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/* Copyright (C) 2000 Damir Zucic */
/*=============================================================================
read_fasta.c
Purpose:
Read a single chain sequence from FASTA file. Return negative
value if file is not in FASTA format. The letters J, O and U
are translated as UNK (unknown) residue, as well as letter X.
Input:
(1) Pointer to RuntimeS structure.
(2) Pointer to input file name.
Output:
(1) Sequence stored to the sequence buffer.
(2) Return value.
Return value:
(1) Positive on success.
(2) Negative on failure.
========includes:============================================================*/
#include <stdio.h>
#include <string.h>
#include <ctype.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:=================================================*/
FILE *OpenFileForReading_ (char *);
void InitHyphob_ (RuntimeS *);
/*======read FASTA file (sequence in one letter code):=======================*/
int ReadFasta_ (RuntimeS *runtimeSP, char *file_nameP)
{
int max_length;
char lineA[STRINGSIZE];
FILE *fileP;
int line_length;
int n;
int lineI = 0;
char *P;
int columnI;
size_t residueI = 0;
size_t offset;
/* The maximal residue name length: */
max_length = RESNAMESIZE - 1;
/* Try to open file: */
fileP = OpenFileForReading_ (file_nameP);
if (fileP == NULL)
{
strcpy (runtimeSP->messageA, "Failed to open file!");
runtimeSP->message_length = strlen (runtimeSP->messageA);
return -1;
}
/* Read file, line by line: */
while (fgets (lineA, STRINGSIZE, fileP))
{
/* Remove the trailing newline: */
line_length = strlen (lineA);
n = line_length - 1;
if (line_length > 0)
{
if (lineA[n] == '\n') lineA[n] = '\0';
line_length--;
}
/* Empty lines are ignored: */
if (line_length == 0) continue;
/* Lines beginning with # are treated as comments: */
if (lineA[0] == '#') continue;
/* If the first character of the first useful line is */
/* not '>', input file format is not FASTA compliant. */
/* If it is, the line contains a protein description. */
if (lineI == 0)
{
if (lineA[0] != '>')
{
fclose (fileP);
return -1;
}
else
{
lineI++;
continue;
}
}
/* If the first character of a line which is not the first useful */
/* line is '>', this signals another sequence. Break from the loop: */
else
{
if (lineA[0] == '>') break;
}
/* Convert to uppercase: */
P = lineA;
while ((n = *P++) != '\0') *(P - 1) = toupper (n);
/* Parse line: */
for (columnI = 0; columnI < line_length; columnI++)
{
/* The current character: */
n = lineA[columnI];
/* Check is there enough place left in the buffer: */
offset = max_length * residueI;
if (offset > runtimeSP->sequence_buffer_size - 10 * max_length)
{
strcpy (runtimeSP->messageA, "Sequence too long!");
runtimeSP->message_length =
strlen (runtimeSP->messageA);
fclose (fileP);
return -2;
}
/* Pointer to the position where */
/* residue name should be copied: */
P = runtimeSP->sequenceP + offset;
/* Identify residue: */
switch (n)
{
case 'A':
strncpy (P, "ALA", max_length);
break;
case 'B':
strncpy (P, "ASX", max_length);
break;
case 'C':
strncpy (P, "CYS", max_length);
break;
case 'D':
strncpy (P, "ASP", max_length);
break;
case 'E':
strncpy (P, "GLU", max_length);
break;
case 'F':
strncpy (P, "PHE", max_length);
break;
case 'G':
strncpy (P, "GLY", max_length);
break;
case 'H':
strncpy (P, "HIS", max_length);
break;
case 'I':
strncpy (P, "ILE", max_length);
break;
case 'J':
strncpy (P, "UNK", max_length);
break;
case 'K':
strncpy (P, "LYS", max_length);
break;
case 'L':
strncpy (P, "LEU", max_length);
break;
case 'M':
strncpy (P, "MET", max_length);
break;
case 'N':
strncpy (P, "ASN", max_length);
break;
case 'O':
strncpy (P, "UNK", max_length);
break;
case 'P':
strncpy (P, "PRO", max_length);
break;
case 'Q':
strncpy (P, "GLN", max_length);
break;
case 'R':
strncpy (P, "ARG", max_length);
break;
case 'S':
strncpy (P, "SER", max_length);
break;
case 'T':
strncpy (P, "THR", max_length);
break;
case 'U':
strncpy (P, "UNK", max_length);
break;
case 'V':
strncpy (P, "VAL", max_length);
break;
case 'W':
strncpy (P, "TRP", max_length);
break;
case 'X':
strncpy (P, "UNK", max_length);
break;
case 'Y':
strncpy (P, "TYR", max_length);
break;
case 'Z':
strncpy (P, "GLX", max_length);
break;
default:
;
}
/* Update the residue index: */
residueI++;
}
/* Update the line index (only useful lines are counted): */
lineI++;
}
/* Close file: */
fclose (fileP);
/* 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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