/*****************************************************************************/
/*                                                                           */
/* UNIT: NTL3_Abs_Corres_2  (Level 3 library routine)                        */
/*                                                                           */
/* Author: Nikola Stojanovic                                                 */
/*                                                                           */
/* Revision:    16 JUL 94   Version 1.0                                      */
/*                                                                           */
/* Function:                                                                 */
/*                                                                           */
/*   Procedure determines the set of pairs of absolute alignment offsets for */
/* a pair of positions, given by some origin and offsets with respect to it; */
/* file names for both the "origins" and "alignment" files are provided as   */
/* input parameters; returns the standard error structure, NULL if there     */
/* were no errors                                                            */
/*                                                                           */
/*****************************************************************************/


#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "ntl3.h"




/*****************************************************************************/
/*                                                                           */
/* Definitions section                                                       */
/*                                                                           */
/*****************************************************************************/


/*****************************************************************************/
/* Definitions of global (static) variables of the unit                      */
/*****************************************************************************/


static int origins_loaded = 0; /* Before first invocation, no origins loaded */
static int alignment_loaded = 0;            /* No alignment initially loaded */

static header_ptr file_data = NULL;        /* Contents of the alignment file */
static align_ptr alignment = NULL;           /* Partially unpacked alignment */
static orgref_ptr origins = NULL;    /* List of defined origins in sequences */

/*****************************************************************************/
/*                                                                           */
/* Code section                                                              */
/*                                                                           */
/*****************************************************************************/

/*****************************************************************************/
/*                                                                           */
/* PROCEDURE: NTL3_Abs_Corres_2                                              */
/*                                                                           */
/* Central procedure for the unit; returns NULL if the absolute positions    */
/*   have been found and set of such pairs allocated, error diagnostics      */
/*   structure otherwise                                                     */

errind NTL3_Abs_Corres_2 (char *reference,
                          long int offset_1, long int offset_2,
                          char *origins_file, char *alignment_file,
                          twoint_ptr *result)
{
 errind load_status;

 /* Check whether this is the first invocation of this routine - if it is,   */
 /*   then load the origins file into internal structure                     */

 if (origins_loaded == 0) {   /* This is the first invocation within program */
  if ((load_status = NTL2_Load_Origins (origins_file, &origins)) != NULL)
   return load_status;
  else origins_loaded = 1;
 }
 /* Check whether the current alignment has already been loaded internally   */

 if (alignment_loaded == 0) {                     /* No alignment loaded yet */

  /* Load the contents of the specified alignment file in appropriate format */
  /*   into internal structure first                                         */

  if ((load_status = NTL2_Load_AlignFile (alignment_file, &file_data)) != NULL)
   return load_status;
  else {      /* Data from the file loaded, now partially expand alignment 1 */
   if ((load_status = NTL1_Load_Alignment (1, file_data, &alignment)) != NULL)
    return load_status;
   else alignment_loaded = 1;
  }
 }
 /* Now when it is guaranteed that both origins and alignments are loaded,   */
 /*   proceed to identify the coresponding positions                         */

 return NTL1_Abs_Corres_2 (reference, offset_1, offset_2,
                           origins, file_data, alignment,
                           result);
}