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NCBI C++ ToolKit: src/algo/cobalt/demo/cobalt_app_util.cpp Source File

objects::CFastaReader::TFlags

)

(!line_reader.

()) {

);

scope->AddTopLevelSeqEntry(*entry);

seqloc->

().Assign(*itr->GetId().front());

seqs.push_back(seqloc);

objects::CFastaReader::TFlags

,

objects::CSeqIdGenerator& id_generator)

);

scope->AddTopLevelSeqEntry(*entry);

(!line_reader.

()) {

= entry->

().front()->GetData().GetAlign().front();

Data loader implementation that uses the blast databases.

Modification of the CFastaReader class that allows for reading a single sequence as a degenarate mult...

CRef< CSeq_entry > ReadAlignedSet(ILineErrorListener *pMessageListener=0)

Read alignment Modified parent class function that allows reading one sequence as aligned set.

CFastaReaderEx(ILineReader &reader, CFastaReader::TFlags flags=0)

Constructor.

Base class for reading FASTA sequences.

const TAnnot & GetAnnot(void) const

Simple implementation of ILineReader for i(o)streams.

Template class for iteration on objects of class C (non-medifiable version)

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

void GetSeqLocFromStream(CNcbiIstream &instream, vector< CRef< objects::CSeq_loc > > &seqs, CRef< objects::CScope > &scope, objects::CFastaReader::TFlags flags)

Reads fasta sequences from stream, adds them to scope, and returns them as the list of Seq_locs.

CRef< objects::CSeq_align > GetAlignmentFromStream(CNcbiIstream &instream, CRef< objects::CScope > &scope, objects::CFastaReader::TFlags flags, objects::CSeqIdGenerator &id_generator)

Reads fasta sequences as multiple sequence alignment.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

CSeqIdGenerator & SetIDGenerator(void)

long TFlags

binary OR of EFlags

CRef< CSeq_entry > x_ReadSeqsToAlign(TIds &ids, ILineErrorListener *pMessageListener)

void x_AddMultiwayAlignment(CSeq_annot &annot, const TIds &ids)

vector< CRef< CSeq_id > > TIds

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

#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.

TSet & SetSet(void)

Select the variant.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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