EnsemblServer/ClientServerUtils.h File Reference

#include <sys/types.h>
#include <sys/wait.h>
#include <sys/socket.h>
#include <sys/time.h>
#include <signal.h>
#include <errno.h>
#include <unistd.h>
#include <netinet/in.h>
#include <netdb.h>
#include <arpa/inet.h>
#include <pthread.h>
#include <stdio.h>
#include <cstdlib>
#include <string>
#include <deque>
#include <exception>
#include "GlobalDefinitions.h"

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Classes
struct	Handshake
struct	QueryHeader
struct	SequenceHeader
struct	MatchHeader
struct	MatchInfo
class	NetworkException
class	BrokenSocketException
class	SocketInterface
Defines
#define	SERV_PORT   9877
#define	SERV_VERSION   4
#define	SA   struct sockaddr
#define	LISTENQ   1024
#define	MAXLINE   4096
#define	__attribute__(x)
Typedefs
typedef void	Sigfunc (int)
Enumerations
enum	TableType { e2bitDNA = 0, e5bitProtein = 1, e5bitTranslatedDNA = 2 }
enum	SortModeType { eNoSort = 0, eSortByMatchLength = 1, eSortByPercentMatch = 2, eSortAndReturnSequence = 3 }
Functions
void	err_sys (const char *fmt,...)
void	sig_chld (int signo)
int	Accept (int fd, sockaddr *sa, socklen_t *salenptr)
void	Bind (int fd, const sockaddr *sa, socklen_t salen)
void	Listen (int fd, int backlog)
Sigfunc *	signal (int signo, Sigfunc *func)
Sigfunc *	Signal (int signo, Sigfunc *func)
void	Close (int fd)
pid_t	Fork (void)
int	Socket (int family, int type, int protocol)
ssize_t	readn (int fd, void *vptr, size_t n)
ssize_t	Readn (int fd, void *ptr, size_t nbytes)
ssize_t	writen (int fd, const void *vptr, size_t n)
void	Writen (int fd, void *ptr, size_t nbytes)
char *	Fgets (char *ptr, int n, FILE *stream)
void	Fputs (const char *ptr, FILE *stream)
void	Connect (int fd, const sockaddr *sa, socklen_t salen)
Variables
Handshake	packed
QueryHeader	packed
SequenceHeader	packed
MatchHeader	packed
MatchInfo	packed

---

Define Documentation

#define __attribute__

(

x

)

Definition at line 70 of file ClientServerUtils.h.

#define LISTENQ   1024

Definition at line 57 of file ClientServerUtils.h.

Referenced by main().

#define MAXLINE   4096

Definition at line 58 of file ClientServerUtils.h.

Referenced by SocketInterface::checkSocketEmpty(), and sendQuery().

#define SA   struct sockaddr

Definition at line 56 of file ClientServerUtils.h.

Referenced by main().

#define SERV_PORT   9877

Definition at line 54 of file ClientServerUtils.h.

#define SERV_VERSION   4

Definition at line 55 of file ClientServerUtils.h.

Referenced by main(), and sendQuery().

---

Typedef Documentation

typedef void Sigfunc(int)

Definition at line 53 of file ClientServerUtils.h.

---

Enumeration Type Documentation

enum SortModeType

Enumerator:

eNoSort
eSortByMatchLength
eSortByPercentMatch
eSortAndReturnSequence

Definition at line 113 of file ClientServerUtils.h.

{
  eNoSort = 0,
  eSortByMatchLength = 1,
  eSortByPercentMatch = 2,
  eSortAndReturnSequence = 3 // return matched ASCII seq to client
};

enum TableType

Enumerator:

e2bitDNA
e5bitProtein
e5bitTranslatedDNA

Definition at line 96 of file ClientServerUtils.h.

{
  e2bitDNA = 0,
  e5bitProtein = 1,
  e5bitTranslatedDNA = 2 
};

---

Function Documentation

int Accept	(	int	fd,
		sockaddr *	sa,
		socklen_t *	salenptr
	)

Definition at line 74 of file ClientServerUtils.cpp.

