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NCBI C++ ToolKit: src/algo/blast/blastinput/blast_asn1_input.cpp Source File

53

: m_InputStream(&

infile

),

54

m_SecondInputStream(

NULL

),

55

m_IsPaired(is_paired),

62

: m_InputStream(&infile1),

63

m_SecondInputStream(&infile2),

102  if

(instream.eof()) {

111  string

message =

"Sequence length not set"

;

113

message += (

string

)

" in the instance of "

+

144  if

(

first

.NotEmpty()) {

146  first

->SetSeq().SetDescr().Set().push_back(seqdesc_first);

152  if

(

first

.NotEmpty()) {

160  if

(

first

.NotEmpty()) {

186  first

->SetSeq().SetDescr().Set().push_back(seqdesc_first);

194  if

(

first

.NotEmpty()) {

Auxiliary classes/functions for BLAST input library.

@ eFirstSegment

The first sequence of a pair with both sequences read and accepted.

Class representing a text or binary file containing sequences in ASN.1 format as a collection of Seq-...

virtual int GetNextSequence(CBioseq_set &bioseq_set)

Get one sequence (or a pair for NGS reads)

CNcbiIstream * m_SecondInputStream

bool x_ReadFromTwoFiles(CBioseq_set &bioseq_set)

Read sequences from two streams.

bool m_IsPaired

Are queries paired.

CASN1InputSourceOMF(CNcbiIstream &infile, bool is_bin=false, bool is_paired=false)

Constructor.

bool m_IsBinary

Is input binary ASN1.

CRef< CSeq_entry > x_ReadOneSeq(CNcbiIstream &instream)

Read one sequence from.

CNcbiIstream * m_InputStream

bool x_ReadFromSingleFile(CBioseq_set &bioseq_set)

Read sequences from one stream.

TSeqPos m_BasesAdded

Number of bases added so far.

const CSeq_id * GetFirstId() const

Defines user input exceptions.

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

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

#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_AsnBinary

#define MSerial_AsnText

I/O stream manipulators –.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

void SetType(TType &value)

Assign a value to Type data member.

const TSeq & GetSeq(void) const

Get the variant data.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

const TInst & GetInst(void) const

Get the Inst member data.

TLength GetLength(void) const

Get the Length member data.

bool IsSetLength(void) const

length of sequence in residues Check if a value has been assigned to Length data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

TUser & SetUser(void)

Select the variant.

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