByPattern

Require full delimiter strings.

static const char label[]

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void SetData(TData &value)

Assign a value to Data data member.

const TSeq & GetSeq(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

TLiteral & SetLiteral(void)

Select the variant.

void SetLength(TLength value)

Assign a value to Length data member.

void SetData(TData &value)

Assign a value to Data data member.

TId & SetId(void)

Assign a value to Id data member.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

const TInst & GetInst(void) const

Get the Inst member data.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

const TIupacna & GetIupacna(void) const

Get the variant data.

void SetExt(TExt &value)

Assign a value to Ext data member.

const TLiteral & GetLiteral(void) const

Get the variant data.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

bool IsLoc(void) const

Check if variant Loc is selected.

E_Choice

Choice variants.

const TId & GetId(void) const

Get the Id member data.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TLength GetLength(void) const

Get the Length member data.

bool IsDelta(void) const

Check if variant Delta is selected.

void SetInst(TInst &value)

Assign a value to Inst data member.

const TExt & GetExt(void) const

Get the Ext member data.

const TDelta & GetDelta(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

bool IsLiteral(void) const

Check if variant Literal is selected.

bool IsSetSeq_data(void) const

may have the data Check if a value has been assigned to Seq_data data member.

void SetLength(TLength value)

Assign a value to Length data member.

list< CRef< CDelta_seq > > Tdata

bool IsGap(void) const

Check if variant Gap is selected.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

E_Choice Which(void) const

Which variant is currently selected.

@ e_Ncbipna

nucleic acid probabilities

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Ncbistdaa

consecutive codes for std aas

@ e_Ncbi2na

2 bit nucleic acid code

@ e_Iupacna

IUPAC 1 letter nuc acid code.

@ e_Ncbipaa

amino acid probabilities

@ e_Ncbi8na

8 bit extended nucleic acid code

@ e_Ncbi4na

4 bit nucleic acid code

@ e_Iupacaa

IUPAC 1 letter amino acid code.

@ e_Ncbi8aa

8 bit extended amino acid codes

static CS_CONTEXT * context

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