--- /dev/null
+#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);
+
+
+
+
+
+
+
+