📄 sim.c
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static char ALINE[51], BLINE[51], CLINE[51];
long display(A,B,M,N,S,AP,BP) char A[], B[]; long M, N; long S[], AP, BP;
{ register char *a, *b, *c;
register long i, j, op;
long lines, ap, bp;
char x, y, z;
i = j = op = lines = 0;
ap = AP;
bp = BP;
a = ALINE;
b = BLINE;
c = CLINE;
while (i < M || j < N)
{ if (op == 0 && *S == 0)
{ op = *S++;
*a = A[++i];
*b = B[++j];
x = *a++;
y = *b++;
z = ' ';
if (x == y)
z = '|';
if (
(x == 'A' && y == 'G') ||
(x == 'C' && y == 'T') ||
(x == 'G' && y == 'A') ||
(x == 'T' && y == 'C')
) z = ':';
*c++ = z;
}
else
{ if (op == 0)
op = *S++;
if (op > 0)
{ *a++ = ' ';
*b++ = B[++j];
op--;
}
else
{ *a++ = A[++i];
*b++ = ' ';
op++;
}
*c++ = '-';
}
if (a >= ALINE+50 || i >= M && j >= N)
{ *a = *b = *c = '\0';
printf("\n%5d ",50*lines++);
for (b = ALINE+10; b <= a; b += 10)
printf(" . :");
if (b <= a+5)
printf(" .");
printf("\n%5d %s\n %s\n%5d %s\n",ap,ALINE,CLINE,bp,BLINE);
ap = AP + i;
bp = BP + j;
a = ALINE;
b = BLINE;
c = CLINE;
}
}
}
/* lib.c - library of C procedures. */
/* fatal - print message and die */
fatal(msg)
char *msg;
{
fprintf(stderr, "%s\n", msg);
exit(1);
}
/* fatalf - format message, print it, and die */
fatalf(msg, val)
char *msg, *val;
{
fprintf(stderr, msg, val);
putc('\n', stderr);
exit(1);
}
/* ckopen - open file; check for success */
FILE *ckopen(name, mode)
char *name, *mode;
{
FILE *fopen(), *fp;
if ((fp = fopen(name, mode)) == NULL)
fatalf("Cannot open %s.", name);
return(fp);
}
/* ckalloc - allocate space; check for success */
char *ckalloc(amount)
long amount;
{
char *malloc(), *p;
if ((p = malloc( (unsigned) amount)) == NULL)
fatal("Ran out of memory.");
return(p);
}
/*****************************************************/
/* Various timer routines. */
/* Al Aburto, aburto@marlin.nosc.mil, 16 Dec 1995 */
/* */
/* t = dtime() outputs the current time in seconds. */
/* Use CAUTION as some of these routines will mess */
/* up when timing across the hour mark!!! */
/* */
/* For timing I use the 'user' time whenever */
/* possible. Using 'user+sys' time is a separate */
/* issue. */
/* */
/* Example Usage: */
/* [timer options added here] */
/* main() */
/* { */
/* double starttime,benchtime,dtime(); */
/* */
/* starttime = dtime(); */
/* [routine to time] */
/* benchtime = dtime() - starttime; */
/* } */
/* */
/* [timer code below added here] */
/*****************************************************/
/*******************/
/* Amiga dtime() */
/*******************/
#ifdef Amiga
#include <ctype.h>
#define HZ 50
double dtime()
{
double q;
struct tt {
long days;
long minutes;
long ticks;
} tt;
DateStamp(&tt);
q = ((double)(tt.ticks + (tt.minutes * 60L * 50L))) / (double)HZ;
return q;
}
#endif
/*****************************************************/
/* UNIX dtime(). This is the preferred UNIX timer. */
/* Provided by: Markku Kolkka, mk59200@cc.tut.fi */
/* HP-UX Addition by: Bo Thide', bt@irfu.se */
/*****************************************************/
#ifdef UNIX
#include <sys/time.h>
#include <sys/resource.h>
#ifdef hpux
#include <sys/syscall.h>
#define getrusage(a,b) syscall(SYS_getrusage,a,b)
#endif
struct rusage rusage;
double dtime()
{
double q;
getrusage(RUSAGE_SELF,&rusage);
q = (double)(rusage.ru_utime.tv_sec);
q = q + (double)(rusage.ru_utime.tv_usec) * 1.0e-06;
return q;
}
#endif
/***************************************************/
/* UNIX_Old dtime(). This is the old UNIX timer. */
/* Use only if absolutely necessary as HZ may be */
/* ill defined on your system. */
/***************************************************/
#ifdef UNIX_Old
#include <sys/types.h>
#include <sys/times.h>
#include <sys/param.h>
#ifndef HZ
#define HZ 60
#endif
struct tms tms;
double dtime()
{
double q;
times(&tms);
q = (double)(tms.tms_utime) / (double)HZ;
return q;
}
#endif
/*********************************************************/
/* VMS dtime() for VMS systems. */
/* Provided by: RAMO@uvphys.phys.UVic.CA */
/* Some people have run into problems with this timer. */
/*********************************************************/
#ifdef VMS
#include time
#ifndef HZ
#define HZ 100
#endif
struct tbuffer_t
{
int proc_user_time;
int proc_system_time;
int child_user_time;
int child_system_time;
};
struct tbuffer_t tms;
double dtime()
{
double q;
times(&tms);
q = (double)(tms.proc_user_time) / (double)HZ;
return q;
}
#endif
/******************************/
/* BORLAND C dtime() for DOS */
/******************************/
#ifdef BORLAND_C
#include <ctype.h>
#include <dos.h>
#include <time.h>
#define HZ 100
struct time tnow;
double dtime()
{
double q;
gettime(&tnow);
