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read_input.c
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#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "read_input.h"
#include "structs.h"
#include "binencode.h"
#include "invdist.h"
#include "condense.h"
#ifdef MPBPA
#include "mpi.h"
#endif
void
check_genes ( int *genes, int num_genes, int at_genome )
{
int i, g0, g1;
int *checkArr;
checkArr = ( int * ) malloc ( ( num_genes + 1 ) * sizeof ( int ) );
if ( checkArr == ( int * ) NULL )
fprintf ( stderr, "ERROR: checkArr NULL\n" );
for ( i = 1; i <= num_genes; i++ )
checkArr[i] = 0;
for ( i = 0; i < num_genes; i++ )
{
g0 = genes[i];
g1 = ( g0 > 0 ? g0 : -g0 );
if ( g1 == 0 )
{
fflush ( outfile );
fclose ( outfile );
fprintf ( stderr, "ERROR: Reading Input Genome %d\n", at_genome );
fprintf ( stderr, "ERROR: Input gene == 0\n" );
exit ( -1 );
}
if ( g1 > num_genes )
{
fflush ( outfile );
fclose ( outfile );
fprintf ( stderr, "ERROR: Reading Input Genome %d\n", at_genome );
fprintf ( stderr,
"ERROR: Input gene (%d) larger than number of genes %d\n",
g0, num_genes );
exit ( -1 );
}
if ( checkArr[g1] != 0 )
{
fflush ( outfile );
fclose ( outfile );
fprintf ( stderr, "ERROR: Reading Input Genome %d\n", at_genome );
fprintf ( stderr, "ERROR: Duplicate gene (%d)\n", g1 );
exit ( -1 );
}
checkArr[g1] = 1;
}
for ( i = 1; i <= num_genes; i++ )
{
if ( checkArr[i] != 1 )
{
fflush ( outfile );
fclose ( outfile );
fprintf ( stderr, "ERROR: Reading Input Genome %d\n", at_genome );
fprintf ( stderr, "ERROR: Missing gene (%d)\n", i );
exit ( -1 );
}
}
free ( checkArr );
return;
}
/* Read data file of gene orders in format:
>genome name 1 2 4 3 5 -6 -10 -9 -8 7
genes 1..n. */
void
read_data ( FILE * input, struct genome_struct **genome_list,
int *num_genes, int *num_genomes, int INVDIST, int CIRCULAR,
int *condense_succ, int *condense_decode, int *orig_num_genes )
{
int genome_num;
int i, j, score;
int a;
int g;
char buf[MAX_STR_LEN];
char genebuf[MAX_STR_LEN];
int readingName;
int gnum;
int NumGenomes, NumGenes;
NumGenomes = 0;
NumGenes = -1;
/************/
readingName = 1;
j = 0;
a = fgetc ( input );
while ( a != EOF )
{
if ( j == MAX_STR_LEN )
{
fflush ( outfile );
fclose ( outfile );
fprintf ( stderr, "ERROR: Buffer overflow reading input\n" );
exit ( -1 );
}
switch ( a )
{
case '\n':
if ( j > 1 )
{
buf[j] = '\0';
j = 0;
if ( readingName )
{
if ( buf[0] != '>' )
{
fflush ( outfile );
fclose ( outfile );
fprintf ( stderr,
"\nERROR: reading genome name from input. " );
fprintf ( stderr,
"Expecting format: \">Name\" \n" );
exit ( -1 );
}
NumGenomes++;
}
else
{
i = 0;
gnum = 0;
while ( i < strlen ( buf ) )
{
while ( buf[i] == ' ' )
i++;
while ( ( buf[i] != ' ' ) && ( buf[i] != '\0' ) )
i++;
gnum++;
i++;
}
if ( NumGenes < 0 )
NumGenes = gnum;
else
{
if ( NumGenes != gnum )
{
fflush ( outfile );
fclose ( outfile );
fprintf ( stderr,
"ERROR: read_data() inconsistent num of genes\n" );
fprintf ( stderr,
"ERROR: Expecting %d genes, but ",
NumGenes );
fprintf ( stderr, "Genome %d has %d genes\n",
NumGenomes, gnum );
exit ( -1 );
}
}
}
readingName = 1 - readingName;
}
break;
case EOF:
fprintf ( outfile, "EOF\n" );
break;
default:
buf[j] = a;
j++;
}
a = fgetc ( input );
}
if ( NumGenomes > MAX_GENOMES )
{
fprintf ( stderr,
"ERROR: \tNumber of genomes in the input is %d, but\n",
NumGenomes );
fprintf ( stderr,
"\tGRAPPA is compiled with a maximum of %d genomes.\n",
MAX_GENOMES );
fprintf ( stderr, "\tPlease edit the header file \"structs.h\", " );
fprintf ( stderr, "increase the value\n" );
fprintf ( stderr, "\tof MAX_GENOMES (currently set to %d), ",
MAX_GENOMES );
fprintf ( stderr, "and recompile.\n" );
exit ( -1 );
}
if ( NumGenes > MAX_NUM_GENES )
{
