12 #include <sys/types.h>
19 #define SHOWVERSION fprintf( stderr, "%s (%s) Version 5.571, model=%s\n", progName( argv[0] ), (dorp=='d')?"nuc":"aa", modelname )
21 #define FFT_THRESHOLD 70
22 #define FFT_WINSIZE_P 20
23 #define FFT_WINSIZE_D 100
26 #define MAXITERATION 500
27 #define M 10000 /* njob no saidaiti */
28 #define N 500000 /* nlen no saidaiti */
31 #define C 60 /* 1 gyou no mojisuu */
33 #define rnd() ( ( 1.0 / ( RAND_MAX + 1.0 ) ) * rand() )
34 #define MAX(X,Y) ( ((X)>(Y))?(X):(Y) )
35 #define MIN(X,Y) ( ((X)<(Y))?(X):(Y) )
36 #define G(X) ( ((X)>(0))?(X):(0) )
37 #define BEFF 1.0 /* 0.6 ni suruto zureru */
42 #define NOTSPECIFIED 100009
43 #define SUEFF 0.1 /* upg/(spg+upg) -> sueff.sed */
45 #define INTMTXSCALE 1000000.0
53 int amino_dis[0x80][0x80];
60 double fastathreshold;
61 int pslocal, ppslocal;
64 int fmodel; // 1-> fmodel 0->default -1->raw
65 int nblosum; // 45, 50, 62, 80
80 int penalty, ppenalty;
81 int penalty_ex, ppenalty_ex;
117 /* sengen no ichi ha koko dake de ha nai */
118 extern void constants();
119 extern char **Calignm1();
120 extern char **Dalignm1();
121 extern char **align0();
122 extern double Cscore_m_1( char **, int, int, double ** );
123 extern double score_m_1( char **, int, int, double ** );
124 extern double score_calc0( char **, int, double **, int );
125 extern char seqcheck( char ** );
126 extern float substitution( char *, char * );
127 extern float substitution_score( char *, char * );
128 extern float substitution_nid( char *, char * );
129 extern float substitution_hosei( char *, char * );
130 extern double ipower( double, int );
131 extern float translate_and_Calign();
132 extern float A__align();
133 extern float A__align11();
134 extern float A__align_gapmap();
135 extern float partA__align();
136 extern float L__align11();
137 extern float G__align11();
138 extern float Falign();
139 extern float Falign_localhom();
140 extern float Conalign();
141 extern float Aalign();
142 extern float imp_match_out_sc( int, int );
143 extern float part_imp_match_out_sc( int, int );
144 extern void ErrorExit();
145 extern void cpmx_calc();
146 extern void intergroup_score( char **, char **, double *, double *, int, int, int, double * );
147 extern int conjuctionfortbfast();
148 extern int fastconjuction();
149 extern char seqcheck( char ** );
151 typedef struct _LocalHom
153 struct _LocalHom *next;
164 typedef struct _NodeInCub
172 struct _Node *children[3];
175 double *weightptr[3];
180 typedef struct _Segment
188 struct _Segment *pair;
192 typedef struct _Segments
200 typedef struct _Achain
210 typedef struct _Fukusosuu
217 #include "functions.h"