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/* $Id: writedb_files.cpp 557074 2018-02-09 14:23:28Z fongah2 $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Kevin Bealer
*
*/
/// @file writedb_files.cpp
/// Implementation for the CWriteDB_Files class.
/// class for WriteDB.
#include <ncbi_pch.hpp>
#include <objtools/blast/seqdb_writer/writedb_files.hpp>
#include <objtools/blast/seqdb_writer/writedb_convert.hpp>
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
#include <serial/serial.hpp>
#include <iostream>
#include <sstream>
BEGIN_NCBI_SCOPE
/// Use standard C++ definitions.
USING_SCOPE(std);
// Blast Database Format Notes (version 4).
// (See below for version 5.)
//
// Integers are 4 bytes stored in big endian format, except for the
// volume length. The volume length is 8 bytes, but is stored in a
// little endian byte order (reason unknown).
// The 'standard' packing for strings in Blast DBs is as follows:
// 0..4: length
// 4..4+length: string data
//
// The title string follows this rule, but the create date has an
// additional detail; if it does not end on an offset that is a
// multiple of 8 bytes, extra 'NUL' characters are added to bring it
// to a multiple of 8 bytes. The NUL characters are added after the
// string bytes, and the stored length of the string is increased to
// include them. After extracting the string, 0-7 NUL bytes will need
// to be stripped from the end of the string (if any are found).
//
// (If this were not done, the offsets in the file would be unaligned;
// on some architectures this could cause a performance penalty or
// other problems. On little endian architectures such as Intel, this
// penalty is always paid.)
// INDEX FILE FORMAT, for "Blast DB Version 4"
//
// 0..4: format version (Blast DB version, current is "4").
// 4..8: seqtype (1 for protein or 0 for nucleotide).
// 8..N1: title (string).
// N1..N2: create date (string).
// N2..N2+4: number of OIDs (#OIDS).
// N2+4..N2+12: number of letters in volume. (note: 8 bytes)
// N2+12..N2+16: maxlength (size of longest sequence in DB)
//
// N2+16..(end): Array data
//
// Array data is 2 or 3 arrays of (#OIDS + 1) four byte integers.
// For protein, 2 arrays are used; for nucleotide, 3 are used.
//
// The first array is header offsets, the second array is sequence
// offsets, and the third (optional) array is offsets of ambiguity
// data. Each array has a final element which is the length of the
// file; this makes it possible to compute the last sequence's length
// without adding a special case.
//
// As shown, the total size of index header =
// 4*4 bytes // 4 int fields (4 bytes each)
// + 8 bytes // 8 byte field
// + 2*4 + strings // 4 bytes length for each plus string data.
// = (32 + strings), rounded up to nearest multiple of 8
//
// "strings" here refers to the unterminated length of both strings.
// Blast Database Format Notes (version 5).
// (See above for version 4.)
//
// Integers are 4 bytes stored in big endian format, except for the
// volume length. The volume length is 8 bytes, but is stored in a
// little endian byte order (reason unknown).
// The 'standard' packing for strings in Blast DBs is as follows:
// 0..4: length
// 4..4+length: string data
//
// The title string and LMDB string follow this rule, but the create
// date has an additional detail; if it does not end on an offset that
// is a multiple of 8 bytes, extra 'NUL' characters are added to bring
// it to a multiple of 8 bytes. The NUL characters are added after the
// string bytes, and the stored length of the string is increased to
// include them. After extracting the string, 0-7 NUL bytes will need
// to be stripped from the end of the string (if any are found).
//
// (If this were not done, the offsets in the file would be unaligned;
// on some architectures this could cause a performance penalty or
// other problems. On little endian architectures such as Intel, this
// penalty is always paid.)
// --------------------------------------------
// INDEX FILE FORMAT, for "Blast DB Version 5"
//
// 0..4: format version (Blast DB version, current is "5").
// 4..8: seqtype (1 for protein or 0 for nucleotide).
// 8..12: this volume number (0 and up).
// 12..N1: title (string).
// N1..N2: name of LMDB database file (string)
// N2..N3: create date (string).
// N3..N3+4: number of OIDs (#OIDS).
// N3+4..N3+12: number of letters in volume. (note: 8 bytes)
// N3+12..N3+16: maxlength (size of longest sequence in DB)
//
// N3+16..(end): Array data
//
// Array data is 2 or 3 arrays of (#OIDS + 1) four byte integers.
