#include <ctype.h>
#include <malloc.h>
#include <stdio.h>
#include <stdlib.h>

#include "global_defs.h"
/*
 *	Alloc.c
 *	Memory functions for Harvard Genome Laboratory.
 *	Last revised 6/3/91
 *
 *       Print error message, and die
 */
void ErrorOut(code, string) int code;
char *string;
{
	if (code == 0) {
		fprintf(stderr, "Error:%s\n", string);
		exit(1);
	}
	return;
}

/*
 *       Calloc count*size bytes with memory aligned to size.
 *	Return pointer to new block.
 */
char *Calloc(count, size)
int count, size;
/*unsigned count,size;*/
{
	char *temp;
	temp = calloc(count, (unsigned)size);

	if (count * size == 0) fprintf(stderr, "Allocate ZERO blocks?\n");
	ErrorOut(temp, "Cannot allocate memory");
	return (temp);
}

/*
 *	Reallocate memory at block, expand to size.
 *	Return pointer to (possibly) new block.
 */
char *Realloc(block, size)
char *block;
unsigned size;
{
	char *temp;
	temp = realloc(block, size);
	ErrorOut(temp, "Cannot change memory size");
	return (temp);
}

/*
 *	Free block Allocated by Calloc.
 *	Return error code from free().
 */

void Cfree(block) char *block;
{
	extern void Warning();
	if (block != NULL) {
#ifdef SUN4
		if (free(block) == 0) Warning("Error in Cfree...");
#endif
	}
	/*        else
			Warning("Error in Cfree, NULL block");
	*/
	return;
}

/*
 *	Print Warning message to stderr.
 */
void Warning(s) char *s;
{
	fprintf(stderr, "Warning:%s\n", s);
	return;
}

/*
 *	Get array element from a sequence structure.  The index
 *	is relative to the alignment.
 */
char GetElem(seq, indx)
Sequence *seq; /*Sequence to search*/
int indx;      /*Index relative to the global offset*/
{
	if ((indx < seq->offset) || (indx >= seq->offset + seq->seqlen))
		return ('-');
	else
		return ((char)(seq->c_elem[indx - seq->offset]));
}

/*
 *	Replace the array element at seq[indx] with elem.  The index
 *       is relative to the alignment.
 */

void ReplaceElem(seq, indx, elem) Sequence *seq; /*Sequence */
int indx;	    /*Position to overwrite (replace) */
unsigned char elem; /*Character to replace with */
{
	int j;
	extern char *Calloc();
	int width;

	/*
	 *	If no c_elem has been allocated yet...
	 */
	/*	if(index("abcdefghijklmnopqrstuvwxyz-0123456789",elem)==0)
			fprintf(stderr,"Warning (ReplaceElem) elem =
	   %c\n",elem);
	*/
	width = seq->offset - indx;
	if (seq->seqlen == 0 && elem != '-') {
		if (seq->seqmaxlen == 0 || seq->c_elem == NULL) {
			seq->c_elem = Calloc(4, sizeof(char));
			seq->offset = indx;
			seq->seqmaxlen = 4;
		}
		seq->seqlen = 1;
		seq->c_elem[0] = elem;
		seq->offset = indx;
	}
	/*
	 *	If inserting before the c_elem (< offset)
	 */
	else if ((indx < seq->offset) && (elem != '-')) {
		seq->seqmaxlen += width;
		seq->c_elem =
		    Realloc(seq->c_elem, seq->seqmaxlen * sizeof(char));
		for (j = seq->seqmaxlen - 1; j >= width; j--)
			seq->c_elem[j] = seq->c_elem[j - width];
		for (j = 0; j < width; j++) seq->c_elem[j] = '-';
		seq->c_elem[0] = elem;
		seq->seqlen += width;
		seq->offset = indx;
	}
	/*
	 * 	if inserting after c_elem (indx > offset + seqlen)
	 */
	else if ((indx >= seq->offset + seq->seqlen) && (elem != '-')) {
		if (indx - seq->offset >= seq->seqmaxlen) {
			seq->seqmaxlen = indx - seq->offset + 256;
			seq->c_elem =
			    Realloc(seq->c_elem, seq->seqmaxlen * sizeof(char));
		}
		for (j = seq->seqlen; j < seq->seqmaxlen; j++)
			seq->c_elem[j] = '-';
		seq->c_elem[indx - seq->offset] = elem;
		seq->seqlen = indx - seq->offset + 1;
	}
	else {
		if (indx - (seq->offset) >= 0 &&
		    indx - (seq->offset) < seq->seqlen)
			seq->c_elem[indx - (seq->offset)] = elem;
		else if (elem != '-')
			fprintf(stderr, "%c better be a -\n", elem);
	}
	return;
}

