/* mdump.c
Program:   mdump.c
Version:   1.0.2
Date:      29-JUL-2002
Author:    David Mathog, Biology Division, Caltech
email:     mathog@caltech.edu
Copyright: 2002 David Mathog and California Institute of Technology (Caltech)
   
Description:  
   Dump data out of binary files.
   Useful among other things for extracting NCBI
   gi values from the .[pn]nd blast database file and
   extracts from it the gi numbers present in that file.
   If the byte order is reversed use -flip to turn them over.
   
   Note that long long (type s) is not always available.  If it isn't
   compile with -D MDUMP_NOLONGLONG.
   
   Note that many older compilers do not support long long or do
   not use lld,llu etc.   gcc supports all of these and is available
   for most platforms.
     
License terms:
    You may run this program on any platform. You may
    redistribute the source code of this program subject to
    the condition that you do not first modify it in any way.
    You may  distribute binary versions of this program so long
    as they were compiled from unmodified source code.  There
    is no charge for using this software.  You may not charge
    others for the use of this software.

Changes:

  1.0.2 29-JUL-2002, Mathog, fixed bugs MDUMP_NOLONGLONG
  1.0.1 30-APR-2002, Mathog, fixed bugs in -show and -offset
  1.0   21-APR-2002, first release

*/
#include <stdlib.h>
#include <stdio.h>
#include <unistd.h>
#include <string.h>
#include <ctype.h>            /* for toupper, tolower */

#define EXVERSTRING "1.0.2  29-JUL-2002"

/* prototypes */
int  lcl_strcasecmp(char *s1, char *s2);
void emit_ds(void);
void emit_help(void);
void flipit(char *carray, int size);
void insane(char *string);
void  process_command_line_args(int argc,char **argv,
  char *dtype, int *offset, int *interval, int *multiple,
  int *blocks, int *usesign, int *flip, int *show,  char **format);
void setinonnegnumeric(int *val,int *numarg,int argc,char **argv,char * label);
void setstring(char **val,int *numarg,int argc,char **argv,char * label);
void setchar(char *val,int *numarg,int argc,char **argv,char * label);

/* globals */

FILE *lcl_stdin;
FILE *lcl_stdout;

/* functions and main */

int  lcl_strcasecmp(char *s1, char *s2){
int c1;
int c2;
  for(; ;s1++,s2++){
    c1=toupper(*s1);
    c2=toupper(*s2);
    if(c1 < c2)return -1;
    if(c1 > c2)return  1;
    if(c1 == 0)return  0;  /*c2 also is 0 in this case */
  }
}

void insane(char *string){
 (void) fprintf(stderr,"%s\n",string);
 exit(EXIT_FAILURE);
}

/* flipit inverts the byte order in an array of characters 
   where size is 2,4,8 or larger (and even) */

void flipit(char *carray, int size){
char ctemp;
int i;
    for(i=0; i<size/2; i++){
      ctemp            =  carray[i];
      carray[i]        =  carray[size-i-1];
      carray[size-i-1] =  ctemp;
    }
}



void setinonnegnumeric(int *val,int *numarg,int argc,char **argv,char * label){
      (*numarg)++;
      if( ( *numarg >= argc ) || (argv[*numarg] == NULL)){
        (void) fprintf( stderr, "%s: missing argument\n",label);
        exit(EXIT_FAILURE);
      }
      if(sscanf(argv[*numarg],"%d",val) != 1){
        (void) fprintf(stderr,"Bad integer argument/parameter [%s %s] \n",label,argv[*numarg]);
        exit(EXIT_FAILURE);
      }
      if(*val < 0){
        (void) fprintf(stderr,"Illegal negative integer argument/parameter [%s %s] \n",label,argv[*numarg]);
        exit(EXIT_FAILURE);
      }
}

void setstring(char **val,int *numarg,int argc,char **argv,char * label){
      (*numarg)++;
      if( ( *numarg >= argc ) || (argv[*numarg] == NULL)){
        (void) fprintf( stderr, "%s: missing argument\n",label);
        exit(EXIT_FAILURE);
      }
      *val = argv[*numarg];
}

void setchar(char *val,int *numarg,int argc,char **argv,char * label){
      (*numarg)++;
      if( ( *numarg >= argc ) || (argv[*numarg] == NULL)){
        (void) fprintf( stderr, "%s: missing argument\n",label);
        exit(EXIT_FAILURE);
      }
      *val = *(argv[*numarg]);
}