// For protein, 2 arrays are used; for nucleotide, 3 are used.
//
// The first array is header offsets, the second array is sequence
// offsets, and the third (optional) array is offsets of ambiguity
// data. Each array has a final element which is the length of the
// file; this makes it possible to compute the last sequence's length
// without adding a special case.
//
// As shown, the total size of index header =
// 5*4 bytes // 5 int fields (4 bytes each)
// + 8 bytes // 8 byte field
// + 3*4 + strings // 4 bytes length for each plus string data.
// = (40 + strings), rounded up to nearest multiple of 8
//
// "strings" here refers to the unterminated length of both strings.
CWriteDB_File::CWriteDB_File(const string & basename,
const string & extension,
int index,
Uint8 max_file_size,
bool always_create)
: m_Created (false),
m_BaseName (basename),
m_Extension (extension),
m_Index (index),
m_Offset (0),
m_MaxFileSize(max_file_size)
{
// Define number of usable bits in m_Offset,
// deducting one for the sign bit.
// Define maximum allowed max_file_size.
#ifdef _DEBUG
static const int MAX_OFFSET_BITS = (sizeof m_Offset * 8);
static const Uint8 MAX_FILE_SIZE = ((Uint8) 1 << MAX_OFFSET_BITS);
#endif
if (m_MaxFileSize == 0) {
m_MaxFileSize = x_DefaultByteLimit();
} else {
#ifdef _DEBUG
_ASSERT(max_file_size <= MAX_FILE_SIZE);
#endif
}
m_Nul.resize(1);
m_Nul[0] = (char) 0;
m_UseIndex = (index >= 0);
x_MakeFileName();
if (always_create) {
Create();
}
}
void CWriteDB_File::Create()
{
_ASSERT(! m_Created);
m_Created = true;
m_RealFile.open(m_Fname.c_str(), ios::out | ios::binary);
}
unsigned int CWriteDB_File::Write(const CTempString & data)
{
// Define maximum allowed max_file_size.
#ifdef _DEBUG
// Define number of usable bits in m_Offset,
// deducting one for the sign bit.
static const int MAX_OFFSET_BITS = (sizeof m_Offset * 8);
static const Uint8 MAX_OFFSET = ((Uint8) 1 << MAX_OFFSET_BITS);
#endif
_ASSERT(m_Created);
#ifdef _DEBUG
_ASSERT(((Uint8) m_Offset + data.length()) <= MAX_OFFSET);
#endif
m_RealFile.write(data.data(), data.length());
m_Offset += data.length();
return m_Offset;
}
string CWriteDB_File::MakeShortName(const string & base, int index)
{
ostringstream fns;
fns << base;
fns << ".";
fns << (index / 10);
fns << (index % 10);
return fns.str();
}
void CWriteDB_File::x_MakeFileName()
{
if (m_UseIndex) {
m_Fname = MakeShortName(m_BaseName, m_Index);
} else {
m_Fname = m_BaseName;
}
m_Fname += ".";
m_Fname += m_Extension;
}
void CWriteDB_File::Close()
{
x_Flush();
if (m_Created) {
m_RealFile.close();
}
}
void CWriteDB_File::RenameSingle()
{
_ASSERT(m_UseIndex == true);
string nm1 = m_Fname;
m_UseIndex = false;
x_MakeFileName();
CDirEntry fn1(nm1);
fn1.Rename(m_Fname, CDirEntry::fRF_Overwrite);
}
CWriteDB_IndexFile::CWriteDB_IndexFile(const string & dbname,
bool protein,
const string & title,
const string & date,
int index,
Uint8 max_file_size,
EBlastDbVersion dbver)
: CWriteDB_File(dbname,
protein ? "pin" : "nin",
index,
max_file_size,
true),
m_Protein (protein),
m_Title (title),
m_Date (date),
m_OIDs (0),
m_DataSize (0),
m_Letters (0),
m_MaxLength (0),
m_Version (dbver)
{
// Compute index overhead, rounding up.
m_Overhead = x_Overhead(title, date);
if (dbver == eBDB_Version5) {
m_Overhead = x_Overhead(title, x_MakeLmdbName(), date);
} else {
m_Overhead = x_Overhead(title, date);
}
m_Overhead = s_RoundUp(m_Overhead, 8);
m_DataSize = m_Overhead;
// The '1' added to the sequence offset array refers to the fact
// that sequence files contain an initial NUL byte. This seems to
// be for the benefit of the protein database scanning code, but
// it is also done for nucleotide databases.
