/////////////////////////////////////////////////////////////////
// Sequence.h
//
// Class for reading/manipulating single sequence character data.
/////////////////////////////////////////////////////////////////

#ifndef SEQUENCE_H
#define SEQUENCE_H

#include <string>
#include <fstream>
#include <iostream>
#include <cctype>
#include <cstdlib>
#include "SafeVector.h"
#include "FileBuffer.h"

/////////////////////////////////////////////////////////////////
// Sequence
//
// Class for storing sequence information.
/////////////////////////////////////////////////////////////////

class Sequence {

	bool isValid; // a boolean indicating whether the sequence data is valid or not
	string header;       // string containing the comment line of the FASTA file
	SafeVector<char> *data;      // pointer to character data
	int length;                  // length of the sequence
	int sequenceLabel; // integer sequence label, typically to indicate the ordering of sequences
					   //   in a Multi-FASTA file
	int inputLabel;              // position of sequence in original input

	/////////////////////////////////////////////////////////////////
	// Sequence::Sequence()
	//
	// Default constructor.  Does nothing.
	/////////////////////////////////////////////////////////////////

	Sequence() :
			isValid(false), header(""), data(NULL), length(0), sequenceLabel(0), inputLabel(
					0) {
	}

public:

	/////////////////////////////////////////////////////////////////
	// Sequence::Sequence()
	//
	// Constructor.  Reads the sequence from a FileBuffer.
	/////////////////////////////////////////////////////////////////

	Sequence(FileBuffer &infile, bool stripGaps = false) :
			isValid(false), header("~"), data(NULL), length(0), sequenceLabel(
					0), inputLabel(0) {

		// read until the first non-blank line
		while (!infile.eof()) {
			infile.GetLine(header);
			if (header.length() != 0)
				break;
		}

		// check to make sure that it is a correct header line
		if (header[0] == '>') {

			// if so, remove the leading ">"
			header = header.substr(1);

			// remove any leading or trailing white space in the header comment
			while (header.length() > 0 && isspace(header[0]))
				header = header.substr(1);
			while (header.length() > 0 && isspace(header[header.length() - 1]))
				header = header.substr(0, header.length() - 1);

			// get ready to read the data[] array; note that data[0] is always '@'
			char ch;
			data = new SafeVector<char>;
			assert(data);
			data->push_back('@');

			// get a character from the file
			while (infile.Get(ch)) {

				// if we've reached a new comment line, put the character back and stop
				if (ch == '>') {
					infile.UnGet();
					break;
				}

				// skip whitespace
				if (isspace(ch))
					continue;

				// substitute gap character
				if (ch == '.')
					ch = '-';
				if (stripGaps && ch == '-')
					continue;

				// check for known characters
				if (!((ch >= 'A' && ch <= 'Z') || (ch >= 'a' && ch <= 'z'))) {
					cerr << "ERROR: Unknown character encountered: " << ch
							<< endl;
					exit(1);
				}

				// everything's ok so far, so just store this character.
				if (ch >= 'a' && ch <= 'z') {
					ch = ch - 'a' + 'A';
				}	//change to upper case. fixed by Liu Yongchao, May 21, 2010

				data->push_back(ch);
				++length;
			}

			// sequence must contain data in order to be valid
			isValid = length > 0;
			if (!isValid) {
				delete data;
				data = NULL;
			}
		}
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::Sequence()
	//
	// Constructor.  Builds a sequence from existing data.  Note
	// that the data must use one-based indexing where data[0] should
	// be set to '@'.
	/////////////////////////////////////////////////////////////////

	Sequence(SafeVector<char> *data, string header, int length,
			int sequenceLabel, int inputLabel) :
			isValid(data != NULL), header(header), data(data), length(length), sequenceLabel(
					sequenceLabel), inputLabel(inputLabel) {
		assert(data);
		assert((*data)[0] == '@');
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::Sequence()
	//
	// Destructor.  Release allocated memory.
	/////////////////////////////////////////////////////////////////

	~Sequence() {
		if (data) {
			assert(isValid);
			delete data;
			data = NULL;
			isValid = false;
		}
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::GetHeader()
	//
	// Return the string comment associated with this sequence.
	/////////////////////////////////////////////////////////////////

	string GetHeader() const {
		return header;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::GetName()
	//
	// Return the first word of the string comment associated with this sequence.
	/////////////////////////////////////////////////////////////////

	string GetName() const {
		char name[1024];
		sscanf(header.c_str(), "%s", name);
		return string(name);
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::GetDataPtr()
	//
	// Return the iterator to data associated with this sequence.
	/////////////////////////////////////////////////////////////////

	SafeVector<char>::iterator GetDataPtr() {
		assert(isValid);
		assert(data);
		return data->begin();
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::GetPosition()
	//
	// Return the character at position i.  Recall that the character
	// data is stored with one-based indexing.
	/////////////////////////////////////////////////////////////////

	char GetPosition(int i) const {
		assert(isValid);
		assert(data);
		assert(i >= 1 && i <= length);
		return (*data)[i];
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::SetLabel()
	//
	// Sets the sequence label to i.
	/////////////////////////////////////////////////////////////////

	void SetLabel(int i) {
		assert(isValid);
		sequenceLabel = i;
		inputLabel = i;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::SetSortLabel()
	//
	// Sets the sequence sorting label to i.
	/////////////////////////////////////////////////////////////////

	void SetSortLabel(int i) {
		assert(isValid);
		sequenceLabel = i;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::GetLabel()
	//
	// Retrieves the input label.
	/////////////////////////////////////////////////////////////////