void emit_ds(void){
    (void) fprintf(stderr,"Data sizes in bytes are:\n");
    (void) fprintf(stderr,"c    %d\n",sizeof(char));
    (void) fprintf(stderr,"w    %d\n",sizeof(short int));
    (void) fprintf(stderr,"l    %d\n",sizeof(int));
#ifdef MDUMP_NOLONGLONG
    (void) fprintf(stderr,"s    unavailable\n");
#else
    (void) fprintf(stderr,"s    %d\n",sizeof(long long));
#endif
    (void) fprintf(stderr,"f    %d\n",sizeof(float));
    (void) fprintf(stderr,"d    %d\n",sizeof(double));
    exit(EXIT_SUCCESS);
}

void emit_help(void){
    (void) fprintf(stderr,"usage: mdump [options] (dump data from stdin/file to stdout/file)\n");
    (void) fprintf(stderr,"\noptions:\n");
    (void) fprintf(stderr,"   -in   file   file to dump, if not specified, from stdin\n");
    (void) fprintf(stderr,"   -out  file   write output to this file, if not specified, to stdout\n");
    (void) fprintf(stderr,"   -dtype    t  c=char, s=short, l=long (default), g=longlong, f=float, d=double\n");
    (void) fprintf(stderr,"   -offset   N  begin this many data elements into file, 0=default\n");
    (void) fprintf(stderr,"   -interval N  number of data elements in each repeat block, 1=default\n");
    (void) fprintf(stderr,"   -multiple N  number of data elements to dump from each block (all to one line)\n");
    (void) fprintf(stderr,"                default is interval value\n");
    (void) fprintf(stderr,"   -blocks   N  number of blocks to dump, 0=all=default\n");
    (void) fprintf(stderr,"   -signed      default is unsigned.  Applies to c,s,l,g data types.\n");
    (void) fprintf(stderr,"                (For g type also change format to lld)\n");
    (void) fprintf(stderr,"   -show     t  show offset to data positions in file (relative to -offset)\n");
    (void) fprintf(stderr,"                as:  (hex) 1: bytes, 2: data elements, 3: blocks\n");
    (void) fprintf(stderr,"                   (octal) 4: bytes, 5: data elements, 6: blocks\n");
    (void) fprintf(stderr,"                 (decimal) 7: bytes, 8: data elements, 9: blocks\n");
    (void) fprintf(stderr,"                anything else = do not show position = default\n");
    (void) fprintf(stderr,"   -format 'string'   C format string for output. ' %%width.precisionType' :\n");
    (void) fprintf(stderr,"                c:   c[har],d[ecimal],o[ctal],[he]x default: ' %%c'\n");
    (void) fprintf(stderr,"                s,l: d,o,x                          default: ' %%9d'\n");
    (void) fprintf(stderr,"                g:   ll(d,u[nsigned],o,x)           default: ' %%20llu'\n");
    (void) fprintf(stderr,"                f,d: f[loat],e[xponent]             default: ' %%9e'\n");
    (void) fprintf(stderr,"   -flip     N  invert byte order, as is=default\n");
    (void) fprintf(stderr,"                Ignored for type c.\n");
    (void) fprintf(stderr,"   -ds          Emit data sizes\n");
    (void) fprintf(stderr,"   -h           print this help message (also -help --h --help -? --?)\n");
    (void) fprintf(stderr,"   -i           emit version, copyright, license and contact information\n\n");
    (void) fprintf(stderr,"\nexamples:\n");
    (void) fprintf(stderr," %% mdump -in somefile -dtype l -format ' %%8.8x' -interval 4 -show 2\n");
    (void) fprintf(stderr,"       Dump in hex format integer elements in blocks of 4 per line\n");
    (void) fprintf(stderr,"       and number the lines by data block.\n");
    (void) fprintf(stderr," %% echo ABCD | mdump -dtype c -format ' %%3.3o' -interval 4 -blocks 1\n");
    (void) fprintf(stderr,"       Emits the octal values for the four characters ABCD.\n");
    exit(EXIT_FAILURE);
}

void  process_command_line_args(int argc,char **argv,
  char *dtype, int *offset, int *interval, int *multiple,
  int *blocks, int *usesign, int *flip, int *show,  char **format){
  
int numarg;
int multset=0;

lcl_stdin=stdin;
lcl_stdout=stdout;
*dtype='l';     /* int4 */
*offset=0;      /* start from first int */
*interval=1;    /* emit in blocks of one */
*multiple=1;    /* emit all in the interval = 1 */
*blocks=0;      /* emit all blocks */
*usesign=0;     /* unsigned int */
*flip=0;        /* do not flip bytes */
*show=0;        /* do not show data offsets */
**format='\0';   /* nothing in format, initially */

