#define NUMBER_METHODS 7
#define NUMBER_PREPROCESSORS 5
#define MAX_ALGOR_NUMBER 32
#define USABLE_ALGOR_NUMBER 32   /* MAX_TABLE_NUMBER*8  where 8 is from      */
                                 /* 4 methods with 2 possible "offset types" */
/*#define USABLE_ALGOR_NUMBER 8 */  /* 4 methods with 2 possible "offset types" */


#define LENGTH_OF_COIL 0   /** For the dimer-trimer likelihood algorithm. */
#define ONCE_PER_COIL 1

    /*  Currently: DimerTrimerSingle, DimerTrimerPair,
                   TableDiffSingle where score coil once
                   TableDiffSingle where score coil length coil times
                   TableDiffPair where score coil once
                   TableDiffPair where score coil lenth coil times for like. */

/** Think of Single=0, Once=0, Length=1, Pair=2 and just add up.... **/
/*
enum {TableDiffSingleOnce, TableDiffSingleLength,
	TableDiffPairOnce, TableDiffPairLength,
	DTSingleLike, DTPairLike};
*/

enum {TDRes, TDCoil};     /*  For computing which number likelihood line to 
			         use in TableDiff method. */
                          /* The algorithm line number is 2*TD? + pairs. */

enum {MultiCoil, PairCoil, NEWCOILS, HMMCoil, ActualCoil, 
	/** TableDiffRes, TableDiffCoil, **/
	PairCoilDiff, PairCoilDiffAvg, STOCK_PAIR};

/*  Can use pairs or singles for first 3.  Singles for PairCoil is NEWCOIL. */
enum {Raw, Percent};

extern char *methodname[];
extern int main_method;
 
/******The following are declared in sc2seq_interface.c ****/
extern double many_pprobs[MAX_TABLE_NUMBER][NUM_RES_TYPE][POSNUM], 
        many_pprobp[MAX_TABLE_NUMBER][NUM_RES_TYPE][NUM_RES_TYPE][POSNUM][POSNUM];
extern double many_weights[MAX_TABLE_NUMBER][AANUM][POSNUM],
             many_weightp[MAX_TABLE_NUMBER][AANUM][AANUM][POSNUM][POSNUM];


extern double (*pprobs)[POSNUM];
extern double (*pprobp)[NUM_RES_TYPE][POSNUM][POSNUM];
extern double (*weights)[POSNUM];
extern double (*weightp)[AANUM][POSNUM][POSNUM];
/*********************************************************/

void output_seq(char lib[MAXFUNCTNUM],
		char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
		double *m,double *b,
		double *m_single, double *b_single, 
		int mode, 
		double log_bound,FILE *flog, 
		FILE *fout_coils,
		FILE *fout,  
		int avg_max,
		int main_method, int main_preprocessor_method,
		int main_table);