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NCBI C++ ToolKit: include/objtools/blast/seqdb_writer/writedb_general.hpp Source File

((

+ (blocksize - 1)) / blocksize);

<

ALLOCSIZE>

((back->size() + length + 1) > back->capacity()) {

* rv = back->data() + back->size();

back->append(

, length);

back->append(&

[0], 1);

* pstr = *iter;

blksz = ALLOCSIZE;

<

ALLOCSIZE>

vector<const char *>

;

(

* x,

length)

<

STR_SIZE>

memset(

, 0, STR_SIZE);

(

= 0;

<STR_SIZE;

++) {

(other) < 0;

(other) == 0;

(

= 0;

<STR_SIZE;

++) {

(

* x,

L);

! ((*this) == other);

Fixed-buffer string type.

CArrayString(const char *x, int L)

Construct from a string in a memory location.

bool operator<(const CArrayString< STR_SIZE > &other) const

Return true if this string is less than 'other'.

char m_Data[STR_SIZE]

Data for this string, NUL terminated iff less than STR_SIZE bytes.

const char * Data() const

Get a pointer to the start of this string's data.

int Cmp(const CArrayString< STR_SIZE > &other) const

Compare two strings (lexicographically).

CArrayString(const CArrayString< STR_SIZE > &other)

Copy constructor.

bool operator==(const CArrayString< STR_SIZE > &other) const

Return true if this string is less than 'other'.

CArrayString< STR_SIZE > & operator=(const CArrayString< STR_SIZE > &other)

Assign this string from another.

int Size() const

Get this string's length.

CArrayString()

Constructor.

Sortable packed array of null terminated strings.

CWriteDB_PackedBuffer< ALLOCSIZE > TThis

This object type.

CWriteDB_PackedBuffer()

Constructor.

void x_AddBlock()

Add an block of ALLOCSIZE bytes to the sorted string vector.

void Clear()

Free all held memory.

~CWriteDB_PackedBuffer()

Destructor.

char m_Zero[1]

Array containing NUL byte for convenience.

CWriteDB_PackedBuffer(const TThis &other)

Prevent copy constructor.

TThis & operator=(const TThis &other)

Prevent copy operator.

const char * Insert(const char *data, int length)

Insert a new string plus a NUL terminator.

vector< string * > m_Packed

Array of pointers to the start of the strings stored here.

Class providing iteration over string data.

Iterator(TPackedMap &pile, TPackedMap::iterator i)

Create an iterator.

TPackedMap::iterator m_Pos1

The iterator for the current TPacked object.

TPackedMap & m_Packed

The CWriteDB_PackedString container.

int m_Pos2

An integer to iterate within the TPacked object.

bool operator!=(Iterator &other)

Compare two iterators for inequality.

void Get(string &data)

Get the string pointed to by this iterator.

bool operator==(Iterator &other)

Compare two iterators for equality.

Iterator & operator++()

Move forward one item (prefix).

Packed string data container with sorting and iteration.

void Insert(const char *x, int L)

Insert string data into the container.

map< CArrayString< PREFIX >, CRef< TPacked > > TPackedMap

A map from the string prefixes to a packed buffer.

CWriteDB_PackedStrings< BLOCK > TPacked

A packed list of buffers.

Iterator End()

Get an iterator to the end of this collection.

void Sort()

Sort all contained data.

int Size() const

Return the number of contained entries.

CWriteDB_PackedBuffer< BLOCK > m_Buffer

Shared list of packed string buffers.

int m_Size

Number of elements stored in this container.

@ BLOCK

This is the amount of string capacity to request.

@ PREFIX

This is the number of bytes for the first level index.

void Clear()

Clear all objects from this container.

Iterator Begin()

Get an iterator to the beginning of this collection.

~CWriteDB_PackedSemiTree()

Destructor.

TPackedMap m_Packed

Map of string prefixes to packed string lists.

CWriteDB_PackedSemiTree()

Constructor.

Comparator for sorting null terminated strings.

bool operator()(const char *a, const char *b) const

Compare two null terminated strings.

Sortable packed array of strings, optimized for space.

const vector< const char * > & GetList()

Get the list of null terminated strings.

CWriteDB_PackedStrings(CWriteDB_PackedBuffer< ALLOCSIZE > &buffer)

Constructor.

CWriteDB_PackedStrings(const TThis &other)

Prevent copy constructor.

~CWriteDB_PackedStrings()

Destructor.

void Insert(const char *x, int length)

Insert string data - must be null terminated.

int Size()

Sort the keyloc array (in place).

CWriteDB_PackedBuffer< ALLOCSIZE > & m_Buffer

Reference to shared packed-buffer object.

TThis & operator=(const TThis &other)

Prevent assignment.

void Sort()

Sort the keyloc array (in place).

vector< const char * > m_KeyLoc

Pointers to the beginning of the strings stored here.

CWriteDB_PackedStrings< ALLOCSIZE > TThis

This object type.

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

constexpr auto sort(_Init &&init)

const GenericPointer< typename T::ValueType > T2 value

int strcmp(const char *str1, const char *str2)

static const BitmapCharRec ch1

static const BitmapCharRec ch2

USING_SCOPE(objects)

Import definitions from the objects namespace.

int s_DivideRoundUp(int value, int blocksize)

Divide by a number, rounding up to a whole integer.

int s_RoundUp(int value, int blocksize)

Round up to the next multiple of some number.

int WriteDB_FindSequenceLength(bool protein, const string &seq)

Compute length of sequence from raw packing.

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