X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=sources%2Fseg%2Fgenwin.h;fp=sources%2Fseg%2Fgenwin.h;h=15f92eb276be5386251d3b45b4059aaad394b517;hb=81362e35a140cd040e948b921053e74267f8a6e3;hp=0000000000000000000000000000000000000000;hpb=2cf032f4b987ba747c04159965aed78e3820d942;p=jpred.git

diff --git a/sources/seg/genwin.h b/sources/seg/genwin.h
new file mode 100644
index 0000000..15f92eb
--- /dev/null
+++ b/sources/seg/genwin.h
@@ -0,0 +1,171 @@
+
+/*****************************************************************************/
+/***   (genwin.h)                                                          ***/
+/*****************************************************************************/
+
+/*--------------------------------------------------------------(includes)---*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <fcntl.h>
+#include <ctype.h>
+#include <math.h>
+
+/*--------------------------------------------------------------(typedefs)---*/
+
+typedef int Bool;
+
+/*---------------------------------------------------------------(defines)---*/
+#ifndef TRUE
+#define TRUE 1
+#define FALSE 0
+#endif
+/*---------------------------------------------------------------(structs)---*/
+
+struct Database
+  {
+   char *filename;
+   FILE *fp;
+   char *indexname;
+   long int filepos;
+  };
+
+struct Sequence
+  {
+   struct Database *db;
+
+   char *id;
+   char *name;
+   char *organism;
+   char *header;
+
+   char *seq;
+   int start;                     /* for windows */
+   int length;
+   struct Alphabet *alphabet;
+
+   struct Sequence *parent;       /* for windows */
+   struct Sequence *root;         /* for subwindows */
+   struct Sequence **children;    /* only the floaters? */
+
+   Bool bogus;
+   Bool punctuation;
+   Bool rubberwin;             /* for windows */
+   Bool floatwin;              /* for subwindows */
+   Bool seedwin;
+
+   int *state;
+   double entropy;
+   int *composition;
+   Bool	*comptst;
+   int	*compindex;
+
+   char *classvec;               /* from ClaVec[aa] */
+   struct Alphabet *clalphabet;
+   double *scorevec;             /* from ScoVec[aa] or ScoFun(pos) */
+   double score;                 /* from ScoFun(win) */
+                          /* union, for integer scores? */
+   struct PerScoreVec *foo;
+   int *bar;
+  };
+
+struct Configuration
+  {
+   char *iseq;
+   int ilength;
+
+   int printper;
+  };
+
+struct Matrix
+  {
+   struct Sequence *parent;
+
+   char **seq;
+   int start;
+   int period;
+   int length;
+
+   int **rowcomp;
+   int **colcomp;
+  };
+
+/*------------------------------------------------------(alphabet structs)---*/
+
+struct Alphabet
+  {
+   char *name;
+   int size;
+
+   int *index[128];
+   char *chars;       /*  [size]  */
+   char **charnames;  /*  [size]  */
+
+   Bool caseinvariant;
+  };
+
+struct TransVector
+  {
+   struct Alphabet *from;
+   struct Alphabet *to;
+
+   int *index;     /*  [from->size]  */
+  };
+
+struct ScoreVector
+  {
+   struct Alphabet *from;
+
+   double *score;   /*  [from->size]  */
+   char *units;
+  };
+
+struct ScoreMatrix
+  {
+   struct Alphabet *from1;
+   struct Alphabet *from2;
+
+   double **score;  /*  [from1->size][from2->size]  */
+   char *units;
+  };
+
+/*---------------------------------------------------------(bogus structs)---*/
+
+struct PerScoreVec
+  {
+   int hits;
+   int tot;
+   double pct;
+   double std;
+   double prob;
+  };
+
+/*----------------------------------------------------------------(protos)---*/
+
+extern struct Database *opendbase();
+extern closedbase();
+
+extern struct Sequence *openseq(), *firstseq(), *nextseq();
+extern closeseq();
+
+extern struct Sequence *openwin(), *nextwin();
+extern shiftwin(), closewin();
+
+extern compon(), stateon(), enton();
+extern double entropy();
+
+extern struct Matrix *openmat();
+extern closemat();
+
+extern upper(), lower(), findchar();
+
+/*----------------------------------------------------------------(macros)---*/
+
+/***   #define bogus(A) (aaindex[A]>=20)   ***/
+
+/*---------------------------------------------------------------(globals)---*/
+
+extern int aaindex[];
+extern char aachar[];
+
+/*---------------------------------------------------------------------------*/