fprintf ( stderr,
"ERROR: \tNumber of genes in the input is %d, but\n",
NumGenes );
fprintf ( stderr,
"\tGRAPPA is compiled with a maximum of %d genes.\n",
MAX_NUM_GENES );
fprintf ( stderr, "\tPlease edit the header file \"structs.h\", " );
fprintf ( stderr, "increase the value\n" );
fprintf ( stderr, "\tof MAX_NUM_GENES (currently set to %d), ",
MAX_NUM_GENES );
fprintf ( stderr, "and recompile.\n" );
exit ( -1 );
}
rewind ( input );
#ifdef MPBPA
if ( MYPROC == 0 )
{
#endif
fprintf ( outfile, "Number of Genomes:\t%d\n", NumGenomes );
fprintf ( outfile, "Number of Genes: \t%d\n", NumGenes );
fflush ( outfile );
#ifdef MPBPA
}
#endif
*genome_list =
( struct genome_struct * ) malloc ( NumGenomes *
sizeof ( struct genome_struct ) );
if ( *genome_list == ( struct genome_struct * ) NULL )
fprintf ( stderr, "ERROR: genome_list NULL\n" );
for ( i = 0; i < NumGenomes; i++ )
{
( *genome_list )[i].gnamePtr =
( char * ) malloc ( MAX_NAME * sizeof ( char ) );
if ( ( *genome_list )[i].gnamePtr == ( char * ) NULL )
{
fprintf ( stderr, "ERROR: gname NULL\n" );
}
}
/************/
genome_num = 0;
readingName = 1;
j = 0;
a = fgetc ( input );
while ( a != EOF )
{
if ( j == MAX_STR_LEN )
{
fprintf ( stderr, "ERROR: Buffer overflow reading input\n" );
exit ( -1 );
}
switch ( a )
{
case '\n':
if ( j > 1 )
{
buf[j] = '\0';
j = 0;
if ( readingName )
{
if ( buf[0] != '>' )
{
fprintf ( stderr,
"\nERROR: reading genome name from input. " );
fprintf ( stderr,
"Expecting format: \">Name\" \n" );
exit ( -1 );
}
if ( strlen ( buf + 1 ) > MAX_STR_LEN )
fprintf ( stderr,
"ERROR: Buffer overflow in genome name\n" );
strcpy ( ( *genome_list )[genome_num].gnamePtr,
buf + 1 );
( *genome_list )[genome_num].genome_num =
genome_num + 1;
( *genome_list )[genome_num].genes =
( int * ) malloc ( NumGenes * sizeof ( int ) );
if ( ( *genome_list )[genome_num].genes == NULL )
fprintf ( stderr,
"ERROR: cannot allocate genes\n" );
}
else
{
i = 0;
gnum = 0;
while ( i < strlen ( buf ) )
{
g = 0;
while ( buf[i] == ' ' )
i++;
while ( ( buf[i] != ' ' ) && ( buf[i] != '\0' ) )
genebuf[g++] = buf[i++];
genebuf[g] = '\0';
( *genome_list )[genome_num].genes[gnum] =
atoi ( genebuf );
gnum++;
g = 0;
i++;
}
check_genes ( ( *genome_list )[genome_num].genes,
NumGenes, genome_num + 1 );
genome_num++;
}
readingName = 1 - readingName;
}
break;
case EOF:
fprintf ( outfile, "EOF\n" );
break;
default:
buf[j] = a;
j++;
}
a = fgetc ( input );
}
fclose ( input );
#ifdef MPBPA
if ( MYPROC == 0 )
{
#endif
/* STACIA REDUCING OUTPUT
printGenomes(*genome_list, NumGenomes, NumGenes);
fprintf(outfile,"\n");
*/
#ifdef MPBPA
}
#endif
if ( INVDIST )
{
#ifdef MPBPA
if ( MYPROC == 0 )
{
#endif
if ( NumGenomes != 2 )
{
fprintf ( stderr, "WARNING: NUM_GENOMES == %3d ",
NumGenomes );
fprintf ( stderr,
" Only the first two genomes will be used\n\n" );
}
score =
invdist_circular_nomem ( *genome_list, *genome_list + 1,
NumGenes );
printf ( "score = %d\n", score );
fprintf ( outfile, "Inversion Distance: %12d\n", score );
fprintf ( outfile, "Breakpoint Distance: %12d\n",
hamming_distance_nomem ( *genome_list, *genome_list + 1,
NumGenes, CIRCULAR ) );
#ifdef MPBPA
}
MPI_Barrier ( MPI_COMM_WORLD );
MPI_Finalize ( );
#endif
fflush ( outfile );
fclose ( outfile );
exit ( 1 );
}
*orig_num_genes = NumGenes;
if ( NumGenomes >= 3 )
condense_genes ( *genome_list, NumGenomes, &NumGenes, CIRCULAR,
condense_succ + NumGenes,
condense_decode + NumGenes );
#ifdef VERYVERBOSE
#ifdef MPBPA
if ( MYPROC == 0 )
{
#endif
fprintf ( outfile, "Condensed Genomes:\n" );
printGenomes ( *genome_list, NumGenomes, NumGenes );
fprintf ( outfile, "\n" );
#ifdef MPBPA
}
MPI_Barrier ( MPI_COMM_WORLD );
#endif
#endif
*num_genes = NumGenes;
*num_genomes = NumGenomes;
return;
}