/*
 *	InsertElem is a modification of InsertElems, and should be
 *	optimized.		s.s.5/6/91
 */
int InsertElem(a, b, ch)
Sequence *a; /* Sequence */
int b;	     /*Position to insert BEFORE*/
char ch;     /*element to insert */
{
	char c[2];
	c[0] = ch;
	c[1] = '\0';

	return (InsertElems(a, b, c));
}

/*
 *	Make a copy of Sequence one, place in Sequence two
 */
void SeqCopy(one, two) Sequence *one, *two;
{
	int j;
	*two = *one;
	if (two->seqmaxlen) two->c_elem = Calloc(one->seqmaxlen, sizeof(char));
	if (two->commentsmaxlen)
		two->comments = Calloc(one->commentsmaxlen, sizeof(char));
	for (j = 0; j < one->seqlen; j++) two->c_elem[j] = one->c_elem[j];
	for (j = 0; j < one->commentslen; j++)
		two->comments[j] = one->comments[j];
	return;
}

/*
 *	Normalize seq (remove leading indels in the c_elem;
 */
void SeqNormal(seq) Sequence *seq;
{
	int len, j, shift_width, trailer;
	char *c_elem;
	len = seq->seqlen;

	c_elem = seq->c_elem;

	if (len == 0) return;

	for (shift_width = 0;
	     (shift_width < len) && (c_elem[shift_width] == '-'); shift_width++)
		;

	for (j = 0; j < len - shift_width; j++)
		c_elem[j] = c_elem[j + shift_width];

	seq->seqlen -= shift_width;
	seq->offset += shift_width;
	for (trailer = seq->seqlen - 1;
	     (c_elem[trailer] == '-' || c_elem[trailer] == '\0') &&
	     trailer >= 0;
	     trailer--)
		c_elem[trailer] = '\0';
	seq->seqlen = trailer + 1;
	return;
}

void SeqRev(seq, min, max) Sequence *seq;
int min, max;
/*
	SeqRev will reverse a given sequence within a window from
	min to max (inclusive).  The idea is to allow several sequences
	to be reversed in such a manner as to allow them to remain aligned.

	    BEFORE				    AFTER
    min |           | max		    min |	    |max
	aaaacccgggttt				tttgggcccaaaa
	aaa-cccg-g				---g-gccc-aaa
	----cccgggt				--tgggccc
*/
{
	int j;
	char temp1, temp2;
	extern char GetElem();
	extern void ReplaceElem();

	for (j = 0; j <= (max - min) / 2; j++) {
		temp1 = GetElem(seq, min + j);
		temp2 = GetElem(seq, max - j);
		ReplaceElem(seq, min + j, (unsigned char)temp2);
		ReplaceElem(seq, max - j, (unsigned char)temp1);
	}

	seq->direction *= -1;

	SeqNormal(seq);
	return;
}

/* sequence complementing. */
void SeqComp(seq) Sequence *seq;
{
	int j;
	unsigned char in, out, case_bit;
	char *c;
	static int tmatr[16] = {'-', 'a', 'c', 'm', 'g', 'r', 's', 'v',
				't', 'w', 'y', 'h', 'k', 'd', 'b', 'n'};

	static int matr[128] = {
	    0,	  0,	0,    0,    0,	  0,	0,    0,    0,	  0,	0,
	    0,	  0,	0,    0,    0,	  0,	0,    0,    0,	  0,	0,
	    0,	  0,	0,    0,    0,	  0,	0,    0,    0,	  0x00, 0,
	    0,	  0,	0,    0,    0,	  0,	0,    0,    0,	  0,	0,
	    0,	  0,	0,    0,    0,	  0,	0,    0,    0,	  0,	0,
	    0,	  0,	0,    0,    0,	  0,	0,    0,    0,	  0,	0x01,
	    0x0e, 0x02, 0x0d, 0,    0,	  0x04, 0x0b, 0,    0,	  0x0c, 0,
	    0x03, 0x0f, 0,    0x05, 0,	  0x05, 0x06, 0x08, 0x08, 0x07, 0x09,
	    0x00, 0x0a, 0,    0,    0,	  0,	0,    0,    0,	  0x01, 0x0e,
	    0x02, 0x0d, 0,    0,    0x04, 0x0b, 0,    0,    0x0c, 0,	0x03,
	    0x0f, 0,	0x05, 0,    0x05, 0x06, 0x08, 0x08, 0x07, 0x09, 0x00,
	    0x0a, 0,	0,    0,    0,	  0x00, 0};

	c = seq->c_elem;
	for (j = 0; j < seq->seqlen; j++) {
		/*
		 *	Save Case bit...
		 */
		case_bit = c[j] & 32;
		out = 0;
		in = matr[c[j]];
		if (in & 1) out |= 8;
		if (in & 2) out |= 4;
		if (in & 4) out |= 2;
		if (in & 8) out |= 1;

		if (case_bit == 0)
			c[j] = toupper(tmatr[out]);
		else
			c[j] = tmatr[out];
	}

	seq->direction *= -1;
	seq->strandedness = (seq->strandedness == 2)   ? 1
			    : (seq->strandedness == 1) ? 2
						       : 0;
	return;
}