4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
7 * Mark Larkin 12 Dec 2005.
8 * Interactive menu class. It uses the object userParameters for
9 * all the session variables.
11 #ifndef INTERACTIVEMENU_H
12 #define INTERACTIVEMENU_H
15 #include "../Clustal.h"
16 #include "../general/clustalw.h"
17 #include "../general/userparams.h"
18 #include "../general/utils.h"
19 #include "../substitutionMatrix/globalmatrix.h"
39 void multipleAlignMenu();
40 void profileAlignMenu();
42 int secStrOutputOptions();
43 void phylogeneticTreeMenu();
44 void treeFormatOptionsMenu();
45 void formatOptionsMenu();
48 void gapPenaltiesMenu();
49 int readMatrix(int alignResidueType, int alignType, MatMenu menu);
50 void clusteringAlgorithmMenu();
62 string secStructOutputTxt[4]; // Changed to a string array
64 MatMenu dnaMatrixMenu;