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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
/*
* The class AlignmentOutput is used to output the Alignment in all the different
* formats that have been selected. It will output all the different file types if
* these have been selected from the menu or the commandline.
* To use this class we must call openAlignmentOutput first. Then we call the function
* createAlignmentOutput with an Alignment to be output and the first and last sequence
* to be output as well.
*/
#ifndef ALIGNMENTOUTPUT_H
#define ALIGNMENTOUTPUT_H
#include <string>
#include <vector>
#include <fstream>
#include <memory>
#include <sstream>
#include <exception>
#include <cassert>
#include "Alignment.h"
namespace clustalw
{
typedef struct rangeNum
{
int start;
int end;
} rangeNum;
typedef struct outputRegion
{
int _firstSeq;
int _lastSeq;
int _firstRes;
int _lastRes;
} outputRegion;
class AlignmentOutput
{
public:
/* Functions */
AlignmentOutput();
bool openAlignmentOutput(string path);
bool QTOpenFilesForOutput(AlignmentFileNames fileNames);
void createAlignmentOutput(Alignment* alignPtr, int firstSeq, int lastSeq);
void printSecStructMask(int prfLength, vector<char>* mask, vector<char>* structMask);
/* Attributes */
private:
/* Functions */
void fastaOut(Alignment* alignPtr, outputRegion partToOutput);
void clustalOut(Alignment* alignPtr, outputRegion partToOutput);
void gcgOut(Alignment* alignPtr, outputRegion partToOutput);
void nexusOut(Alignment* alignPtr, outputRegion partToOutput);
void phylipOut(Alignment* alignPtr, outputRegion partToOutput);
void nbrfOut(Alignment* alignPtr, outputRegion partToOutput);
void gdeOut(Alignment* alignPtr, outputRegion partToOutput);
string nameonly(string s);
void findRangeValues(Alignment* alignPtr, rangeNum *rnum, int firstRes, int lastRes,
int firstSeq);
bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
string fileExtension);
int SeqGCGCheckSum(vector<char>* sequence, int length);
void showAlign();
/* Attributes */
auto_ptr<ofstream> clustalOutFile;
auto_ptr<ofstream> gcgOutFile;
auto_ptr<ofstream> nbrfOutFile;
auto_ptr<ofstream> phylipOutFile;
auto_ptr<ofstream> gdeOutFile;
auto_ptr<ofstream> nexusOutFile;
auto_ptr<ofstream> fastaOutFile;
string clustalOutName;
string gcgOutName;
string phylipOutName;
string nbrfOutName;
string gdeOutName;
string nexusOutName;
string fastaOutName;
vector<string> strongGroup;
vector<string> weakGroup;
int clusSecStructOffset;
int clusSequenceOffset;
};
}
#endif
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