// PdbFinderParser.cpp


#include <cctype>
#include <cstring>
#include "PdbFinderParser.hpp"


namespace NGBW {


// PdbFinderParser


bool PdbFinderParser::Parse(PdbFinderRecord &record)
{
	record.clear();

	while (1) {
		ReadNextLine();

		if (m_input.Eof())
			return false;

		if (std::memcmp(m_line, "ID ", 3) == 0) {
			ParseIdentity(record);

			break;
		}
	}

	while (1) {
		if (m_input.Eof())
			return false;

		if (std::memcmp(m_line, "Header ", 7) == 0)
			ParseHeader(record);
		else if (std::memcmp(m_line, "Source ", 7) == 0)
			ParseSource(record);
		else if (std::memcmp(m_line, "Chain ", 6) == 0)
			ParseChain(record);
		else if (FindEndToken())
			break;
		else
			ReadNextLine();
	}

	return true;
}

void PdbFinderParser::ParseIdentity(PdbFinderRecord &record)
{
	GetFieldValue(3, record.identity);

	ReadNextLine();
}

void PdbFinderParser::ParseHeader(PdbFinderRecord &record)
{
	GetFieldValue(7, record.description);

	ReadNextLine();
}

void PdbFinderParser::ParseSource(PdbFinderRecord &record)
{
	GetFieldValue(7, record.organism);

	while (1) {
		ReadNextLine();

		if (m_input.Eof() || std::memcmp(m_line, "Source ", 7) != 0)
			break;

		std::string value;

		GetFieldValue(7, value);

		record.organism.push_back(' ');
		record.organism.append(value);
	}
}

void PdbFinderParser::ParseChain(PdbFinderRecord &record)
{
	while (1) {
		PdbChain new_chain;

		GetFieldValue(6, new_chain.identity);

		if (new_chain.identity[0] != '_') {
			while (1) {
				ReadNextLine();

				if (m_input.Eof() || !std::isspace(m_line[0]))
					break;

				size_t first = FindFirstNotSpace(1);

				if (first == std::string::npos || std::memcmp(m_line + first, "Sequence ", 9) != 0)
					continue;

				GetFieldValue(first + 9, new_chain.sequence);
			}

			if (new_chain.sequence.length() > 0)
				record.chains.push_back(new_chain);
		}
		else
			ReadNextLine();

		if (m_input.Eof() || std::memcmp(m_line, "Chain ", 6) != 0)
			break;
	}
}

void PdbFinderParser::GetFieldValue(size_t offset, std::string &value)
{
	size_t first = FindFirstOf(':', offset);

	if (first == std::string::npos)
		return;

	first = FindFirstNotSpace(first + 1);

	size_t last = std::strlen(m_line);

	value.assign(m_line + first, last - first);
}

bool PdbFinderParser::FindEndToken()
{
	size_t first = FindFirstNotSpace();

	if (first == std::string::npos)
		return false;

	if (m_line[first] == '/' && m_line[first + 1] == '/')
		return true;

	return false;
}


} // namespace NGBW