2 /*****************************************************************************/
4 /*****************************************************************************/
6 /*--------------------------------------------------------------(includes)---*/
14 /*--------------------------------------------------------------(typedefs)---*/
18 /*---------------------------------------------------------------(defines)---*/
23 /*---------------------------------------------------------------(structs)---*/
43 int start; /* for windows */
45 struct Alphabet *alphabet;
47 struct Sequence *parent; /* for windows */
48 struct Sequence *root; /* for subwindows */
49 struct Sequence **children; /* only the floaters? */
53 Bool rubberwin; /* for windows */
54 Bool floatwin; /* for subwindows */
63 char *classvec; /* from ClaVec[aa] */
64 struct Alphabet *clalphabet;
65 double *scorevec; /* from ScoVec[aa] or ScoFun(pos) */
66 double score; /* from ScoFun(win) */
67 /* union, for integer scores? */
68 struct PerScoreVec *foo;
82 struct Sequence *parent;
93 /*------------------------------------------------------(alphabet structs)---*/
101 char *chars; /* [size] */
102 char **charnames; /* [size] */
109 struct Alphabet *from;
112 int *index; /* [from->size] */
117 struct Alphabet *from;
119 double *score; /* [from->size] */
125 struct Alphabet *from1;
126 struct Alphabet *from2;
128 double **score; /* [from1->size][from2->size] */
132 /*---------------------------------------------------------(bogus structs)---*/
143 /*----------------------------------------------------------------(protos)---*/
145 extern struct Database *opendbase();
148 extern struct Sequence *openseq(), *firstseq(), *nextseq();
151 extern struct Sequence *openwin(), *nextwin();
152 extern shiftwin(), closewin();
154 extern compon(), stateon(), enton();
155 extern double entropy();
157 extern struct Matrix *openmat();
160 extern upper(), lower(), findchar();
162 /*----------------------------------------------------------------(macros)---*/
164 /*** #define bogus(A) (aaindex[A]>=20) ***/
166 /*---------------------------------------------------------------(globals)---*/
168 extern int aaindex[];
169 extern char aachar[];
171 /*---------------------------------------------------------------------------*/