	int GetLabel() const {
		assert(isValid);
		return inputLabel;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::GetSortLabel()
	//
	// Retrieves the sorting label.
	/////////////////////////////////////////////////////////////////

	int GetSortLabel() const {
		assert(isValid);
		return sequenceLabel;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::Fail()
	//
	// Checks to see if the sequence successfully loaded.
	/////////////////////////////////////////////////////////////////

	bool Fail() const {
		return !isValid;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::Length()
	//
	// Returns the length of the sequence.
	/////////////////////////////////////////////////////////////////

	int GetLength() const {
		assert(isValid);
		assert(data);
		return length;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::WriteMFA()
	//
	// Writes the sequence to outfile in MFA format.  Uses numColumns
	// columns per line.  If useIndex is set to false, then the
	// header is printed as normal, but if useIndex is true, then
	// ">S###" is printed where ### represents the sequence label.
	/////////////////////////////////////////////////////////////////

	void WriteMFA(ostream &outfile, int numColumns,
			bool useIndex = false) const {
		assert(isValid);
		assert(data);
		assert(!outfile.fail());

		// print out heading
		if (useIndex)
			outfile << ">S" << GetLabel() << endl;
		else
			outfile << ">" << header << endl;

		// print out character data
		int ct = 1;
		for (; ct <= length; ct++) {
			outfile << (*data)[ct];
			if (ct % numColumns == 0)
				outfile << endl;
		}
		if ((ct - 1) % numColumns != 0)
			outfile << endl;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::Clone()
	//
	// Returns a new deep copy of the seqeuence.
	/////////////////////////////////////////////////////////////////

	Sequence *Clone() const {
		Sequence *ret = new Sequence();
		assert(ret);

		ret->isValid = isValid;
		ret->header = header;
		ret->data = new SafeVector<char>;
		assert(ret->data);
		*(ret->data) = *data;
		ret->length = length;
		ret->sequenceLabel = sequenceLabel;
		ret->inputLabel = inputLabel;

		return ret;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::GetRange()
	//
	// Returns a new sequence object consisting of a range of
	// characters from the current seuquence.
	/////////////////////////////////////////////////////////////////

	Sequence *GetRange(int start, int end) const {
		Sequence *ret = new Sequence();
		assert(ret);

		assert(start >= 1 && start <= length);
		assert(end >= 1 && end <= length);
		assert(start <= end);

		ret->isValid = isValid;
		ret->header = header;
		ret->data = new SafeVector<char>;
		assert(ret->data);
		ret->data->push_back('@');
		for (int i = start; i <= end; i++)
			ret->data->push_back((*data)[i]);
		ret->length = end - start + 1;
		ret->sequenceLabel = sequenceLabel;
		ret->inputLabel = inputLabel;

		return ret;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::AddGaps()
	//
	// Given an SafeVector<char> containing the skeleton for an
	// alignment and the identity of the current character, this
	// routine will create a new sequence with all necesssary gaps added.
	// For instance,
	//    alignment = "XXXBBYYYBBYYXX"
	//    id = 'X'
	// will perform the transformation
	//    "ATGCAGTCA" --> "ATGCC---GT--CA"
	//                    (XXXBBYYYBBYYXX)
	/////////////////////////////////////////////////////////////////

	Sequence *AddGaps(SafeVector<char> *alignment, char id) {
		Sequence *ret = new Sequence();
		assert(ret);

		ret->isValid = isValid;
		ret->header = header;
		ret->data = new SafeVector<char>;
		assert(ret->data);
		ret->length = (int) alignment->size();
		ret->sequenceLabel = sequenceLabel;
		ret->inputLabel = inputLabel;
		ret->data->push_back('@');

		SafeVector<char>::iterator dataIter = data->begin() + 1;
		for (SafeVector<char>::iterator iter = alignment->begin();
				iter != alignment->end(); ++iter) {
			if (*iter == 'B' || *iter == id) {
				ret->data->push_back(*dataIter);
				++dataIter;
			} else
				ret->data->push_back('-');
		}

		return ret;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::GetString()
	//
	// Returns the sequence as a string with gaps removed.
	/////////////////////////////////////////////////////////////////

	string GetString() {
		string s = "";
		for (int i = 1; i <= length; i++) {
			if ((*data)[i] != '-')
				s += (*data)[i];
		}
		return s;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::GetMapping()
	//
	// Returns a SafeVector<int> containing the indices of every
	// character in the sequence.  For instance, if the data is
	// "ATGCC---GT--CA", the method returns {1,2,3,4,5,9,10,13,14}.
	/////////////////////////////////////////////////////////////////

	SafeVector<int> *GetMapping() const {
		SafeVector<int> *ret = new SafeVector<int>(1, 0);
		for (int i = 1; i <= length; i++) {
			if ((*data)[i] != '-')
				ret->push_back(i);
		}
		return ret;
	}

	/////////////////////////////////////////////////////////////////
	// Sequence::Highlight()
	//
	// Changes all positions with score >= cutoff to upper case and
	// all positions with score < cutoff to lower case.
	/////////////////////////////////////////////////////////////////

	void Highlight(const SafeVector<float> &scores, const float cutoff) {
		for (int i = 1; i <= length; i++) {
			if (scores[i - 1] >= cutoff)
				(*data)[i] = toupper((*data)[i]);
			else
				(*data)[i] = tolower((*data)[i]);
		}
	}
};

#endif