// UniprotParser.cpp


#include <string>
#include <cctype>
#include <cstring>
#include "UniprotParser.hpp"


namespace NGBW {


// UniprotParser


bool UniprotParser::Parse(FastaRecord &record)
{
	record.clear();

	while (1) {
		ReadNextLine();

		if (m_input.Eof())
			return false;

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

			break;
		}
	}

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

		if (std::memcmp(m_line, "AC ", 3) == 0) {
			ParseAccession(record);

			break;
		}

		ReadNextLine();
	}

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

		if (std::memcmp(m_line, "DE ", 3) == 0) {
			ParseDescription(record);

			break;
		}

		ReadNextLine();
	}

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

		if (std::memcmp(m_line, "OS ", 3) == 0) {
			ParseOrganism(record);

			break;
		}

		ReadNextLine();
	}

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

		if (std::memcmp(m_line, "SQ ", 3) == 0) {
			ParseSequence(record);

			break;
		}

		ReadNextLine();
	}

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

		if (FindEndToken())
			break;

		ReadNextLine();
	}

	return true;
}

void UniprotParser::ParseAccession(FastaRecord &record)
{
	size_t first = FindFirstNotSpace(3);

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

	size_t last = FindFirstOf(';', first + 1);

	if (last == std::string::npos)
		last = std::strlen(m_line);

	record.identity.assign(m_line + first, last - first);

	ReadNextLine();
}

void UniprotParser::ParseDescription(FastaRecord &record)
{
	size_t first = FindFirstNotSpace(3);

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

	size_t last;

	if (std::memcmp(m_line + first, "RecName:", 8) == 0) {
		first = FindFirstOf('=', first + 8) + 1;
		last = FindFirstOf(';', first);

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

	while (1) {
		ReadNextLine();

		if (m_input.Eof() || std::memcmp(m_line, "DE ", 3) != 0)
			break;

		first = FindFirstNotSpace(3);

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

		if (std::memcmp(m_line + first, "Flags:", 6) == 0) {
			first = FindFirstNotSpace(first + 6);
			last = FindFirstOf(';', first);

			record.description.push_back(' ');
			record.description.append(m_line + first, last - first);
		}
	}
}

void UniprotParser::ParseOrganism(FastaRecord &record)
{
	size_t first = FindFirstNotSpace(3);

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

	size_t last = std::strlen(m_line);

	record.organism.assign(m_line + first, last - first);

	ReadNextLine();
}

void UniprotParser::ParseSequence(FastaRecord &record)
{
	while (1) {
		ReadNextLine();

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

		size_t first = FindFirstNotSpace(1);

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

		size_t last = first - 1;
		size_t length = std::strlen(m_line);

		while (1) {
			first = FindFirstNotSpace(last + 1);
			last = FindFirstSpace(first + 1);

			if (last == std::string::npos)
				last = length;

			record.sequence.append(m_line + first, last - first);

			if (last == length)
				break;
		}
	}
}

bool UniprotParser::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