/*  File: blxview.h
 *  Author: Erik Sonnhammer, 92-02-20
 *  Copyright (c) J Thierry-Mieg and R Durbin, 1999
 * -------------------------------------------------------------------
 * Acedb is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
 * -------------------------------------------------------------------
 * This file is part of the ACEDB genome database package, written by
 * 	Richard Durbin (Sanger Centre, UK) rd@sanger.ac.uk, and
 *	Jean Thierry-Mieg (CRBM du CNRS, France) mieg@kaa.crbm.cnrs-mop.fr
 *
 * Description: include file for BLXVIEW.C
 * Other files: iupac.h, blxview.c, translate.c
 * Exported functions: 
 * HISTORY:
 * Last edited: Nov 29 11:21 2001 (edgrif)
 * * Aug 26 16:57 1999 (fw): added this header
 * Created: Thu Aug 26 16:57:17 1999 (fw)
 * CVS info:   $Id: blxview.h,v 1.34 2001/11/29 12:30:59 edgrif Exp $
 *-------------------------------------------------------------------
 */
#ifndef DEF_BLXVIEW_H
#define DEF_BLXVIEW_H

#define NAMESIZE    12
#define FULLNAMESIZE 255
#define INITDBSEQLEN 50000   /* Initial estimate of max database sequence length */
#define MAXLINE 10000


#define max(a,b)        (((a) > (b)) ? (a) : (b))
#define min(a,b)        (((a) < (b)) ? (a) : (b))

#define selectFeaturesStr     "Feature series selection tool"
#define FS(msp) (msp->type == FSSEG || msp->type == XY)
#define XY_NOT_FILLED -1000  /* Magic value meaning "value not provided" */

/* Shapes of XY data */
enum { XY_PARTIAL, XY_INTERPOLATE, XY_BADSHAPE };

/* Types of MSP */
enum { EXBLX, SEQBL, /* Old, discontinue some time */
       HSP, GSP, GSPdata, GFF, FSSEG, XY, XYdata, SEQ, SEQdata };

/* Remember to ALWAYS update blxview.c:mspcpy() when changing this !!! */
typedef struct _MSP
{
struct _MSP *next;
    int      type;		/* See enum above */
    int      score;
    int      id;

    char    *qname;		/* For Dotter, the MSP can belong to either sequence */
    char     qframe[8];		
    int      qstart;
    int      qend;

    char    *sname;		
    char     sframe[8];
    int      sstart; 
    int      send;
    char    *sseq;

    char    *desc;
    int      box ;
    Graph    graph;

    int      color;   
    int      shape;   /* For SFS data, e.g. XY type PARTIAL or INTERPOLATE shapes */
    int      fs;      /* Ordinal number of the series that this MSP belongs to. */

    Array    xy;      /* For XY plot series */

    Array    gaps;    /* gaps in this homolgy */

#ifdef ACEDB
    KEY      key;
#endif
} MSP;

  
typedef struct featureSeries_ {
    char  *name;
    int    nr;
    int    on;
    float  x;	      /* Series offset on x axis, to bump series on the screen */
    float  y;	      /* Series offset on y axis */
    int    xy;	      /* Flag for XY plot series */
} FEATURESERIES;


/* blixem can use either efetch (default) or a pfetch server to get          */
/* sequences, to use pfetch you need node/port information.                  */
typedef struct
{
  char *net_id ;
  int port ;
} PfetchParams ;


/* Dotter/Blixem Package-wide variables */
extern char *blixemVersion ;
extern char *stdcode1[];        /* 1-letter amino acid translation code */
extern int   aa_atob[];
extern int PAM120[23][23];
extern Array fsArr;		/* in dotter.c */
extern Graph dotterGraph;
extern float fsPlotHeight;
extern GtkWidget *blixemWindow;


/* Dotter/Blixem Package-wide functions */

Graph blxview (char *seq, char *seqname,
	       int dispStart, int offset, MSP *msp, char *opts, PfetchParams *pfetch) ;
Graph blxreadhsp(FILE *seqfile, FILE *exblxfile, char *featurefile, char *qname, 
		 int dispstart, int qoffset, char *opts, int *argc, char **argv);
char *translate(char *seq, char **code);
char *revcomp(char *comp, char *seq);
void *compl(char *seq);
void  argvAdd(int *argc, char ***argv, char *s);
void  loadFeatures(FILE* fil, MSP **msp);
float fs2y(MSP *msp, float *maxy, float height);
char  Seqtype(char *seq);
void  blviewRedraw(void);
void  selectFeatures(void);
float fsTotalHeight(MSP *msplist);
void  parseFS(MSP **MSPlist, FILE *file, char *opts,
	      char **seq1, char *seq1name, char **seq2, char *seq2name) ;
void insertFS(MSP *msp, char *series);
char *readFastaSeq(FILE *seqfile, char *qname);

#endif /*  !defined DEF_BLXVIEW_H */