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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
/**
* Mark Larkin 12 Dec 2005.
* Interactive menu class. It uses the object userParameters for
* all the session variables.
*/
#ifndef INTERACTIVEMENU_H
#define INTERACTIVEMENU_H
#include <string>
#include "../Clustal.h"
#include "../general/clustalw.h"
#include "../general/userparams.h"
#include "../general/utils.h"
#include "../substitutionMatrix/globalmatrix.h"
namespace clustalw
{
using namespace std;
class InteractiveMenu
{
public:
/* Functions */
InteractiveMenu();
~InteractiveMenu();
void mainMenu();
/* Attributes */
private:
/* Functions */
void doSystem();
void multipleAlignMenu();
void profileAlignMenu();
void ssOptionsMenu();
int secStrOutputOptions();
void phylogeneticTreeMenu();
void treeFormatOptionsMenu();
void formatOptionsMenu();
void pairwiseMenu();
void multiMenu();
void gapPenaltiesMenu();
int readMatrix(int alignResidueType, int alignType, MatMenu menu);
void clusteringAlgorithmMenu();
void iterationMenu();
/* Attributes */
Clustal* clustalObj;
string phylipName;
string clustalName;
string distName;
string nexusName;
//string fasta_name;
string p1TreeName;
string p2TreeName;
string secStructOutputTxt[4]; // Changed to a string array
string lin1;
MatMenu dnaMatrixMenu;
MatMenu matrixMenu;
MatMenu pwMatrixMenu;
char choice;
};
}
#endif
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