// fileio.cpp (166 lines)
//
// Coded by: Joseph Bertolami 
// Email: jbertola@uci.edu
//
// ICS 175A, Winter 2004
//

#include "fileio.h"


// Author: Joseph Bertolami
// Email: jbertola@uci.edu
int DFile::ReadFile(char *filename)
{
	if ( !filename ) return 0;

	long f_size = 0;
	FILE *f = fopen(filename, "r");
	if ( !f ) printf("Error: Unable to open %s\n", filename);

	// read file size (avoid Win32!)
	fseek(f, 0, SEEK_END);
	f_size = ftell(f);
	fclose(f);

	f = fopen(filename, "r");
	if ( !f ) printf("Error: Unable to open %s\n", filename);

	char *data = (char *) malloc(f_size+1);
	memset(data, 0, f_size);

	int read = (int) fread(data, 1, (size_t) f_size, f);
	if ( read == 0 ) printf("Error: Unable to read bytes from %s\n", filename);
	else printf("Read %i bytes\n", read);

	data[f_size] = '\0';
		
	fclose(f);
		
	if ( buffer ) delete buffer;
	buffer = new DString(data);

	return buffer->length;
}

// Author: Joseph Bertolami
// Email: jbertola@uci.edu
int DFile::WriteFile(char *filename)
{
	if ( !filename || !buffer ) return 0;

	FILE *f = fopen(filename, "w");
	if ( !f ) printf("Error: Unable to open file %s\n", filename);

	int wrote = (int) fwrite(buffer->buffer, 1, (size_t) buffer->length, f);
		
	if ( wrote == 0 ) printf("Unable to write bytes to %s\n", filename);
	else printf("Wrote %i bytes\n", wrote);

	fclose(f);
	return wrote;
}

// Author: Joseph Bertolami
// Email: jbertola@uci.edu
// Modified by: Nicholas Urrea (just added case insensivitiy for reading in genes)
int DGFile::ReadGeneFile(char *filename)
{
	if ( ReadFile(filename) == 0 )
		return 0;

	unsigned long cur_gene = -1;

	// now buffer is valid and contains full file data, we simply must parse 
	// tokenize by newline, a line is either a gene header, or gene data
	// if it is a gene header, parse it, if it is data, add it to current gene's data
	char * backup = strdup(buffer->buffer);
	char * token = strtok(backup, "\r\n");

	// first lets gather the number of genomic sequences since we lack a good
	// data structure basecode

	do
	{
		if ( token[0] == '>' )
			num_genes++;
	} while ( token = strtok(NULL, "\r\n") );

	printf("Number of genes in file: %i\n", num_genes);
	genes = new CGene[num_genes];

	if ( backup ) free(backup);
	backup = strdup(buffer->buffer);
	token = strtok(backup, "\r\n");

	do 
	{
		if ( token[0] == '>' )
		{ // parsing header
			cur_gene++;

			if ( cur_gene >= num_genes )
			{
				printf("Critical error: gene buffer overrun\n");
				return -1;
			}

			char gname[80]; memset(gname, 0, 80);
			int ret = sscanf(token, "> %s from %i to %i, size %i", gname, genes[cur_gene].neg_range, genes[cur_gene].pos_range, genes[cur_gene].size);
			genes[cur_gene].name.set(gname);

			printf("Read Gene %i: %s\n", cur_gene, genes[cur_gene].name.buffer);
		}
		// this check really isnt necessary... but for security
		else if ( token[0] == 'A' || token[0] == 'T' || 
				  token[0] == 'G' || token[0] == 'C' || 
				  token[0] == 'a' || token[0] == 't' ||
				  token[0] == 'g' || token[0] == 'c' )
		{
			// if speed becomes an issue, pre-size the sequence buffers as specified
			// by the size parameter in the gene header.. this isnt done for now b/c
			// we arent assuming the header is necessarily correct

			// Case insensitivity added by Nicholas Urrea:
			// convert all chars to upper case !!
			for(unsigned int i=0; i<strlen(token); i++)
			{
				// detected lower case letters, convert to upper case
				if( token[i] == 'a' ) token[i] = 'A';
				else if( token[i] == 't' ) token[i] = 'T';
				else if( token[i] == 'g' ) token[i] = 'G';
				else if( token[i] == 'c' ) token[i] = 'C';
			}	

			// parsing genomic sequence
			char * temp = strdup(token);
			if ( genes[cur_gene].sequence.length == 0 )
				genes[cur_gene].sequence.set(temp);
			else
			{
				DString addTo(temp); // will free itself at scope exit
				genes[cur_gene].sequence += addTo;
			}
		}

	} while ( token = strtok(NULL, "\r\n") );

	return 0;
}

// Author: Joseph Bertolami
// Email: jbertola@uci.edu
CGene * DGFile::GetGene(int gene)
{
	if ( gene >= 0 && gene < num_genes )
		return &genes[gene];
}

// Author: Joseph Bertolami
// Email: jbertola@uci.edu
DString * DGFile::GetGeneData(int gene)
{
	if ( gene >= 0 && gene < num_genes )
		return &genes[gene].sequence;
}