+++ /dev/null
-/* list_db.c - report values from map_db.c */
-
-/* copyright (c) 1999 William R. Pearson */
-
-/* format of the index file:
-
-1) map_db version number ["MP"+2 bytes]
-2) number of sequences in database [4 bytes]
-3) total length of database [8 bytes]
-4) longest sequence in database [8 bytes]
-5) list of offsets to definitions [num_seq+1] int*8
-6) list of offsets to sequences [num_seq+1] int*8
-7) list of flag characters for sequences [num_seq+1] bytes
- (used for GCG binary to encode 2bit or 4 bit representation)
-
- sequence files will be as defined by their format
-*/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include "uascii.h"
-#include "ncbl2_head.h"
-
-void src_int4_write(FILE *, int);
-void src_int4_read(FILE *, int *);
-void src_long4_read(FILE *, long *);
-void src_long8_write(FILE *, long);
-void src_long8_read(FILE *, long *);
-
-void newname(char *nname, char *oname, char *suff, int maxn);
-
-main(int argc, char **argv)
-{
- FILE *libi;
- char lname[256];
- char iname[256];
- char format[4];
- char *bp;
-
- int i;
- int d_pos; /* start of description */
- int s_pos; /* start of sequence */
- int attr; /* sequence attribute */
- int lib_aa; /* 0 => DNA, 1 => protein */
- int nlib; /* number of entries */
- long f_size;
- long max_len; /* longest sequence */
- long tot_len; /* total sequence length */
- int n1;
-
- int lib_size; /* current space available - may be realloc'ed */
- int lib_inc;
- int lib_type; /* 1 for protein, 0 for DNA */
- int lib_dna; /* dna=1; prot=0; */
- long *d_pos_arr; /* array of description pointers */
- long *s_pos_arr; /* array of description pointers */
- char *attr_arr; /* array of attribute chars */
-
- int mm64_flag;
-
- lib_type = 0;
- lib_dna = 0;
-
- /* open the database */
- if (argc > 1) strncpy(lname, argv[1],sizeof(lname));
- else {
- fprintf(stderr," Entry library name: ");
- fgets(lname,sizeof(lname),stdin);
- if ((bp=strchr(lname,'\n'))!=NULL) *bp='\0';
- }
-
- if ((bp=strchr(lname,' '))!=NULL) {
- lib_type = atoi(bp+1);
- *bp='\0';
- }
- else lib_type = 0;
-
- newname(iname,lname,"xin",sizeof(iname));
-
- if ((libi=fopen(iname,"r"))==NULL) {
- fprintf(stderr," cannot open %s\n",iname);
- exit(1);
- }
-
- fread(format,1,sizeof(format),libi);
- printf("%c%c%d %d\n",format[0],format[1],format[2],format[3]);
- mm64_flag = (format[2]==1);
-
- src_int4_read(libi,&lib_aa);
-
- if (mm64_flag) src_long8_read(libi,&f_size);
- else src_long4_read(libi,&f_size);
-
- src_int4_read(libi,&nlib);
-
- if (mm64_flag) {
- src_long8_read(libi,&tot_len);
- src_long8_read(libi,&max_len);
- }
- else {
- src_long4_read(libi,&tot_len);
- src_long4_read(libi,&max_len);
- }
-
- printf(" %d entries; tot: %ld; max: %ld\n",nlib,tot_len,max_len);
-
- /* allocate array of description pointers */
- if ((d_pos_arr=(long *)calloc(nlib+1, sizeof(long)))==NULL) {
- fprintf(stderr," cannot allocate %d for desc. array\n",nlib+1);
- exit(1);
- }
- /* allocate array of sequence pointers */
- if ((s_pos_arr=(long *)calloc(nlib+1, sizeof(long)))==NULL) {
- fprintf(stderr," cannot allocate %d for seq. array\n",nlib+1);
- exit(1);
- }
- if ((attr_arr=(char *)calloc(nlib+1, sizeof(char)))==NULL) {
- fprintf(stderr," cannot allocate %d for attr. array\n",nlib+1);
- exit(1);
- }
-
- if (mm64_flag) {
- for (i=0; i<=nlib; i++) src_long8_read(libi,&d_pos_arr[i]);
- for (i=0; i<=nlib; i++) src_long8_read(libi,&s_pos_arr[i]);
- }
- else {
- for (i=0; i<=nlib; i++) src_long4_read(libi,&d_pos_arr[i]);
- for (i=0; i<=nlib; i++) src_long4_read(libi,&s_pos_arr[i]);
- }
-
- fread(attr_arr,nlib+1,sizeof(char),libi);
- fclose(libi);
-
- printf("header\tseq\n");
-
- for (i=0; i<nlib; i++) printf("%ld\t%ld\n",d_pos_arr[i],s_pos_arr[i]);
-}
-
-void src_int4_read(FILE *fd, int *val)
-{
- int tval;
-#ifdef IS_BIG_ENDIAN
- fread(&tval,(size_t)4,(size_t)1,fd);
- *val = tval;
-#else
- unsigned char b[4];
-
- fread((char *)&b[0],(size_t)1,(size_t)4,fd);
- *val = 0;
- *val = (int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8)
- +(int)b[3];
-#endif
-}
-
-void src_long4_read(FILE *fd, long *val)
-{
- int tval;
-#ifdef IS_BIG_ENDIAN
- fread(&tval,(size_t)4,(size_t)1,fd);
- *val = tval;
-#else
- unsigned char b[4];
-
- fread((char *)&b[0],(size_t)1,(size_t)4,fd);
- *val = 0;
- *val = (int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8)
- +(int)b[3];
-#endif
-}
-
-void src_long8_read(FILE *fd, long *val)
-{
-#ifdef IS_BIG_ENDIAN
- fread((char *)val,(size_t)8,(size_t)1,fd);
-#else
- unsigned char b[8];
-
- fread((char *)&b[0],(size_t)1,(size_t)8,fd);
- *val = 0;
- *val = (int)
- ((((((((int)b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8)+(int)b[3]<<8)+
- (int)b[4]<<8)+(int)b[5]<<8)+(int)b[6]<<8)+(int)b[7];
-#endif
-}
-
-void src_int4_write(FILE *fd, int val)
-{
-#ifdef IS_BIG_ENDIAN
- fwrite(&val,(size_t)4,(size_t)1,fd);
-#else
- unsigned char b[4];
-
- b[3] = val & 255;
- b[2] = (val=val>>8)&255;
- b[1] = (val=val>>8)&255;
- b[0] = (val=val>>8)&255;
-
- fwrite(b,(size_t)1,(size_t)4,fd);
-#endif
-}
-
-void
-newname(char *nname, char *oname, char *suff, int maxn)
-{
- strncpy(nname,oname,maxn-1);
- strncat(nname,".",1);
- strncat(nname,suff,maxn-strlen(nname));
-}
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