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NCBI C++ ToolKit: src/objtools/blast/seqdb_writer/writedb_convert.cpp Source File

(

= 0;

< 16;

++) {

new_format =

;

amb_words = (new_format

? (0x80000000 | (num_amb * 2))

(

= 0;

< num_amb;

++) {

length_m1 =

.Length() - 1;

((length_m1 >> 12) == 0);

= (

.Value() << 4) | (length_m1 >> 8);

= length_m1 & 0xFF;

length_m1 =

.Length() - 1;

off =

.Offset();

((length_m1 >> 4) == 0);

= (

.Value() << 4) | length_m1;

[1] = (off >> 16) & 0xFF;

[2] = (off >> 8) & 0xFF;

[3] = (off ) & 0xFF;

cerr <<

<< endl;

bitcount = ((

& 1) +

((

>> 1) & 1) +

((

>> 2) & 1) +

((

>> 3) & 1));

(

= 0;

< 4;

++) {

((

& (1 <<

)) == 0)

vector<unsigned char>

;

(

= 0;

<4;

++) {

;

last_byte = blast_bytes - 1;

(!((

)inp_bytes == (

)byte_length)) {

cout <<

<< inp_bytes <<

<< byte_length << endl;

((

)inp_bytes == (

)byte_length);

seq.resize(blast_bytes);

(

= 0;

< inp_bytes;

++) {

b2 = inp & 0xF;

(((c1 | c2) & 0x80) == 0) {

half = (c1 << 2) | c2;

half |= ambiguities.

(b1,

*2) << 2;

half |= ambiguities.

(b2,

*2+1);

seq[

/2] |= (

& 1) ? half : (half << 4);

seq[last_byte] &= 255-3;

seq[last_byte] |= remainder;

vector<char> & v =

.GetSeq_data().GetNcbistdaa().Get();

seq.assign(& v[0], v.size());

& v =

.GetSeq_data().GetNcbieaa().Get();

& v =

.GetSeq_data().GetIupacaa().Get();

last_byte = blast_bytes - 1;

vector<char> & v =

.GetSeq_data().GetNcbi2na().Get();

((

)data_bytes == (

)v.size());

seq.reserve(blast_bytes);

seq.assign(& v[0], data_bytes);

seq.resize(blast_bytes);

seq[last_byte] &= 255-3;

seq[last_byte] |= remainder;

& v =

.GetSeq_data().GetIupacna().Get();

(

)

.GetLength(),

Encode ambiguities in blast database format.

int m_Log2[16]

Table mapping 1248 to 0123.

void x_AddAmbig(int value, int offset)

Add an ambiguity letter.

CAmbigDataBuilder(int sz)

Constructor.

void GetAmbig(string &amb)

Compute and return the encoded list of ambiguities.

void x_PackOldAmbig(string &amb, CAmbiguousRegion &r)

Append the 'old' encoding of one ambiguous region to a string.

vector< CAmbiguousRegion > m_Regions

Ambiguous regions for the sequence.

int Check(int data, int offset)

Check (and maybe store) a possibly ambiguous letter.

int x_Random(int value)

Pick a random letter from the set represented by an ambiguity.

CRandom m_Random

Random number generator.

void x_PackNewAmbig(string &amb, const CAmbiguousRegion &r)

Append the 'new' encoding of one ambiguous region to a string.

int m_Size

Size of the input sequence.

Ambiguous portion of a sequence.

CAmbiguousRegion(int value, int offset, int length)

Construct a new ambiguous region of a specified length.

int m_Value

Value of base (ambiguity letter).

int Length() const

Get the length of this ambiguous region.

CAmbiguousRegion(int value, int offset)

Construct a new ambiguous region one letter in length.

@ eMaxLength

Maximum length of a region.

bool Append(int value, int offset)

Try to append a letter to an ambiguous region.

int m_Start

Starting offset (offset of first base).

int m_End

End offset (offset of first disincluded base.)

int Value() const

Get the letter value for this region.

CAmbiguousRegion()

Construct a new, empty, ambiguous region.

int Offset() const

Get the starting offset of the region.

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

static int base_length[29]

static const char si[8][64]

static unsigned char ctable[16]

const TPrim & Get(void) const

uint32_t Uint4

4-byte (32-bit) unsigned integer

TValue GetRand(void)

Get the next random number in the interval [0..GetMax()] (inclusive)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TLength GetLength(void) const

Get the Length member data.

const TNcbi4na & GetNcbi4na(void) const

Get the variant data.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

unsigned int

A callback function used to compare two keys in a database.

const GenericPointer< typename T::ValueType > T2 value

static const BitmapCharRec ch1

static const BitmapCharRec ch0

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

void WriteDB_Ncbi4naToBinary(const char *ncbi4na, int byte_length, int base_length, string &seq, string &amb)

Build binary blast2na + ambig encoding based on ncbi4na input.

void WriteDB_Ncbi2naToBinary(const CSeq_inst &si, string &seq)

Build blast db nucleotide format from Ncbi2na Seq-inst.

vector< unsigned char > s_BuildNa4ToNa2Table()

Builds a table from NA4 to NA2 (with ambiguities marked as 0xFF.)

void WriteDB_EaaToBinary(const CSeq_inst &si, string &seq)

Build blast db protein format from Eaa protein Seq-inst.

void WriteDB_IupacaaToBinary(const CSeq_inst &si, string &seq)

Build blast db protein format from Iupacaa protein Seq-inst.

void WriteDB_StdaaToBinary(const CSeq_inst &si, string &seq)

Build blast db protein format from Stdaa protein Seq-inst.

void WriteDB_IupacnaToBinary(const CSeq_inst &si, string &seq, string &amb)

Build blast db nucleotide format from Iupacna Seq-inst.

Data conversion tools for CWriteDB and associated code.

void s_AppendInt4(string &outp, int x)

Append a value to a string as a 4 byte big-endian integer.

Implementation for general purpose utilities for WriteDB.

int s_DivideRoundUp(int value, int blocksize)

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

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