4 int AddString (char ***list, int len, char *token);
5 BitsLong Expecting (int y);
6 int CheckString (char **list, int len, char *token, int *matchIndex);
7 int CheckStringValidity (char *s);
10 int GetToken (char *token, int *tokenType, char **sourceH);
11 int FindValidCommand (char *tk, int *numMatches);
12 int IsArgValid (char *s, char *validArg);
13 int IsIn (char ch, char *s);
14 int IsSame (char *s1, char *s2);
16 int ParseCommand (char *s);
17 void ResetCharacterFlags (void);
18 void ResetTaxaFlags (void);
19 int RootUserTree (TreeNode *p);
20 void SetUpParms (void);
21 void ShowNodes (TreeNode *p, int indent, int isThisTreeRooted);
22 int ShowTree (Tree *t);
23 void State_CODON (char *state, int code, int division);
24 void State_DOUBLET (char *state, int code);
25 int StateCode_AA (int n);
26 int StateCode_NUC4 (int n);
27 int StateCode_Std (int n);
29 char WhichNuc (int x);
30 char WhichRes (int x);
31 char WhichStand (int x);
33 #endif /* __COMMAND_H__ */