q = 60.0 * (double)(tnow.ti_min);
q = q + (double)(tnow.ti_sec);
q = q + (double)(tnow.ti_hund)/(double)HZ;
return q;
}
#endif
/**************************************/
/* Microsoft C (MSC) dtime() for DOS */
/**************************************/
#ifdef MSC
#include <time.h>
#include <ctype.h>
#define HZ CLOCKS_PER_SEC
clock_t tnow;
double dtime()
{
double q;
tnow = clock();
q = (double)tnow / (double)HZ;
return q;
}
#endif
/*************************************/
/* Macintosh (MAC) Think C dtime() */
/*************************************/
#ifdef MAC
#include <time.h>
#define HZ 60
double dtime()
{
double q;
q = (double)clock() / (double)HZ;
return q;
}
#endif
/************************************************************/
/* iPSC/860 (IPSC) dtime() for i860. */
/* Provided by: Dan Yergeau, yergeau@gloworm.Stanford.EDU */
/************************************************************/
#ifdef IPSC
extern double dclock();
double dtime()
{
double q;
q = dclock();
return q;
}
#endif
/**************************************************/
/* FORTRAN dtime() for Cray type systems. */
/* This is the preferred timer for Cray systems. */
/**************************************************/
#ifdef FORTRAN_SEC
fortran double second();
double dtime()
{
double q;
second(&q);
return q;
}
#endif
/***********************************************************/
/* UNICOS C dtime() for Cray UNICOS systems. Don't use */
/* unless absolutely necessary as returned time includes */
/* 'user+system' time. Provided by: R. Mike Dority, */
/* dority@craysea.cray.com */
/***********************************************************/
#ifdef CTimer
#include <time.h>
double dtime()
{
double q;
clock_t clock(void);
q = (double)clock() / (double)CLOCKS_PER_SEC;
return q;
}
#endif
/********************************************/
/* Another UNIX timer using gettimeofday(). */
/* However, getrusage() is preferred. */
/********************************************/
#ifdef GTODay
#include <sys/time.h>
struct timeval tnow;
double dtime()
{
double q;
gettimeofday(&tnow,NULL);
q = (double)tnow.tv_sec + (double)tnow.tv_usec * 1.0e-6;
return q;
}
#endif
/*****************************************************/
/* Fujitsu UXP/M timer. */
/* Provided by: Mathew Lim, ANUSF, M.Lim@anu.edu.au */
/*****************************************************/
#ifdef UXPM
#include <sys/types.h>
#include <sys/timesu.h>
struct tmsu rusage;
double dtime()
{
double q;
timesu(&rusage);
q = (double)(rusage.tms_utime) * 1.0e-06;
return q;
}
#endif
/**********************************************/
/* Macintosh (MAC_TMgr) Think C dtime() */
/* requires Think C Language Extensions or */
/* #include <MacHeaders> in the prefix */
/* provided by Francis H Schiffer 3rd (fhs) */
/* skipschiffer@genie.geis.com */
/**********************************************/
#ifdef MAC_TMgr
#include <Timer.h>
#include <stdlib.h>
static TMTask mgrTimer;
static Boolean mgrInited = false;
static double mgrClock;
#define RMV_TIMER RmvTime( (QElemPtr)&mgrTimer )
#define MAX_TIME 1800000000L
/* MAX_TIME limits time between calls to */
/* dtime( ) to no more than 30 minutes */
/* this limitation could be removed by */
/* creating a completion routine to sum */
/* 30 minute segments (fhs 1994 feb 9) */
static void Remove_timer( )
{
RMV_TIMER;
mgrInited = false;
}
double dtime( )
{
if( mgrInited ) {
RMV_TIMER;
mgrClock += (MAX_TIME + mgrTimer.tmCount)*1.0e-6;
} else {
if( _atexit( &Remove_timer ) == 0 ) mgrInited = true;
mgrClock = 0.0;
}
if( mgrInited ) {
mgrTimer.tmAddr = NULL;
mgrTimer.tmCount = 0;
mgrTimer.tmWakeUp = 0;
mgrTimer.tmReserved = 0;
InsTime( (QElemPtr)&mgrTimer );
PrimeTime( (QElemPtr)&mgrTimer, -MAX_TIME );
}
return( mgrClock );
}
#endif
/***********************************************************/
/* Parsytec GCel timer. */
/* Provided by: Georg Wambach, gw@informatik.uni-koeln.de */
/***********************************************************/
#ifdef PARIX
#include <sys/time.h>
double dtime()
{
double q;
q = (double) (TimeNowHigh()) / (double) CLK_TCK_HIGH;
return q;
}
#endif
/************************************************/
/* Sun Solaris POSIX dtime() routine */
/* Provided by: Case Larsen, CTLarsen.lbl.gov */
/************************************************/
#ifdef POSIX
#include <sys/time.h>
#include <sys/resource.h>
#include <sys/rusage.h>
#ifdef __hpux
#include <sys/syscall.h>
#endif
struct rusage rusage;
double dtime()
{
double q;
getrusage(RUSAGE_SELF,&rusage);
q = (double)(rusage.ru_utime.tv_sec);
q = q + (double)(rusage.ru_utime.tv_nsec) * 1.0e-09;
return q;
}
#endif
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