// PdbSeqresParser.cpp


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


namespace NGBW {


// PdbSeqresParser


bool PdbSeqresParser::Parse(PdbSeqresRecord &record)
{
	record.clear();

	if (m_line == NULL)
		ReadNextLine();

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

		if (m_line[0] == '>') {
			ParseHeader(record);

			break;
		}

		ReadNextLine();
	}

	while (1) {
		if (m_input.Eof() || m_line[0] == '>')
			break;

		record.sequence.append(m_line);

		ReadNextLine();
	}

	return true;
}

void PdbSeqresParser::ParseHeader(PdbSeqresRecord &record)
{
	size_t length = std::strlen(m_line);
	size_t last = FindFirstSpace(1);

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

	size_t index = 1;

	while (index < last) {
		record.protein_id.push_back(std::toupper(m_line[index]));

		index += 1;

		if (m_line[index] == '_') {
			index += 1;

			break;
		}
	}

	while (index < last) {
		record.chain_id.push_back(m_line[index]);

		index += 1;
	}

	if (last < length) {
		const char *sub_string = std::strstr(m_line + last, "length:");

		if (sub_string != NULL) {
			size_t first = (sub_string - m_line) + 7;

			last = FindFirstSpace(first + 1);

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

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

	ReadNextLine();
}


} // namespace NGBW