  for(numarg=1;numarg<argc;numarg++){
    if(0==lcl_strcasecmp(argv[numarg], "-flip")){
      *flip=1;
    }
    else if(0==lcl_strcasecmp(argv[numarg], "-signed")){
      *usesign=1;
    }
    else if(lcl_strcasecmp(argv[numarg], "-in")==0){
      lcl_stdin=fopen(argv[++numarg],"r");
      if(lcl_stdin==NULL)insane("mdump: fatal error: could not open input file");
      continue;
    }
    else if(lcl_strcasecmp(argv[numarg], "-out")==0){
      lcl_stdout=fopen(argv[++numarg],"w");
      if(lcl_stdout==NULL)insane("mdump: fatal error: could not open output file");
      continue;
    }
    else if(0==lcl_strcasecmp(argv[numarg], "-show")){
      setinonnegnumeric(show,&numarg,argc,argv,"-show");
    }
    else if(0==lcl_strcasecmp(argv[numarg], "-dtype")){
      setchar(dtype,&numarg,argc,argv,"-dtype");
    }
    else if(0==lcl_strcasecmp(argv[numarg], "-offset")){
      setinonnegnumeric(offset,&numarg,argc,argv,"-offset");
    }
    else if(0==lcl_strcasecmp(argv[numarg], "-interval")){
      setinonnegnumeric(interval,&numarg,argc,argv,"-interval");
    }
    else if(0==lcl_strcasecmp(argv[numarg], "-multiple")){
      setinonnegnumeric(multiple,&numarg,argc,argv,"-multiple");
      multset=1;
    }
    else if(0==lcl_strcasecmp(argv[numarg], "-blocks")){
      setinonnegnumeric(blocks,&numarg,argc,argv,"-blocks");
    }
    else if(0==lcl_strcasecmp(argv[numarg], "-format")){
      setstring(format,&numarg,argc,argv,"-format");
    }
    else if(lcl_strcasecmp(argv[numarg], "-i")==0){
      (void)fprintf(stderr,"Version:   %s\n",EXVERSTRING);
      (void)fprintf(stderr,"bugs to:   mathog@caltech.edu\n");
      (void)fprintf(stderr,"Copyright: 2002 David Mathog and California Institute of Technology\n");
      (void)fprintf(stderr,"License terms:\n");
      (void)fprintf(stderr,"    You may run this program on any platform. You may\n");
      (void)fprintf(stderr,"    redistribute the source code of this program subject to\n");
      (void)fprintf(stderr,"    the condition that you do not first modify it in any way.\n");
      (void)fprintf(stderr,"    You may  distribute binary versions of this program so long\n");
      (void)fprintf(stderr,"    as they were compiled from unmodified source code.  There\n");
      (void)fprintf(stderr,"    is no charge for using this software.  You may not charge\n");
      (void)fprintf(stderr,"    others for the use of this software.\n");
      exit(EXIT_SUCCESS);
    }
    else if( (lcl_strcasecmp(argv[numarg], "-h")==0)     ||
             (lcl_strcasecmp(argv[numarg], "--h")==0)    ||
             (lcl_strcasecmp(argv[numarg], "-?")==0)     ||
             (lcl_strcasecmp(argv[numarg], "--?")==0)    ||
             (lcl_strcasecmp(argv[numarg], "-help")==0)  ||
             (lcl_strcasecmp(argv[numarg], "--help")==0) ){
       emit_help();
    }
    else{
      (void) fprintf(stderr,"mdump:fatal error:no such parameter [%s]\n",argv[numarg]);
      emit_help();
    }
  }
  if(multset==0)*multiple=*interval;
}

int main(int argc, char *argv[]){
int   count,repcount,mcount,bcount,dangle;
int   offset, interval, multiple;
int   blocks, usesign, flip,show;
int   dsize,dformat;
char  dtype;
char  *carray;
char  cformat[100];
char *format=&cformat[0];

char      cv;
short int sv;
int       lv;
#ifdef MDUMP_NOLONGLONG
/* long long not supported on this platform */
#else
long long gv;
#endif
float     fv;
double    dv;

  process_command_line_args(argc,argv,
     &dtype, &offset, &interval, &multiple,
     &blocks, &usesign, &flip, &show, &format);
    
