// PdbFinderWriter.cpp


#if defined(_WIN32) || defined(_WIN64)

// C4290 - the compiler ignores exception specifications
#pragma warning(disable: 4290)

#endif


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


namespace NGBW {


// PdbFinderWriter


void PdbFinderWriter::Write(const SeqresMap &sequences) throw(std::ios_base::failure)
{
	while (1) {
		while (1) {
			ReadNextLine();

			if (m_input.Eof())
				return;

			if (std::memcmp(m_line, "ID ", 3) == 0)
				break;
		}

		std::string protein_id;

		GetFieldValue(3, protein_id);

		for (std::string::iterator i = protein_id.begin() ; i != protein_id.end() ; i++)
			*i = std::toupper(*i);

		SeqresMap::const_iterator entry(sequences.find(protein_id));

		if (entry == sequences.end())
			continue;

		const ChainSet &chains = (*entry).second;

		m_output << m_line;

		m_output.put('\n');

		ReadNextLine();

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

			m_output << m_line;

			m_output.put('\n');

			if (std::memcmp(m_line, "Chain ", 6) == 0)
				ParseChain(chains);
			else if (FindEndToken())
				break;
			else
				ReadNextLine();
		}
	}
}

void PdbFinderWriter::ParseChain(const ChainSet &chains)
{
	std::string chain_id;

	GetFieldValue(6, chain_id);

	PdbSeqresRecord key;

	key.chain_id.assign(chain_id);

	ChainSet::const_iterator entry(chains.find(key));

	if (entry == chains.end()) {
		ReadNextLine();

		return;
	}

	const PdbSeqresRecord &record = *entry;

	while (1) {
		ReadNextLine();

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

		size_t first = FindFirstNotSpace(1);

		if (first == std::string::npos) {
			m_output.put('\n');

			continue;
		}

		if (std::memcmp(m_line + first, "Sequence ", 9) == 0) {
			size_t last = FindFirstOf(':');

			m_output.write(m_line, last + 1);
			m_output.put(' ');

			m_output << record.sequence;

			m_output.put('\n');
		}
		else if (std::strstr(m_line + first, "-Acids") != NULL) {
			size_t last = FindFirstOf(':');

			m_output.write(m_line, last + 1);
			m_output.put(' ');

			m_output << record.length;

			m_output.put('\n');
		}
		else {
			m_output << m_line;

			m_output.put('\n');
		}
	}
}

void PdbFinderWriter::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 PdbFinderWriter::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