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#ifndef __COMMAND_H__
#define __COMMAND_H__
int AddString (char ***list, int len, char *token);
BitsLong Expecting (int y);
int CheckString (char **list, int len, char *token, int *matchIndex);
int CheckStringValidity (char *s);
int DoExecute (void);
int FreeMatrix (void);
int GetToken (char *token, int *tokenType, char **sourceH);
int FindValidCommand (char *tk, int *numMatches);
int IsArgValid (char *s, char *validArg);
int IsIn (char ch, char *s);
int IsSame (char *s1, char *s2);
int IsWhite (char c);
int ParseCommand (char *s);
void ResetCharacterFlags (void);
void ResetTaxaFlags (void);
int RootUserTree (TreeNode *p);
void SetUpParms (void);
void ShowNodes (TreeNode *p, int indent, int isThisTreeRooted);
int ShowTree (Tree *t);
void State_CODON (char *state, int code, int division);
void State_DOUBLET (char *state, int code);
int StateCode_AA (int n);
int StateCode_NUC4 (int n);
int StateCode_Std (int n);
char WhichAA (int x);
char WhichNuc (int x);
char WhichRes (int x);
char WhichStand (int x);
#endif /* __COMMAND_H__ */
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