Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / interface / InteractiveMenu.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/interface/InteractiveMenu.h b/website/archive/binaries/mac/src/clustalw/src/interface/InteractiveMenu.h
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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
+