gde_linux/CORE/Genbank.c

#include <malloc.h>
#include <stdio.h>
#include <sys/time.h>
#include <time.h>
#include <xview/panel.h>
#include <xview/xview.h>

#include "defines.h"
#include "menudefs.h"

/*
Copyright (c) 1989-1990, University of Illinois board of trustees.  All
rights reserved.  Written by Steven Smith at the Center for Prokaryote Genome
Analysis.  Design and implementation guidance by Dr. Gary Olsen and Dr.
Carl Woese.

Copyright (c) 1990,1991,1992 Steven Smith at the Harvard Genome Laboratory.
all rights reserved.

Copyright (c) 1993, Steven Smith, all rights reserved.

*/

ReadGen(filename, dataset, type) char *filename;
NA_Alignment *dataset;
int type;
{
	register int done = FALSE, len = 0, j = 0;
	int count, IS_REALLY_AA = FALSE;
	char Inline[GBUFSIZ], c;
	char *buffer, *gencomments = NULL, fields[8][GBUFSIZ];
	int buflen = 0, genclen = 0, curelem = 0, n = 0, flag = 0;
	int start_col = -1;

	NA_Sequence *this_elem;
	FILE *file;
	extern int Default_DNA_Trans[], Default_RNA_Trans[];
	extern int Default_NA_RTrans[];
	extern int Default_PROColor_LKUP[], Default_NAColor_LKUP[];

	ErrorOut("No such file", file = fopen(filename, "r"));

	for (; fgets(Inline, GBUFSIZ, file) != 0;) {
		if (Inline[strlen(Inline) - 1] == '\n')
			Inline[strlen(Inline) - 1] = '\0';
		if (Find(Inline, "LOCUS")) {
			curelem = dataset->numelements++;
			if (curelem == 0) {
				dataset->element = (NA_Sequence *)Calloc(
				    5, sizeof(NA_Sequence));
				dataset->maxnumelements = 5;
			}
			else if (curelem == dataset->maxnumelements) {
				(dataset->maxnumelements) *= 2;
				dataset->element = (NA_Sequence *)Realloc(
				    dataset->element, dataset->maxnumelements *
							  sizeof(NA_Sequence));
			}
			this_elem = &(dataset->element[curelem]);
			n = sscanf(Inline, "%s %s %s %s %s %s %s %s", fields[0],
				   fields[1], fields[2], fields[3], fields[4],
				   fields[5], fields[6], fields[7]);
			if (IS_REALLY_AA) {
				InitNASeq(this_elem, PROTEIN);
			}
			else if (Find(Inline, "DNA")) {
				InitNASeq(this_elem, DNA);
			}
			else if (Find(Inline, "RNA")) {
				InitNASeq(this_elem, RNA);
			}
			else if (Find(Inline, "MASK")) {
				InitNASeq(this_elem, MASK);
			}
			else if (Find(Inline, "TEXT")) {
				InitNASeq(this_elem, TEXT);
			}
			else if (Find(Inline, "PROT")) {
				InitNASeq(this_elem, PROTEIN);
			}
			else
				InitNASeq(this_elem, DNA);

			strncpy(this_elem->short_name, fields[1], 31);
			AsciiTime(&(this_elem->t_stamp.origin), fields[n - 1]);
			this_elem->attr = DEFAULT_X_ATTR;

			if (Find(Inline, "Circular"))
				this_elem->attr |= IS_CIRCULAR;

			gencomments = NULL;
			genclen = 0;
		}
		else if (Find(Inline, "DEFINITION"))
			strncpy(this_elem->description, &(Inline[12]), 79);

		else if (Find(Inline, "AUTHOR"))
			strncpy(this_elem->authority, &(Inline[12]), 79);

		else if (Find(Inline, "  ORGANISM"))
			strncpy(this_elem->seq_name, &(Inline[12]), 79);

		else if (Find(Inline, "ACCESSION"))
			strncpy(this_elem->id, &(Inline[12]), 79);

		else if (Find(Inline, "ORIGIN")) {
			done = FALSE;
			len = 0;
			for (; done == FALSE &&
			       fgets(Inline, GBUFSIZ, file) != 0;) {
				if (Inline[0] != '/') {
					if (buflen == 0) {
						buflen = GBUFSIZ;
						buffer = Calloc(sizeof(char),
								buflen);
					}

					else if (len + strlen(Inline) >=
						 buflen) {
						buflen += GBUFSIZ;
						buffer = Realloc(
						    buffer,
						    sizeof(char) * buflen);
						for (j = buflen - GBUFSIZ;
						     j < buflen; j++)
							buffer[j] = '\0';
					}
					/*
					 *	Search for the fist column of
					 *data
					 *(whitespace-number-whitespace)data
					 */
					if (start_col == -1) {
						for (start_col = 0;
						     Inline[start_col] == ' ' ||
						     Inline[start_col] == '\t';
						     start_col++)
							;

