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NCBI C++ ToolKit: src/algo/cobalt/unit_test/cobalt_test_util.cpp Source File

objects::CSeqIdGenerator* id_generator

)

(!parse_deflines) {

(!line_reader.

()) {

scope->AddTopLevelSeqEntry(*entry);

seqloc->

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

seqs.push_back(seqloc);

objects::CSeqIdGenerator* id_generator

)

(scope.

()) {

(!parse_deflines) {

(entry.

()) {

(!line_reader.

()) {

align = entry->

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

Data loader implementation that uses the blast databases.

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)

@ eProblem_ModifierFoundButNoneExpected

Interface for CMultiAligner.

int ReadFastaQueries(const string &filename, vector< CRef< objects::CSeq_loc > > &seqs, CRef< objects::CScope > &scope, bool parse_deflines, objects::CSeqIdGenerator *id_generator)

int ReadMsa(const string &filename, CRef< CSeq_align > &align, CRef< CScope > scope, bool parse_deflines, objects::CSeqIdGenerator *id_generator)

Operators to edit gaps in sequences.

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 > ReadAlignedSet(int reference_row, ILineErrorListener *pMessageListener=nullptr)

Read as many sequences as are available, and interpret them as an alignment, with hyphens marking rel...

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

void IgnoreProblem(ILineError::EProblem problem)

@ fNoParseID

Generate an ID (whole defline -> title)

@ fForceType

Force specified type regardless of accession.

@ fValidate

Check (alphabetic) residue validity.

@ fAssumeProt

Assume prots unless accns indicate otherwise.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

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 Empty(void) const THROWS_NONE

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

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

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