{
  int             n;

 again:
  if ( (n = accept(fd, sa, salenptr)) < 0) 
  {
    if (errno == ECONNABORTED)
      goto again;
    else
      throw NetworkException
      ( (string)"accept error: " + (string)strerror(errno) ); 
  }
  return(n);
} // ~Accept

void Bind	(	int	fd,
		const sockaddr *	sa,
		socklen_t	salen
	)

void Close

(

int

fd

)

Definition at line 144 of file ClientServerUtils.cpp.

Referenced by main(), and threadWrapper().

{  
  if (close(fd) == -1) 
  {
    throw NetworkException
      ( (string)"close error: " + (string)strerror(errno) ); 
  }
}

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void Connect	(	int	fd,
		const sockaddr *	sa,
		socklen_t	salen
	)

void err_sys	(	const char *	fmt,
			...
	)

Definition at line 66 of file ClientServerUtils.cpp.

Referenced by main().

{
        printf("error: %s\n", fmt);
        exit(1);
}

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char* Fgets	(	char *	ptr,
		int	n,
		FILE *	stream
	)

Definition at line 328 of file ClientServerUtils.cpp.

{
  char  *rptr;
  if ( (rptr = fgets(ptr, n, stream)) == NULL && ferror(stream))
    throw NetworkException("fgets error");
  return (rptr);
}

pid_t Fork

(

void

)

Definition at line 154 of file ClientServerUtils.cpp.

Referenced by main().

{
  pid_t pid;
  if ( (pid = fork()) == -1) throw NetworkException("fork error");
  return(pid);
}

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void Fputs	(	const char *	ptr,
		FILE *	stream
	)

Definition at line 336 of file ClientServerUtils.cpp.

{
  if (fputs(ptr, stream) == EOF) throw NetworkException("fputs error");
}

void Listen	(	int	fd,
		int	backlog
	)

Definition at line 99 of file ClientServerUtils.cpp.

Referenced by main().

{
  char  *ptr;

  /*4can override 2nd argument with environment variable */
  if ( (ptr = getenv("LISTENQ")) != NULL)
    backlog = atoi(ptr);

  if (listen(fd, backlog) < 0)
    throw NetworkException
      ( (string)"listen error: " + (string)strerror(errno) ); 
} // ~Listen

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ssize_t Readn	(	int	fd,
		void *	ptr,
		size_t	nbytes
	)

Definition at line 196 of file ClientServerUtils.cpp.

References readn().

{
  ssize_t               n;
  
  if ( (n = readn(fd, ptr, nbytes)) < 0)
    throw NetworkException("readn error");
  return(n);
}

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ssize_t readn	(	int	fd,
		void *	vptr,
		size_t	n
	)

Definition at line 169 of file ClientServerUtils.cpp.

Referenced by Readn().

{
  size_t        nleft;
  ssize_t       nread;
  char  *ptr;
  
  ptr = (char*) vptr;
  nleft = n;
  while (nleft > 0) 
  {
    if ( (nread = read(fd, ptr, nleft)) < 0) 
    {
      if (errno == EINTR)
        nread = 0;              /* and call read() again */
      else
        return(-1);
    } else if (nread == 0)
      break;                            /* EOF */
    
    nleft -= nread;
    ptr   += nread;
  }
  return(n - nleft);            /* return >= 0 */
}

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void sig_chld

(

int

signo

)

Definition at line 107 of file SSAHAServer.cpp.

References myPID.

Referenced by main().

{
  pid_t pid;
  int           stat;
  
  while ( (pid = waitpid(-1, &stat, WNOHANG)) > 0)
    cout << myPID << ": terminated child " << pid << endl;
    //    printf("child %d terminated\n", pid);
  return;
}

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Sigfunc* Signal	(	int	signo,
		Sigfunc *	func
	)

Definition at line 134 of file ClientServerUtils.cpp.