  dangle=0;
  count=0;
  repcount=0;
  mcount=0;
  bcount=0;
  switch (dtype) {
    case 'c':
    case 'C':
      dsize=sizeof(char);
      dformat=0;
      carray = &cv;
      if(*format=='\0')(void) strcpy(format," %c");
      break;
    case 's':
    case 'S':
      dsize=sizeof(short int);
      dformat=2;
      carray = (char *) &sv;
      if(*format=='\0')(void) strcpy(format," %9d");
      break;
    case 'l':
    case 'L':
      dsize=sizeof(int);
      dformat=4;
      carray = (char *) &lv;
      if(*format=='\0')(void) strcpy(format," %9d");
      break;
    case 'f':
    case 'F':
      dsize=sizeof(float);
      dformat=6;
      carray = (char *) &fv;
      if(*format=='\0')(void) strcpy(format," %9e");
      break;
    case 'd':
    case 'D':
      dsize=sizeof(double);
      dformat=8;
      carray = (char *) &dv;
      if(*format=='\0')(void) strcpy(format," %9e");
      break;
    case 'g':
    case 'G':
#ifdef MDUMP_NOLONGLONG
      (void) fprintf(stderr,"mdump, fatal error: type s is not supported on this platform\n");
      exit(EXIT_FAILURE);
#else /* MDUMP_NOLONGLONG */
      dsize=sizeof(long long);
      dformat=10;
      carray = (char *) &gv;
      if(*format=='\0')(void) strcpy(format," %20llu");
      break;
#endif /* MDUMP_NOLONGLONG */
    default:
      (void)fprintf(stderr,"mtype, fatal error, unknown data type %c\n",dtype);
      exit(EXIT_FAILURE);
  }
  if(usesign)dformat++;
  
  while(fread(carray,dsize,1,lcl_stdin)>0){
  

    count++;
    if(count<offset+1)continue;
    if(mcount < multiple){
       if(mcount==0){
         switch(show){
           case 1:   /* byte offsets, hex */
             (void) fprintf(lcl_stdout,"%8.8x ",(count-offset-1)*dsize);
             break;
           case 2:   /* data element offsets, hex */
             (void) fprintf(lcl_stdout,"%8.8x ",(count-offset-1));
             break;
           case 3:   /* block offsets, hex */
             (void) fprintf(lcl_stdout,"%8.8x ",(count-offset-1)/interval);
             break;
           case 4:   /* byte offsets, octal */
             (void) fprintf(lcl_stdout,"%11.11o ",(count-offset-1)*dsize);
             break;
           case 5:   /* data element offsets, octal */
             (void) fprintf(lcl_stdout,"%11.11o ",(count-offset-1));
             break;
           case 6:   /* block offsets, octal */
             (void) fprintf(lcl_stdout,"%11.11o ",(count-offset-1)/interval);
             break;
           case 7:   /* byte offsets, decimal */
             (void) fprintf(lcl_stdout,"%9d ",(count-offset-1)*dsize);
             break;
           case 8:   /* data element offsets, decimal */
             (void) fprintf(lcl_stdout,"%9d ",(count-offset-1));
             break;
           case 9:   /* block offsets, decimal */
             (void) fprintf(lcl_stdout,"%9d ",(count-offset-1)/interval);
             break;
         }         
       }
       if(flip){ flipit(carray,dsize); }
       switch (dformat) {
          case 0: 
            (void) fprintf(lcl_stdout,format,(unsigned char) cv);
            break;
          case 1:
            (void) fprintf(lcl_stdout,format,(char) cv);
            break;
          case 2: 
            (void) fprintf(lcl_stdout,format,(unsigned short int) sv);
            break;
          case 3:
            (void) fprintf(lcl_stdout,format, sv);
            break;
          case 4: 
            (void) fprintf(lcl_stdout,format, (unsigned int) lv);
            break;
          case 5:
            (void) fprintf(lcl_stdout,format, lv);
            break;
          case 6: /* no unsigned for float */ 
          case 7:
            (void) fprintf(lcl_stdout,format, fv);
            break;
          case 8: /* no unsigned for double */
          case 9:
            (void) fprintf(lcl_stdout,format, dv);
            break;
          case 10: 
#ifndef  MDUMP_NOLONGLONG
           (void) fprintf(lcl_stdout,format, (unsigned long long) gv);
#endif
            break;
          case 11:
#ifndef  MDUMP_NOLONGLONG
            (void) fprintf(lcl_stdout,format, gv);
#endif
            break;
       }
       dangle=1;
    }
    repcount++;
    mcount++;
    if(repcount>=interval){
       repcount=0;
       mcount=0;
       bcount++;
       (void) fprintf(lcl_stdout,"\n");
       dangle=0;
       if(blocks != 0 && bcount >= blocks)break;
    }
  }
  
  if(dangle)(void) fprintf(lcl_stdout,"\n");
  exit(EXIT_SUCCESS);
}