/*  File: blxmain.c
 *  Author: Erik Sonnhammer
 *  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: BLXMAIN - Standalone calling program for blxview.
 * Exported functions: 
 * HISTORY:
 * Last edited: Oct 28 09:10 2003 (edgrif)
 * * Aug 26 16:57 1999 (fw): added this header
 * Created: Thu Aug 26 16:56:45 1999 (fw)
 * CVS info:   $Id: blxmain.c,v 1.48 2003/10/28 09:54:30 edgrif Exp $
 *-------------------------------------------------------------------
 */

#include <wh/regular.h>
#include <wh/graph.h>
#include <wh/gex.h>
#include <w9/blixem_.h>


/*                                                                           */
/*            blixem copyright string, use "what" on the executable.         */
/*                                                                           */
UT_COPYRIGHT_STRING(BLIXEM_TITLE, BLIXEM_VERSION, BLIXEM_RELEASE, BLIXEM_UPDATE, BLIXEM_DESC)

/* Set up  scrolled window message lists if required by user. */ 
enum {BLIXEM_MESG_NUM = 50} ;
static void msgPopupsCB(BOOL msg_list) ;


/* global debug flag for blixem, set TRUE to get debugging output.           */
BOOL blixem_debug_G = FALSE ;


static char *usageText = "\
\n\
 Blixem - display Blast matches as a multiple alignment.\n\
\n\
 Reference:  Sonnhammer ELL & Durbin R (1994). A workbench for Large Scale\n\
 Sequence Homology Analysis. Comput. Applic. Biosci. 10:301-307.\n\
\n\
  Usage: blixem [options] <sequencefile> <datafile> [X options] \n\
\n\
 Both <sequencefile> and <datafile> can be substituted by \"-\"\n\
 for reading from stdin (pipe).  If <sequencefile> is piped, the first\n\
 line should contain the sequence name and the second the sequence itself.\n\
\n\
 Options:\n\
 -s <mode>  Sorting mode at startup.\n\
               s = by Score\n\
               i = by Identity\n\
               n = by Name\n\
               p = by Position\n\
 -I         Inverted sorting order\n\
 -b         Don't start with Big Picture.\n\
 -S <#>     Start display at position #.\n\
 -F <file>  Read in query sequence and data from <file> (replaces sequencefile).\n\
 -h         Help and more options.\n\
 -o <optstring>\n\
            Blixem options,  e.g. -o \"MBr\" you'll have to read the source code for details.\n\
 -O <#>     sequence offset.\n\
 -P nodeid<:port>\n\
            Causes Blixem to get sequences from a pfetch server at machine nodeid on the given port (default 22100).\n\
 -r         Remove input files after parsing, used by xace when calling blixem as a\n\
            standalone program.\n\
 -x <file>  Read in extra data (to that in datafile) from from <file>, data may be in a\n\
            different format.\n\
\n\
 Some X options:\n\
 -acefont <font> Main font.\n\
 -font    <font> Menu font.\n\
\n\
 To make the datafile from blast output, run MSPcrunch with option -q.\n\n\
\n\
 by Erik.Sonnhammer@cgr.ki.se\n\
 Version" ;

static char *help_string = "\n\
 o To pipe MSPcrunch output directly to Blixem, use \"-\"\n\
   as the second parameter ([datafile]).  Example:\n\
\n\
   MSPcrunch -q <my.blast_output> | blixem <my.seq> -\n\
\n\
\n\
 o The BLAST program (blastp, blastn, blastx, tblastn, tblastx)\n\
   is automatically detected from the Blast output header by MSPcrunch\n\
   and is passed on to Blixem in the seqbl format (-q).  If\n\
   your output lacks the header, set the program with these options:\n\
\n\
   -p    Use blastp output (blastx is default)\n\
   -n    Use blastn output\n\
   -t    Use tblastn output\n\
   -l    Use tblastx output\n\n" ;