m_Hdr.push_back(0);
m_Seq.push_back(1);
}
int CWriteDB_IndexFile::x_Overhead(const string & T,
const string & lmdbName,
const string & D)
{
return 5 * sizeof(int) + sizeof(long)
+ 3 * sizeof(int) + T.size() + lmdbName.size() + D.size();
}
int CWriteDB_IndexFile::x_Overhead(const string & T,
const string & D)
{
return 4 * sizeof(int) + sizeof(long)
+ 2 * sizeof(int) + T.size() + D.size();
}
void CWriteDB_IndexFile::x_Flush()
{
_ASSERT(m_Created);
bool use_lmdb = (m_Version == eBDB_Version5);
int format_version = (int) m_Version;
int seq_type = (m_Protein ? 1 : 0);
// Pad the date string (see comments at top.)
string pad_date = m_Date;
int count = 0;
const string lmdb_name = use_lmdb ? x_MakeLmdbName() : "";
int overhead = use_lmdb
? x_Overhead(m_Title, lmdb_name, pad_date)
: x_Overhead(m_Title, pad_date);
while (overhead & 0x7) {
pad_date.append(m_Nul);
if (count != -1) {
_ASSERT(count++ < 8);
}
overhead = use_lmdb
? x_Overhead(m_Title, lmdb_name, pad_date)
: x_Overhead(m_Title, pad_date);
}
// Write header
ostream & F = m_RealFile;
s_WriteInt4 (F, format_version);
s_WriteInt4 (F, seq_type);
if (!lmdb_name.empty()) {
s_WriteInt4 (F, m_Index);
s_WriteString(F, m_Title);
s_WriteString(F, lmdb_name);
} else {
s_WriteString(F, m_Title);
}
s_WriteString(F, pad_date);
s_WriteInt4 (F, m_OIDs);
s_WriteInt8LE(F, m_Letters);
s_WriteInt4 (F, m_MaxLength);
for(unsigned i = 0; i < m_Hdr.size(); i++) {
s_WriteInt4(F, m_Hdr[i]);
}
for(unsigned i = 0; i < m_Seq.size(); i++) {
s_WriteInt4(F, m_Seq[i]);
}
// Should loop m_OID times, or not at all.
for(unsigned i = 0; i < m_Amb.size(); i++) {
s_WriteInt4(F, m_Amb[i]);
}
// This extra index is added here because formatdb adds it. SeqDB
// depends on its existence, but I don't think anyone reads (or
// needs) the data. The last offset in the ambiguity column
// represents the position of the set of ambiguities corresponding
// to the last offset in the sequence column. But the last
// sequence offset is not really a sequence start, it is the
// 'extra' offset used by sequence length computations.
if (m_Amb.size()) {
s_WriteInt4(F, m_Seq.back());
}
vector<unsigned int> tmp1, tmp2, tmp3;
m_Hdr.swap(tmp1);
m_Seq.swap(tmp2);
m_Amb.swap(tmp3);
}
/// Form name of lmdb database file.
const string CWriteDB_IndexFile::x_MakeLmdbName()
{
string suffix = (m_Protein ? ".pdb" : ".ndb");
size_t last_slash = m_BaseName.find_last_of('/');
if (last_slash == m_BaseName.npos) {
return m_BaseName + suffix;
} else {
return m_BaseName.substr(last_slash + 1) + suffix;
}
}
CWriteDB_HeaderFile::CWriteDB_HeaderFile(const string & dbname,
bool protein,
int index,
Uint8 max_file_size)
: CWriteDB_File(dbname,
protein ? "phr" : "nhr",
index,
max_file_size,
true),
m_DataSize(0)
{
}
CWriteDB_SequenceFile::CWriteDB_SequenceFile(const string & dbname,
bool protein,
int index,
Uint8 max_file_size,
Uint8 max_letters)
: CWriteDB_File(dbname,
protein ? "psq" : "nsq",
index,
max_file_size,
true),
m_Letters (0),
#ifdef _DEBUG
m_BaseLimit(max_letters),
m_Protein (protein)
#else
m_BaseLimit(max_letters)
#endif
{
// Only protein sequences need the inter-sequence NUL bytes.
// The first null written here is for nucleotide sequences.
// It doesn't seem necessary, but formatdb provides it, so I
// will too.
WriteWithNull(string());
}
END_NCBI_SCOPE
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