Program Listing for File parser.hpp
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/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#pragma once
#include "cif++/row.hpp"
#include <map>
namespace cif
{
// --------------------------------------------------------------------
class parse_error : public std::runtime_error
{
public:
parse_error(uint32_t line_nr, const std::string &message)
: std::runtime_error("parse error at line " + std::to_string(line_nr) + ": " + message)
{
}
};
// --------------------------------------------------------------------
// TODO: Need to implement support for transformed long lines
class sac_parser
{
public:
using datablock_index = std::map<std::string, std::size_t>;
virtual ~sac_parser() = default;
enum CharTraitsMask : uint8_t
{
kOrdinaryMask = 1 << 0,
kNonBlankMask = 1 << 1,
kTextLeadMask = 1 << 2,
kAnyPrintMask = 1 << 3
};
static constexpr bool is_space(int ch)
{
return ch == ' ' or ch == '\t' or ch == '\r' or ch == '\n';
}
static constexpr bool is_white(int ch)
{
return is_space(ch) or ch == '#';
}
static constexpr bool is_ordinary(int ch)
{
return ch >= 0x20 and ch <= 0x7f and (kCharTraitsTable[ch - 0x20] & kOrdinaryMask) != 0;
}
static constexpr bool is_non_blank(int ch)
{
return ch > 0x20 and ch <= 0x7f and (kCharTraitsTable[ch - 0x20] & kNonBlankMask) != 0;
}
static constexpr bool is_text_lead(int ch)
{
return ch >= 0x20 and ch <= 0x7f and (kCharTraitsTable[ch - 0x20] & kTextLeadMask) != 0;
}
static constexpr bool is_any_print(int ch)
{
return ch == '\t' or
(ch >= 0x20 and ch <= 0x7f and (kCharTraitsTable[ch - 0x20] & kAnyPrintMask) != 0);
}
static bool is_unquoted_string(std::string_view text);
protected:
static constexpr uint8_t kCharTraitsTable[128] = {
// 0 1 2 3 4 5 6 7 8 9 a b c d e f
14, 15, 14, 14, 14, 15, 15, 14, 15, 15, 15, 15, 15, 15, 15, 15, // 2
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 15, 15, 15, 15, // 3
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, // 4
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 15, 14, 15, 14, // 5
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, // 6
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 0, // 7
};
enum class CIFToken
{
Unknown,
Eof,
DATA,
LOOP,
GLOBAL,
SAVE_,
SAVE_NAME,
STOP,
Tag,
Value
};
static constexpr const char *get_token_name(CIFToken token)
{
switch (token)
{
case CIFToken::Unknown: return "Unknown";
case CIFToken::Eof: return "Eof";
case CIFToken::DATA: return "DATA";
case CIFToken::LOOP: return "LOOP";
case CIFToken::GLOBAL: return "GLOBAL";
case CIFToken::SAVE_: return "SAVE";
case CIFToken::SAVE_NAME: return "SAVE+name";
case CIFToken::STOP: return "STOP";
case CIFToken::Tag: return "Tag";
case CIFToken::Value: return "Value";
default: return "Invalid token parameter";
}
}
// get_next_char takes the next character from the istream.
// This function also does carriage/linefeed translation.
int get_next_char();
// Put the last read character back into the istream
void retract();
CIFToken get_next_token();
void match(CIFToken token);
public:
bool parse_single_datablock(const std::string &datablock);
datablock_index index_datablocks();
bool parse_single_datablock(const std::string &datablock, const datablock_index &index);
void parse_file();
protected:
sac_parser(std::istream &is, bool init = true);
void parse_global();
void parse_datablock();
virtual void parse_save_frame();
void error(const std::string &msg)
{
if (cif::VERBOSE > 0)
std::cerr << "Error parsing mmCIF: " << msg << '\n';
throw parse_error(m_line_nr, msg);
}
void warning(const std::string &msg)
{
if (cif::VERBOSE > 0)
std::cerr << "parser warning at line " << m_line_nr << ": " << msg << '\n';
}
// production methods, these are pure virtual here
virtual void produce_datablock(std::string_view name) = 0;
virtual void produce_category(std::string_view name) = 0;
virtual void produce_row() = 0;
virtual void produce_item(std::string_view category, std::string_view item, std::string_view value) = 0;
protected:
enum class State
{
Start,
White,
Esc,
Comment,
QuestionMark,
Dot,
QuotedString,
QuotedStringQuote,
UnquotedString,
Tag,
TextField,
TextFieldNL,
Reserved,
Value
};
std::streambuf &m_source;
// Parser state
uint32_t m_line_nr;
bool m_bol;
CIFToken m_lookahead;
// token buffer
std::vector<char> m_token_buffer;
std::string_view m_token_value;
};
// --------------------------------------------------------------------
class parser : public sac_parser
{
public:
parser(std::istream &is, file &file)
: sac_parser(is)
, m_file(file)
{
}
void produce_datablock(std::string_view name) override;
void produce_category(std::string_view name) override;
void produce_row() override;
void produce_item(std::string_view category, std::string_view item, std::string_view value) override;
protected:
file &m_file;
datablock *m_datablock = nullptr;
category *m_category = nullptr;
row_handle m_row;
};
} // namespace cif