/* Entry point for blixem standalone program, you should be aware when       */
/* altering this that blxview.c is also compiled into acedb and that         */
/* blxview() is called directly by acedb code.                               */
/*                                                                           */
int main(int argc, char **argv)
{
  FILE        *seqfile, *FSfile;
  char seqfilename[1000] = {'\0'}, FSfilename[1000] = {'\0'} ;
  char  *qseq = NULL, 
    *dummyseq = NULL,					    /* Needed for blxparser to handle both */
							    /* dotter and blixem */
    line[MAXLINE+1],
    ch, *cp, *cq, *c;
  MSP         *MSPlist = NULL ;
  static char opts[32]=" MBr Z   ",	/* 0 L|N|P|T|X
					   1 M
					   2 B|b
					   3 R|r (blxparser.c)
					   4    (available)
					   5 Z (blxparser.c)
					   6 I 
					   7 G (blxparser.c)
					   8    sorting mode
					*/
    qname[FULLNAMESIZE+1],
    dummyseqname[FULLNAMESIZE+1];
  int dispstart = 0, offset = 0, install = 1, seqInSFS = 0 ;

#if !defined(MACINTOSH)
  int          optc;
  extern int   optind;
  extern char *optarg;
  char        *optstring="bF:hIilno:O:pP:rS:s:tx:";
  
  static char *cc_date = 
#if defined(__DATE__)
    __DATE__
#else
    ""
#endif
    ;

  char *usage;

  BOOL rm_input_files = FALSE ;
  PfetchParams *pfetch = NULL ;
  BOOL xtra_data = FALSE ;
  FILE *xtra_file = NULL ;
  char xtra_filename[1000] = {'\0'} ;


  /* Set up the message package to report program/user details in messages.  */
  messSetMsgInfo(argv[0], BLIXEM_TITLE_STRING) ;

  usage = messalloc(strlen(usageText) + strlen(blixemVersion) + strlen(cc_date) + 10);
  sprintf(usage, "%s %s, %s\n", usageText, blixemVersion, cc_date);

  while ((optc = getopt(argc, argv, optstring)) != EOF )
    {
      switch (optc)
	{
	case 'b':
	  opts[2] = 'b';
	  break;
	case 'F': 
	  seqInSFS = 1;        
	  strcpy(FSfilename, optarg);
	  break;
	case 'h': 
	  fprintf(stderr, "%s\n%s\n", usage, help_string) ;
	  exit(EXIT_FAILURE) ;
	  break;
	case 'I':
	  opts[6] = 'I';
	  break;
	case 'i':
	  install = 0;
	  break;
	case 'l':
	  opts[0] = 'L';
	  break;
	case 'n':
	  opts[0] = 'N';
	  break;
	case 'o':
	  {
	    int i ;

	    memset(opts, ' ', strlen(opts)) ;

	    for (i = 0 ; i < strlen(optarg) ; i++)
	      {
		opts[i] = optarg[i] ;
	      }
	  }
	  break;
	case 'O':
	  /* Note that I don't do any checking of the value, this is in line */
	  /* with the way blxview() accepts any value of offset, I just check*/
	  /* its actually an integer.                                        */
	  if (!(utStr2Int(optarg, &offset)))
	    messcrash("Bad offset argument: \"-%c %s\"", optc, optarg) ;
	  break;
	case 'p':
	  opts[0] = 'P';
	  break;
	case 'P':
	  pfetch = messalloc(sizeof(PfetchParams)) ;
	  pfetch->net_id = strtok(optarg, ":") ;
	  pfetch->port = atoi(strtok(NULL, ":")) ;
	  break;
	case 'r':
	  rm_input_files = TRUE ;
	  break ;
	case 'S': 
	  if (!(dispstart = atoi(optarg)))
	    messcrash("Bad diplay start position: %s", optarg); 
	  opts[1] = ' ';
	  break;
	case 's': 
	  if (*optarg != 's' && *optarg != 'i' && *optarg != 'n' && *optarg != 'p')
	    {
	      fprintf(stderr,"Bad sorting mode: %s\n", optarg); 
	      exit(EXIT_FAILURE) ;
	    }
	  opts[8] = *optarg;
	  break;
	case 't':
	  opts[0] = 'T';
	  break;
	case 'x': 
	  xtra_data = TRUE ;
	  strcpy(xtra_filename, optarg);
	  break;

	default : messcrash("Illegal option");
	}
    }

  if (argc-optind < 2 && !seqInSFS)
    {
      fprintf(stderr, "%s\n", usage); 
      exit(EXIT_FAILURE);
    }

#else  /* Macintosh */
    printf("Seq file: "); scanf("%s", seqfilename);
    printf("FS file: "); scanf("%s", FSfilename);
#endif
 
