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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seq__formatter_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/blast/blastdb_format/seq_formatter.cpp Source File

: m_Out(

), m_FmtSpec(format_spec), m_BlastDb(blastdb), m_GetDefline(

), m_OtherFields(0)

);

os <<

<<

[

] <<

;

(

.m_SeqRange.NotEmpty()) {

(

.m_FiltAlgoId >= 0) {

(!masks.

()) {

(df_set.

()) {

(oid, defline_data, other_fields);

(oid, defline_data, other_fields);

(oid, defline_data, other_fields);

kStandardSeparator(

);

(use_ctrl_a ?

: kStandardSeparator);

(

token : tokens) {

kPossibleId(token, 0, pos !=

? pos : token.length());

(!seqids.empty()) {

retval += kStandardSeparator + token;

old_title = (*desc)->GetTitle();

: m_BlastDb(blastdb), m_Out(

), m_fasta(

), m_UseLongSeqIds(useLongSeqId)

->SetInt().SetFrom(itr->first);

->SetInt().SetTo(itr->second-1);

(bioseq.

()) {

(

.m_FiltAlgoId != -1) {

(!masks.

()) {

(

.m_SeqRange.NotEmpty()) {

(

.m_UseCtrlA) {

(range.

()) {

(range.

()) {

<< fasta_deflines;

(range.

()) {

: m_BlastDb(blastdb), m_Out(

)

simpler =

;

(id_type ==

) {

(bioseq.

()) {

+

.size();

ncbi::TMaskedQueryRegions mask

void DumpAll(const CBlastDB_FormatterConfig &config)

CBlastDB_BioseqFormatter(CSeqDB &blastdb, CNcbiOstream &out)

Constructor.

int Write(CSeqDB::TOID oid, const CBlastDB_FormatterConfig &config, string target_id=kEmptyStr)

Retun 0 if Sucess otherwise -1.

CSeqDB & m_BlastDb

The BLAST database from which to extract data.

void DumpAll(const CBlastDB_FormatterConfig &config)

CSeqDB & m_BlastDb

The BLAST database from which to extract data.

int Write(CSeqDB::TOID oid, const CBlastDB_FormatterConfig &config, string target_id=kEmptyStr)

Retun 0 if Sucess otherwise -1.

CBlastDB_FastaFormatter(CSeqDB &blastdb, CNcbiOstream &out, TSeqPos width=80, bool useLongSeqId=false)

Constructor.

void x_GetSeq(CSeqDB::TOID oid, const CBlastDB_FormatterConfig &config, string &seq)

CNcbiOstream & m_Out

Stream to write output.

vector< char > m_ReplTypes

Vector of convertor objects.

string m_FmtSpec

The output format specification.

int Write(CSeqDB::TOID oid, const CBlastDB_FormatterConfig &config, string target_id=kEmptyStr)

unsigned int m_OtherFields

Bit Mask for other fields.

CBlastDeflineUtil::BlastDeflineFields m_DeflineFields

vector< string > m_Seperators

Vector of offsets where the replacements will take place.

CBlastDB_SeqFormatter(const string &fmt_spec, CSeqDB &blastdb, CNcbiOstream &out)

Constructor.

CSeqDB & m_BlastDb

The BLAST database from which to extract data.

string x_GetSeqMask(CSeqDB::TOID oid, int algo_id)

string x_GetSeqHash(CSeqDB::TOID oid)

void x_Print(CSeqDB::TOID oid, vector< string > &defline_data, vector< string > &other_fields)

Build data for write.

void DumpAll(const CBlastDB_FormatterConfig &config)

@ leaf_node_scientific_names

static void ExtractDataFromBlastDeflineSet(const CBlast_def_line_set &dl_set, vector< string > &results, BlastDeflineFields fields, string target_id, bool use_long_id)

static void ProcessFastaDeflines(CBioseq &bioseq, string &out, bool use_ctrla)

static void ExtractDataFromBlastDefline(const CBlast_def_line &dl, vector< string > &results, BlastDeflineFields fields, bool use_long_id)

static void ApplySeqMask(string &seq, const CSeqDB::TSequenceRanges &masks, const TSeqRange r=TSeqRange::GetEmpty())

static Uint4 GetSeqHash(const char *buffer, int length)

static string GetMasksString(const CSeqDB::TSequenceRanges &masks)

static void GetReverseStrandSeq(string &seq)

Defines invalid user input exceptions.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

int TOID

Sequence type accepted and returned for OID indices.

void GetSequenceAsString(int oid, CSeqUtil::ECoding coding, string &output, TSeqRange range=TSeqRange()) const

Get a sequence in a given encoding.

int GetSeqLength(int oid) const

Returns the sequence length in base pairs or residues.

