cuddl::detail::fastx_mapped_file Class Reference

Read-only contiguous file payload for in-memory FASTX parsing. More...

#include <fastx_sequence_file.hpp>

Public Member Functions
	fastx_mapped_file ()=default
	fastx_mapped_file (fastx_mapped_file const &)=delete
fastx_mapped_file &	operator= (fastx_mapped_file const &)=delete
	fastx_mapped_file (fastx_mapped_file &&other) noexcept
fastx_mapped_file &	operator= (fastx_mapped_file &&other) noexcept
	~fastx_mapped_file ()
std::string_view	data () const noexcept
	Contiguous read-only file bytes.
bool	empty () const noexcept
	True when the file is empty or load produced no bytes.

Static Public Member Functions
static Result< std::unique_ptr< fastx_mapped_file > >	load (std::string const &path, bool read=false, bool direct=false)
	Maps or reads a file.

Detailed Description

Read-only contiguous file payload for in-memory FASTX parsing.

On Linux a plain file is memory-mapped by default, so FASTA extents reference the mapping with no copy, or read into memory it owns on request. Other platforms always read.

Definition at line 254 of file fastx_sequence_file.hpp.

Constructor & Destructor Documentation

fastx_mapped_file() [1/3]

cuddl::detail::fastx_mapped_file::fastx_mapped_file ( )

default

fastx_mapped_file() [2/3]

cuddl::detail::fastx_mapped_file::fastx_mapped_file ( fastx_mapped_file const &  )

delete

fastx_mapped_file() [3/3]

cuddl::detail::fastx_mapped_file::fastx_mapped_file ( fastx_mapped_file &&  other )

inlinenoexcept

Definition at line 259 of file fastx_sequence_file.hpp.

                                                          {
        *this = std::move(other);
    }

~fastx_mapped_file()

cuddl::detail::fastx_mapped_file::~fastx_mapped_file ( )

inline

Definition at line 281 of file fastx_sequence_file.hpp.

                         {
        release();
    }

Member Function Documentation

data()

std::string_view cuddl::detail::fastx_mapped_file::data ( ) const

inlinenoexcept

Contiguous read-only file bytes.

Definition at line 316 of file fastx_sequence_file.hpp.

                                                       {
        return std::string_view{data_, size_};
    }

empty()

bool cuddl::detail::fastx_mapped_file::empty ( ) const

inlinenoexcept

True when the file is empty or load produced no bytes.

Definition at line 321 of file fastx_sequence_file.hpp.

                                              {
        return size_ == 0;
    }

load()

static Result< std::unique_ptr< fastx_mapped_file > > cuddl::detail::fastx_mapped_file::load ( std::string const &  path, bool  read = false, bool  direct = false  )

inlinestatic

Maps or reads a file.

Empty files succeed with empty data. Any failure carries the reason; the FASTX loader maps it to its stable "cannot open" error.

Parameters

read	Read into owned memory instead of mapping. Unmapping write-locks the address space and shoots down TLBs on every core, which serialises a consumer that frees files loaded by dozens of threads; a single thread mapping ahead of others is better off mapping.
direct	Read with O_DIRECT, as read_whole_file does.

Definition at line 297 of file fastx_sequence_file.hpp.

                                                                        {
        auto buffer = std::make_unique<fastx_mapped_file>();
        auto loaded = buffer->load_from_path(path, read, direct);
        if (!loaded) return Err(loaded.error());
        return buffer;
    }

Here is the call graph for this function:

operator=() [1/2]

fastx_mapped_file & cuddl::detail::fastx_mapped_file::operator= ( fastx_mapped_file &&  other )

inlinenoexcept

Definition at line 263 of file fastx_sequence_file.hpp.

                                                                     {
        if (this != &other) {
            release();
            owned_storage_ = std::move(other.owned_storage_);
            data_ = other.data_;
            size_ = other.size_;
            other.data_ = nullptr;
            other.size_ = 0;
#if defined(__linux__)
            mapped_ = other.mapped_;
            mapped_size_ = other.mapped_size_;
            other.mapped_ = nullptr;
            other.mapped_size_ = 0;
#endif
        }
        return *this;
    }

operator=() [2/2]

fastx_mapped_file & cuddl::detail::fastx_mapped_file::operator= ( fastx_mapped_file const &  )

delete

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The documentation for this class was generated from the following file:

• fastx_sequence_file.hpp