    /* Add -install for private colormaps */
    if (install)
      argvAdd(&argc, &argv, "-install");
    graphInit(&argc, argv) ;
    gexInit(&argc, argv);
    gexSetMessPrefs(FALSE, BLIXEM_MESG_NUM, msgPopupsCB) ;  /* for control of popup or mesglist */

    if (!seqInSFS)
      {
	strcpy(seqfilename, argv[optind]);
	strcpy(FSfilename, argv[optind+1]);

	if (!strcmp(seqfilename, "-"))
	  {
	    seqfile = stdin;
	  }
	else if(!(seqfile = fopen(seqfilename, "r")))
	  {
	    messcrash("Cannot open %s\n", seqfilename);
	  }
	
	/* Read in query sequence */
	if (seqfile == stdin)
	  {
	    /* Same file for query and FS data - sequence on first two lines */
	    Array arr = arrayCreate(5000, char);
	    int i=0;
	    
	    if (!fgets(line, MAXLINE, seqfile))
	      messcrash("Error reading seqFile");;

	    sscanf(line, "%s", qname);
	    
	    while ((ch = fgetc(seqfile)) != '\n') {
		/*if (isAlnRes(ch) || isAlnNonres(ch))*/
		array(arr, i++, char) = ch;
	    }
	    qseq = messalloc(arrayMax(arr)+1);
	    cq = qseq;
	    for (i = 0; i < arrayMax(arr);) *cq++ = arr(arr, i++, char);
	    arrayDestroy(arr);
	  }
	else
	  {
	    fseek(seqfile, 0, SEEK_END);
	    qseq = messalloc(ftell(seqfile)+1);
	    cq = qseq;
	    fseek(seqfile, 0, SEEK_SET);
	    while (!feof(seqfile))
		{
		    if (!fgets(line, MAXLINE, seqfile))
		      break;
		    if ((c = (char *)strchr(line, '\n')))
		      *c = 0;
		    
		    if (*line == '>')
		      {
			strncpy(qname, line+1, 255);
			qname[255]=0;
			if ((c = (char *)strchr(qname, ' ')))
			  *c = 0;
			continue;
		      }
		    
		    for (cp = line; *cp; cp++) 
			/*if (isAlnRes(*cp) || isAlnNonres(*cp))*/ *cq++ = *cp;
		    *cq = 0;
		}
	    fclose(seqfile);
	}
    }

    /* Parse the data file containing the homol descriptions.                */
    if (!strcmp(FSfilename, "-"))
      {
	FSfile = stdin;
      }
    else if(!(FSfile = fopen(FSfilename, "r")))
      {
	messcrash("Cannot open %s\n", FSfilename);
      }
    parseFS(&MSPlist, FSfile, opts, &qseq, qname, &dummyseq, dummyseqname) ;
    if (FSfile != stdin)
      fclose(FSfile) ;

    /* There may an additional file containing homol data in an alternative format. */
    if (xtra_data)
      {
	if(!(xtra_file = fopen(xtra_filename, "r")))
	  {
	    messcrash("Cannot open %s\n", xtra_filename) ;
	  }
	parseFS(&MSPlist, xtra_file, opts, &qseq, qname, &dummyseq, dummyseqname) ;
	fclose(xtra_file) ;
      }


    /* Remove the input files if requested.                                  */
    if (rm_input_files)
      {
	if(seqfilename[0] != '\0' && unlink(seqfilename) != 0)
	  messerror("Unlink of sequence input file \"%s\" failed: %s\n",
		    seqfilename, messSysErrorText()) ;
	if(FSfilename[0] != '\0' && unlink(FSfilename) != 0)
	  messerror("Unlink of MSP input file \"%s\" failed: %s\n",
		    FSfilename, messSysErrorText()) ;
	if (xtra_filename[0] != '\0' && unlink(xtra_filename) != 0)
	  messerror("Unlink of extra MSP sequence input file \"%s\" failed: %s\n",
		    xtra_filename, messSysErrorText()) ;
      }


    if (GRAPH_NULL != blxview(qseq, qname, dispstart, offset, MSPlist, opts, pfetch, TRUE))	/* TRUE means it's an external call */
      graphLoop(TRUE);
    
    
    /* We should not get here....                                            */
    return (EXIT_FAILURE) ;
}



/* Enables user to switch between seeing informational messages in popups
 * or in a scrolled window. */
static void msgPopupsCB(BOOL msg_list)
{
  int list_length ;

  if (msg_list)
    list_length = BLIXEM_MESG_NUM ;
  else
    list_length = 0 ;

  gexSetMessPopUps(msg_list, list_length) ;

  return ;
}