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NCBI C++ ToolKit: src/algo/winmask/win_mask_util.cpp Source File

<<

<< id_str <<

<< e.

() <<

);

objects::CBioseq_Handle & bsh )

( idset.find( *iter ) != idset.end() ) {

( !

.empty() &&

[

.length() - 1] ==

)

=

.substr( 0,

.length() - 1 );

( !

.empty() ) {

string::size_type pos = (

[0] ==

) ? 1 : 0;

string::size_type

=

.length();

( pos != string::npos && pos <

) {

( (pos =

.find_first_of(

, pos )) != string::npos ) {

<<

<< id_str <<

);

( nword_sets_.size() < nwords ) {

nword_sets_.resize( nwords );

( id_str[id_str.length() - 1] !=

) {

nword_sets_[nwords - 1].insert( id_str );

nword_sets_[nwords - 1].insert(

id_str.substr( 0, id_str.length() - 1 ) );

objects::CBioseq_Handle & bsh )

( !id_str.empty() ) {

string::size_type pos = id_str.find_first_of(

);

id_str = id_str.substr( 0, pos );

( find( id_str ) )

;

( id_str.substr( 0, 4 ) ==

) {

id_str = id_str.substr( 4, string::npos );

find( id_str );

& id_str,

nwords )

nword_sets_[nwords].find( id_str ) != nword_sets_[nwords].end();

vector< Uint4 > word_starts =

( id_str );

< nword_sets_.size() &&

< word_starts.size() - 1; ++

) {

( !nword_sets_[

].

() ) {

(

j = 0; j < word_starts.size() -

- 1; ++j ) {

pattern = id_str.substr(

word_starts[j +

+ 1] - word_starts[j] - 1 );

( find( pattern,

) ) {

& input_format)

( input_format ==

) {

( input_format ==

) {

}

( input_format !=

) {

+ input_format);

m_CurrentBioseq.Reset();

(

.

() ||

[0] ==

)

( (ids == 0 || ids->

()) &&

(exclude_ids == 0 || exclude_ids->

()) ) {

( ids != 0 && !ids->

() )

( ids->

( bsh ) ) {

( exclude_ids != 0 && !exclude_ids->

() )

( exclude_ids->

( bsh ) ) {

static CRef< CScope > m_Scope

Class for reading sequences from BLAST databases.

Class for reading sequences from fasta files.

virtual void insert(const string &id_str)

See documentation for CIdSet::insert().

set< objects::CSeq_id_Handle > idset

virtual bool find(const objects::CBioseq_Handle &) const

See documentation for CIdSet::find().

virtual bool find(const objects::CBioseq_Handle &) const

See documentation for CIdSet::find().

virtual void insert(const string &id_str)

See documentation for CIdSet::insert().

static const vector< Uint4 > split(const string &id_str)

\brief Split a string into words and return an array of word start offsets.

Base class for sets of seq_id representations used with -ids and -exclude-ids options.

virtual bool find(const objects::CBioseq_Handle &bsh) const =0

Check if the id of the given bioseq is in the id set.

virtual bool empty() const =0

Check if the id set is empty.

Function iterating over bioseqs in input.

CInputBioseq_CI(const string &input_file, const string &input_format)

unique_ptr< CNcbiIstream > m_InputFile

CInputBioseq_CI & operator++(void)

Move to the next object in iterated sequence.

unique_ptr< CMaskReader > m_Reader

static bool consider(const objects::CBioseq_Handle &bsh, const CIdSet *ids, const CIdSet *exclude_ids)

Check if the given bioseq should be considered for processing.

iterator_bool insert(const value_type &val)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_ASSERT(expr, mess)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

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...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

vector< CSeq_id_Handle > TId

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

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

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

bool IsSeq(void) const

Check if variant Seq is selected.

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

void split(std::vector< std::string > *strVec, const std::string &str_, const std::string &split_)

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