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NCBI C++ ToolKit: src/util/stream_source.cpp Source File

&description,

(prefix ==

) {

+ description,

arg_desc.

(

,

);

arg_desc.

(prefix,

,

+ description,

+ description,

+ description,

+ description,

+ description,

prefix +

);

(prefix ==

) {

arg_desc.

(

,

);

(args[prefix +

].

()) {

.push_back(

+ prefix +

);

.push_back(args[prefix +

].AsString());

(args[prefix +

]) {

.push_back(

+ prefix +

);

.push_back(args[prefix +

].AsString());

(args[prefix +

].

()) {

.push_back(

+ prefix +

);

.push_back(args[prefix +

].AsString());

.push_back(

+ prefix);

.push_back(args[prefix].AsString());

: m_Istr(

), m_CurrIndex(0)

: m_Istr(

), m_CurrIndex(0)

path =

[prefix +

].AsString();

(

[prefix +

]) {

);

);

);

(

<<

.size() <<

);

& file_mask)

);

+ file_path +

);

vector<string> paths;

paths.push_back(file_path);

vector<string> masks;

( !file_mask.empty() ) {

masks.push_back(file_mask);

masks.push_back(

);

paths.begin(), paths.end(),

masks.begin(), masks.end(),

(

<<

.size() <<

);

);

(

);

(

);

CInputStreamSource::operator

()

(m_Istr || m_IstrOwned.get() || m_CurrIndex < m_Files.size());

ncbi::TMaskedQueryRegions mask

vector< string > GetAllFilePaths() const

Returns all the file paths referenced by the manifest.

class CInputStreamSource encapsulates details of how we supply applications with input data through s...

void InitManifest(const string &manifest)

Initialize from a manifest file.

CInputStreamSource & operator++()

Advance to the next stream in the class.

CInputStreamSource & JumpToFile(unsigned index)

Jump to specified file in input list.

virtual void x_OpenNextFile()

static bool HaveArgsForPrefix(const string &prefix="input")

Check whether the arguments for a specific prefix have been set up in this application.

size_t GetCurrentStreamIndex(size_t *count=nullptr) const

Returns the current file index and the total number of files.

string GetCurrentFileName(void) const

Returns the current file name.

virtual ~CInputStreamSource()

void x_OpenOwnedStream(CNcbiIstream *is)

static vector< string > RecreateInputArgs(const CArgs &args, const string &prefix="input")

Get the standard input arguments that are present in args so we can pass them on to some other progra...

CNcbiIstream & operator*()

Dereferencing the stream class returns the current stream.

CInputStreamSource()

Default ctor This ctor leaves the stream source empty.

CNcbiIstream & GetStream(void)

Access the current stream.

CInputStreamSource & Rewind(void)

Resets the iterator to the first stream in the class.

static void SetStandardInputArgs(CArgDescriptions &arg_desc, const string &prefix="input", const string &description="data to process", bool is_mandatory=false)

Supply a standard set of arguments via argument descriptions to an application.

void InitFilesInDirSubtree(const string &file_path, const string &file_mask=kEmptyStr)

Initialize from a file search path.

unique_ptr< CNcbiIstream > m_IstrOwned

virtual void InitArgs(const CArgs &args, const string &prefix="input")

Initialize from a set of arguments.

void InitStream(CNcbiIstream &istr, const string &fname=kEmptyStr)

Initialize from a stream No ownership is claimed by this class - lifetime management of the stream is...

void InitFile(const string &file_path)

Initialize from a single file path.

iterator_bool insert(const value_type &val)

void SetDependency(const string &arg1, EDependency dep, const string &arg2)

Define a dependency.

void AddKey(const string &name, const string &synopsis, const string &comment, EType type, TFlags flags=0)

Add description for mandatory key.

void AddAlias(const string &alias, const string &arg_name)

Add argument alias.

CArgs & Assign(const CArgs &other)

Copy contents of another object into this one.

void AddOptionalKey(const string &name, const string &synopsis, const string &comment, EType type, TFlags flags=0)

Add description for optional key without default value.

void SetCurrentGroup(const string &group)

Set current arguments group name.

void AddDefaultKey(const string &name, const string &synopsis, const string &comment, EType type, const string &default_value, TFlags flags=0, const string &env_var=kEmptyStr, const char *display_value=nullptr)

Add description for optional key with default value.

@ eRequires

One argument requires another.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

#define NCBI_THROW(exception_class, err_code, message)

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

void FindFiles(TPathIterator path_begin, TPathIterator path_end, const vector< string > &masks, TFindFunc &find_func, TFindFiles flags=fFF_Default)

Generic algorithm for file search.

virtual bool Exists(void) const

Check if directory "dirname" exists.

@ fFF_Recursive

descend into sub-dirs

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static set< string > s_InputStreamSourcePrefixes

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