						for (start_col++;
						     strchr(
							 "1234567890",
							 Inline[start_col]) !=
						     NULL;
						     start_col++)
							;

						for (start_col++;
						     Inline[start_col] == ' ' ||
						     Inline[start_col] == '\t';
						     start_col++)
							;
					}
					for (j = start_col;
					     (c = Inline[j]) != '\0'; j++) {
						if ((c != '\n') &&
						    ((j - start_col + 1) % 11 !=
						     0))
							buffer[len++] = c;
					}
				}
				else {
					AppendNA(buffer, len,
						 &(dataset->element[curelem]));
					for (j = 0; j < len; j++)
						buffer[j] = '\0';
					len = 0;
					done = TRUE;
					dataset->element[curelem].comments =
					    gencomments;
					dataset->element[curelem].comments_len =
					    genclen - 1;
					dataset->element[curelem]
					    .comments_maxlen = genclen;

					gencomments = NULL;
					genclen = 0;
				}
			}
			/*
			 *		Test if sequence should be converted by
			 *the translation table If it looks like a protein...
			 */
			if (dataset->element[curelem].rmatrix &&
			    IS_REALLY_AA == FALSE) {
				IS_REALLY_AA = CheckType(
				    dataset->element[curelem].sequence,
				    dataset->element[curelem].seqlen);

				if (IS_REALLY_AA == FALSE)
					Ascii2NA(
					    dataset->element[curelem].sequence,
					    dataset->element[curelem].seqlen,
					    dataset->element[curelem].rmatrix);
				else
				/*
				 *		Force the sequence to be AA
				 */
				{
					dataset->element[curelem].elementtype =
					    PROTEIN;
					dataset->element[curelem].rmatrix =
					    NULL;
					dataset->element[curelem].tmatrix =
					    NULL;
					dataset->element[curelem].col_lut =
					    Default_PROColor_LKUP;
				}
			}
		}
		else if (Find(Inline, "ZZZZZ")) {
			Cfree(gencomments);
			genclen = 0;
		}
		else {
			if (gencomments == NULL) {
				gencomments = String(Inline);
				genclen = strlen(gencomments) + 1;
			}
			else {
				genclen += strlen(Inline) + 1;
				gencomments = Realloc(gencomments,
						      genclen * sizeof(char));
				strncat(gencomments, Inline, GBUFSIZ);
				strncat(gencomments, "\n", GBUFSIZ);
			}
		}
	}
	Cfree(buffer);
	fclose(file);
	for (j = 0; j < dataset->numelements; j++)
		dataset->maxlen =
		    MAX(dataset->maxlen, dataset->element[j].seqlen +
					     dataset->element[j].offset);
	return;
}

typedef struct mya {
	int yy;
	int mm;
	int dd;
	int hr;
	int mn;
	int sc;
} sA;

AsciiTime(sA *a, char *asciitime)
{
	int j;
	char temp[GBUFSIZ];
	extern char month[12][6];

	a->dd = 0;
	a->yy = 0;
	a->mm = 0;
	sscanf(asciitime, "%d%5c%d", &(a->dd), temp, &(a->yy));
	temp[5] = '\0';
	for (j = 0; j < 12; j++)
		if (strcmp(temp, month[j]) == 0) a->mm = j + 1;
	if (a->dd < 0 || a->dd > 31 || a->yy < 0 || a->mm > 11) SetTime(a);
	return;
}

WriteGen(aln, filename, method, maskable) NA_Alignment *aln;
char *filename;
int method, maskable;
{
	int i, j, k, mask = -1;
	FILE *file;
	NA_Sequence *this_elem;
	extern char month[12][6];
	char c;
	if (aln == NULL) return;
	if (aln->na_ddata == NULL) return;

	file = fopen(filename, "w");
	if (file == NULL) {
		Warning("Cannot open file for output");
		return (1);
	}

	if (maskable && method != SELECT_REGION)
		for (j = 0; j < aln->numelements; j++)
			if (aln->element[j].elementtype == MASK &&
			    aln->element[j].selected)
				mask = j;