References signal().

Referenced by main().

{
  Sigfunc       *sigfunc;
  if ( (sigfunc = signal(signo, func)) == SIG_ERR) 
    throw NetworkException
      ( (string)"signal error: " + (string)strerror(errno) ); 
  return(sigfunc);
}

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Sigfunc* signal	(	int	signo,
		Sigfunc *	func
	)

Definition at line 112 of file ClientServerUtils.cpp.

Referenced by Signal().

{
  struct sigaction      act, oact;
  
  act.sa_handler = func;
  sigemptyset(&act.sa_mask);
  act.sa_flags = 0;
  if (signo == SIGALRM) {
#ifdef  SA_INTERRUPT
    act.sa_flags |= SA_INTERRUPT;       /* SunOS 4.x */
#endif
  } else {
#ifdef  SA_RESTART
    act.sa_flags |= SA_RESTART;         /* SVR4, 44BSD */
#endif
  }
  if (sigaction(signo, &act, &oact) < 0)
    return(SIG_ERR);
  return(oact.sa_handler);
}

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int Socket	(	int	family,
		int	type,
		int	protocol
	)

Definition at line 161 of file ClientServerUtils.cpp.

Referenced by main().

{
  int           n;
  if ( (n = socket(family, type, protocol)) < 0) throw NetworkException("socket error");
  return(n);
}

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void Writen	(	int	fd,
		void *	ptr,
		size_t	nbytes
	)

Definition at line 315 of file ClientServerUtils.cpp.

References writen().

Referenced by SocketInterface::sendChars(), SocketInterface::sendSequence(), SocketInterface::sendString(), and SocketInterface::sendStruct().

{


  if (writen(fd, ptr, nbytes) != nbytes) 
  {
    //    cout << "Error no :"<< errno << endl;
    throw BrokenSocketException();
    //    else throw NetworkException("writen error");
  }
}

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ssize_t writen	(	int	fd,
		const void *	vptr,
		size_t	n
	)

Definition at line 270 of file ClientServerUtils.cpp.

Referenced by Writen().

{
  size_t                nleft;
  ssize_t               nwritten;
  const char    *ptr;

  //  pollfd pollDetails;
  //  pollDetails.fd=fd;
  //  pollDetails.events=POLLIN|POLLRDNORM|POLLRDBAND|POLLPRI|POLLOUT|POLLWRNORM|POLLWRBAND;
  //  int pollOut(0);


  ptr = (char *) vptr;
  nleft = n;
  while (nleft > 0) {

    //    do { pollOut=poll(&pollDetails,1,10); } while (pollOut==0);
    //  cout << "POLL Writen: " <<   pollOut
    //   << ((pollDetails.revents|POLLIN!=0)?'1':'0')
    //    << ((pollDetails.revents|POLLRDNORM!=0)?'1':'0')
    //    << ((pollDetails.revents|POLLRDBAND!=0)?'1':'0')
    //   << ((pollDetails.revents|POLLPRI!=0)?'1':'0')
    //   << ((pollDetails.revents|POLLOUT!=0)?'1':'0')
    //   << ((pollDetails.revents|POLLWRNORM!=0)?'1':'0')
    //   << ((pollDetails.revents|POLLWRBAND!=0)?'1':'0')
    //   << ((pollDetails.revents|POLLERR!=0)?'1':'0')
    //   << ((pollDetails.revents|POLLHUP!=0)?'1':'0')
    //   << ((pollDetails.revents|POLLNVAL!=0)?'1':'0') << endl;


    if ( (nwritten = write(fd, ptr, nleft)) <= 0) {
      if (errno == EINTR)
        nwritten = 0;           /* and call write() again */
      else
        return(-1);                     /* error */
    }
    
    nleft -= nwritten;
    ptr   += nwritten;
  }
  return(n);
}

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Variable Documentation

struct MatchInfo packed

struct MatchHeader packed

struct SequenceHeader packed

struct QueryHeader packed

struct Handshake packed

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