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/* Copyright (C) 2000-2003 Damir Zucic */
/*=============================================================================
parse_sequence.c
Purpose:
Parse the sequence string.
Input:
(1) Pointer to RuntimeS structure.
(2) Pointer to the string which contains the sequence.
Output:
(1) Sequence stored to the sequence buffer.
(2) Return value.
Return value:
(1) Positive on success.
(2) Negative on failure.
Notes:
(1) The sequence is expected in three letters code. One letter
code may be missinterpreted as valid three letters code.
(2) Space, comma, tab and semicolon may be used as separators.
========includes:============================================================*/
#include <stdio.h>
#include <string.h>
#include <X11/Xlib.h>
#include <X11/Xutil.h>
#include <X11/Xos.h>
#include <X11/Xatom.h>
#include "defines.h"
#include "commands.h"
#include "typedefs.h"
/*======function prototypes:=================================================*/
char *ExtractToken_ (char *, int, char *, char *);
void InitHyphob_ (RuntimeS *);
/*======parse sequence string:===============================================*/
int ParseSequence_ (RuntimeS *runtimeSP, char *stringP)
{
int max_length, i;
char *remainderP;
char tokenA[SHORTSTRINGSIZE];
char *P;
size_t residueI = 0;
/* The maximal residue name length: */
max_length = RESNAMESIZE - 1;
/* Reset the number of residues in sequence: */
runtimeSP->residuesN = 0;
/* Zero initialize the sequence buffer: */
for (i = 0; i < (int) runtimeSP->sequence_buffer_size; i++)
{
*(runtimeSP->sequenceP + i) = '\0';
}
/* Parse the string: */
remainderP = stringP;
while ((remainderP = ExtractToken_ (tokenA, SHORTSTRINGSIZE,
remainderP, " ,;\t\n")) != NULL)
{
/* Check the residue name size: */
if ((int) strlen (tokenA) > max_length)
{
sprintf (runtimeSP->messageA,
"Residue name %s too long!",
tokenA);
runtimeSP->message_length = strlen (runtimeSP->messageA);
return -1;
}
/* Copy the residue name to the sequence buffer: */
P = runtimeSP->sequenceP + max_length * residueI;
strcpy (P, tokenA);
/* Update the residue index: */
residueI++;
}
/* Store the number of residues: */
runtimeSP->residuesN = residueI;
/* Reinitialize serial numbers: */
for (residueI = 0; residueI < runtimeSP->residuesN; residueI++)
{
*(runtimeSP->serialIP + residueI) = residueI + 1;
}
/* Reinitialize disulfide flags: */
for (residueI = 0; residueI < runtimeSP->residuesN; residueI++)
{
*(runtimeSP->disulfideFP + residueI) = 0;
}
/* Initialize hydrophobicity values: */
InitHyphob_ (runtimeSP);
/* Return positive value on success: */
return 1;
}
/*===========================================================================*/
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