	for (j = 0; j < aln->numelements; j++) {
		if ((aln->element[j].selected && j != mask &&
		     method != SELECT_REGION) ||
		    (aln->element[j].subselected && method == SELECT_REGION) ||
		    (method == ALL)) {
			this_elem = &(aln->element[j]);
			fprintf(
			    file,
			    "LOCUS       %10s%8d bp    %4s  %10s   %2d%5s%4d\n",
			    this_elem->short_name,
			    this_elem->seqlen + this_elem->offset,
			    (this_elem->elementtype == DNA)	  ? "DNA"
			    : (this_elem->elementtype == RNA)	  ? "RNA"
			    : (this_elem->elementtype == MASK)	  ? "MASK"
			    : (this_elem->elementtype == PROTEIN) ? "PROT"
								  : "TEXT",
			    this_elem->attr & IS_CIRCULAR ? "Circular" : "",
			    this_elem->t_stamp.origin.dd,
			    month[this_elem->t_stamp.origin.mm - 1],
			    this_elem->t_stamp.origin.yy > 1900
				? this_elem->t_stamp.origin.yy
				: this_elem->t_stamp.origin.yy + 1900);
			if (this_elem->description[0])
				fprintf(file, "DEFINITION  %s\n",
					this_elem->description);
			if (this_elem->seq_name[0])
				fprintf(file, "  ORGANISM  %s\n",
					this_elem->seq_name);
			if (this_elem->id[0])
				fprintf(file, " ACCESSION  %s\n",
					this_elem->id);
			if (this_elem->authority[0])
				fprintf(file, "   AUTHORS  %s\n",
					this_elem->authority);
			if (this_elem->comments)
				fprintf(file, "%s\n", this_elem->comments);
			fprintf(file, "ORIGIN");
			if (this_elem->tmatrix) {
				if (mask == -1) {
					for (i = 0, k = 0;
					     k < this_elem->seqlen +
						     this_elem->offset;
					     k++) {
						if (method == SELECT_REGION) {
							if (aln->selection_mask
								[k] == '1') {
								if (i % 60 == 0)
									fprintf(
									    file,
									    "\n"
									    "%9"
									    "d",
									    i + 1);
								if (i % 10 == 0)
									fprintf(
									    file,
									    " ");
								fprintf(
								    file, "%c",
								    this_elem->tmatrix
									[getelem(
									    this_elem,
									    k)]);
								i++;
							}
						}
						else {
							if (i % 60 == 0)
								fprintf(file,
									"\n%9d",
									i + 1);
							if (i % 10 == 0)
								fprintf(file,
									" ");
							fprintf(
							    file, "%c",
							    this_elem->tmatrix
								[getelem(
								    this_elem,
								    k)]);
							i++;
						}
					}
				}
				else {
					for (k = 0; k < this_elem->seqlen +
							    this_elem->offset;
					     k++) {
						c = (char)getelem(
						    &(aln->element[mask]), k);
						if (c != '0' && c != '-') {
							if (k % 60 == 0)
								fprintf(file,
									"\n%9d",
									k + 1);
							if (k % 10 == 0)
								fprintf(file,
									" ");
							fprintf(
							    file, "%c",
							    this_elem->tmatrix
								[getelem(
								    this_elem,
								    k)]);
						}
					}
				}
			}
			else {
				if (mask == -1) {
					for (i = 0, k = 0;
					     k < this_elem->seqlen +
						     this_elem->offset;
					     k++) {
						if (method == SELECT_REGION) {
							if (aln->selection_mask
								[k] == '1') {
								if (i % 60 == 0)
									fprintf(
									    file,
									    "\n"
									    "%9"
									    "d",
									    i + 1);
								if (i % 10 == 0)
									fprintf(
									    file,
									    " ");
								fprintf(
								    file, "%c",
								    getelem(
									this_elem,
									k));
								i++;
							}
						}
						else {
							if (i % 60 == 0)
								fprintf(file,
									"\n%9d",
									i + 1);
							if (i % 10 == 0)
								fprintf(file,
									" ");
							fprintf(
							    file, "%c",
							    getelem(this_elem,
								    k));
							i++;
						}
					}
				}
				else {
					for (k = 0; k < this_elem->seqlen +
							    this_elem->offset;
					     k++) {
						c = (char)getelem(
						    &(aln->element[mask]), k);
						if (c != '0' && c != '-') {
							if (k % 60 == 0)
								fprintf(file,
									"\n%9d",
									k + 1);
							if (k % 10 == 0)
								fprintf(file,
									" ");
							fprintf(
							    file, "%c",
							    getelem(this_elem,
								    k));
						}
					}
				}
			}
			fprintf(file, "\n//\n");
		}
	}
	fclose(file);
	return;
}

SetTime(sA *a)
{
	struct tm *tim, *localtime();
	long clock;

	clock = time(0);
	tim = localtime(&clock);

	a->yy = tim->tm_year;
	a->mm = tim->tm_mon + 1;
	a->dd = tim->tm_mday;
	a->hr = tim->tm_hour;
	a->mn = tim->tm_min;
	a->sc = tim->tm_sec;
	return;
}

/*
 *	CheckType:  Check base composition to see if the sequence
 *	appears to be an amino acid sequence.  If it is, pass back
 *	TRUE, else FALSE.
 */
CheckType(seq, len) char *seq;
int len;
{
	int j, count1 = 0, count2 = 0;

	for (j = 0; j < len; j++)
		if (((seq[j] | 32) < 'z') && ((seq[j] | 32) > 'a')) {
			count1++;
			if (index("ACGTUNacgtun", seq[j]) == NULL) count2++;
		}

	return ((count2 > count1 / 4) ? TRUE : FALSE);
}