Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__sra__input_8cpp_source.html below:

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

check_for_paires

,

: m_Accessions(accessions),

m_IsPaired(check_for_paires)

m_ItAcc = m_Accessions.begin();

VResolverCacheEnable(resolver.

(), vrAlwaysDisable);

m_SraDb.reset(

(mgr, *m_ItAcc));

(

->IsTechnicalRead()) {

bioseq.

().push_back(

->GetShortSeq_id());

bioseq.

().SetSeq_data().SetIupacna(

((

)sequence));

bioseq.

().push_back(quality_scores);

bioseq_set.

().push_back(seq_entry);

bioseq_set.

().back().GetNonNullPointer();

spot =

->GetSpotId();

(

->GetSpotId() == spot) {

(

&& second) {

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

(seq_entry.

()) {

seqloc->

().SetFrom(0);

retval(*seqloc, scope);

Auxiliary classes/functions for BLAST input library.

Definitions and functions associated with the BlastQueryInfo structure.

@ eFirstSegment

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

const CSeq_id * GetFirstId() const

Class for reading sequences from SRA respository or SRA file.

virtual int GetNextSequence(CBioseq_set &bioseq_set)

Get one sequence (or a pair for NGS reads)

virtual bool End(void)

Signal whether there are any unread sequence left.

void x_ReadPairs(CBioseq_set &bioseq_set)

Read one batch of sequences and mark pairs.

TSeqPos m_BasesAdded

Number of bases added so far.

bool m_IsPaired

Are queries paired.

void x_NextAccession(void)

Advance to the next SRA accession.

unique_ptr< CCSraShortReadIterator > m_It

unique_ptr< CCSraDb > m_SraDb

vector< string >::iterator m_ItAcc

vector< string > m_Accessions

CRef< CSeq_entry > x_ReadOneSeq(void)

Read one sequence pointed by the iterator.

virtual SSeqLoc GetNextSSeqLoc(CScope &scope)

Retrieve a single sequence (in an SSeqLoc container)

CRef< CSeq_loc > x_GetNextSeq_loc(CScope &scope)

Read the next sequence, add it to scope and return Seq-loc object.

TObject * GetPointer(void) const

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)

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

bool NotEmpty(void) const THROWS_NONE

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

bool Empty(void) const THROWS_NONE

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

size_type length(void) const

Return the length of the represented array.

void SetType(TType &value)

Assign a value to Type data member.

@ eNa_strand_both

in forward orientation

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.

TId & SetId(void)

Assign a value to Id data member.

const TInst & GetInst(void) const

Get the Inst member data.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

TLength GetLength(void) const

Get the Length member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

TUser & SetUser(void)

Select the variant.

@ eRepr_raw

continuous sequence

@ eMol_na

just a nucleic acid

Definition of SSeqLoc structure.

Structure to represent a single sequence to be fed to BLAST.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4