CRef< CBioseq > GetBioseq(int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_seq_id=NULL) const

Get a CBioseq for a sequence.

bool CheckOrFindOID(int &next_oid) const

Find an included OID, incrementing next_oid if necessary.

CRef< CBlast_def_line_set > GetHdr(int oid) const

Get the ASN.1 header for the sequence.

void GetMaskData(int oid, const vector< int > &algo_ids, TSequenceRanges &ranges)

Get masked ranges of a sequence.

std::ofstream out("events_result.xml")

main entry point for tests

#define GI_FROM(T, value)

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

#define MSerial_AsnText

I/O stream manipulators –.

static SIZE_TYPE ParseIDs(CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default)

Parse a string representing one or more Seq-ids, appending the results to IDS.

static int BestRank(const CRef< CSeq_id > &id)

@ fParse_PartialOK

Warn rather than throwing an exception when a FASTA-style ID set contains unparsable portions,...

@ fParse_Default

By default in ParseIDs and IsValid, allow raw parsable non-numeric accessions and plausible local acc...

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

void SetMask(EMaskType type, CConstRef< CSeq_loc > location)

virtual void Write(const CSeq_entry_Handle &handle, const CSeq_loc *location=0)

Unspecified locations designate complete sequences; non-empty custom titles override the usual title ...

void SetWidth(TSeqPos width)

virtual void WriteSequence(const CBioseq_Handle &handle, const CSeq_loc *location=0, CSeq_loc::EOpFlags merge_flags=CSeq_loc::fMerge_AbuttingOnly)

void SetFlag(EFlags flag)

void SetAllFlags(TFlags flags)

void ResetFlag(EFlags flag)

@ fNoExpensiveOps

don't try too hard to find titles

@ fKeepGTSigns

don't convert '>' to '_' in title

@ fEnableGI

Use this flag to enable GI output in the defline.

@ fReverseStrand

flip the (implicit) location

@ eSoftMask

write as lowercase rather than uppercase

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

NCBI_NS_STD::string::size_type SIZE_TYPE

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.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_ByPattern

Require full delimiter strings.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

const Tdata & Get(void) const

Get the member data.

list< CRef< CBlast_def_line > > Tdata

list< CRef< CSeqdesc > > Tdata

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

void SetDescr(TDescr &value)

Assign a value to Descr data member.

@ e_Title

a title for this sequence

static void hex(unsigned char c)

constexpr bool empty(list< Ts... >) noexcept

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static void s_ReplaceCtrlAsInTitle(CBioseq &bioseq)

static void s_GetMaskSeqLoc(const CSeqDB::TSequenceRanges &mask_ranges, CSeq_loc &seq_loc)

static string s_RejoinDeflineTitle(const string &title, bool use_ctrl_a)

Auxiliary function to format the defline by rejoining multiple deflines using standard or <CNTRL>-A.

static void s_GetSeqMask(CSeqDB &db, CSeqDB::TOID oid, int algo_id, CSeqDB::TSequenceRanges &masks)

static const string kNoMask

Definition of a blastdb formatter interfaces.

ESeqDBIdType SeqDB_SimplifySeqid(CSeq_id &bestid, const string *acc, Int8 &num_id, string &str_id, bool &simpler)

Seq-id simplification.

ESeqDBIdType

Various identifier formats used in Id lookup.

Configuration object for CBlastDB_Formatter classes.

unsigned int leaf_node_tax_ids

unsigned int leaf_node_tax_names

List of sequence offset ranges.

Auxiliary functor to compute the length of a string (shamlessly copied from seq_writer....

SIZE_TYPE operator()(SIZE_TYPE a, const string &b) const

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