void io_close(struct io_file *f) {
if (NULL != f) {
unbuffer(f);
close(f->fd);
if (NULL != f->map) munmap(f->map,f->map_size);
free(f);
}
}
int io_out(struct io_file *f,int pos,const void *o,int len) {
int end = pos + len;
if (0 == len) return pos;
if (NULL == f || -1 == pos) return -1;
if (NULL == o) return pos + len;
if (remap(f,pos,len)) return -1;
if (pos < f->file_size) {
assert(pos >= f->map_offset);
if (pos >= f->buffer_offset && unbuffer(f))
return -1;
if (end > (int)(f->map_offset + f->map_size))
end = f->map_offset + f->map_size;
if (end > f->file_size)
end = f->file_size;
memcpy(pos - f->map_offset + (char *) f->map,o,end - pos);
}
else {
if (pos < f->buffer_offset
|| pos > (int)(f->buffer_offset + f->buffer_size)) {
if (unbuffer(f)) return -1;
if (lseek(f->fd,pos,SEEK_SET) == (off_t) -1) {
perror("lseek");
return -1;
}
assert(0 == f->buffer_size);
f->buffer_offset = pos;
}
else if (pos == (int)(f->buffer_offset + sizeof f->buffer))
if (unbuffer(f)) return -1;
assert(pos >= f->buffer_offset
&& pos <= (int)(f->buffer_offset + f->buffer_size));
if (end > (int)(f->buffer_offset + sizeof f->buffer))
end = f->buffer_offset + sizeof f->buffer;
memcpy(&f->buffer[pos - f->buffer_offset],o,end - pos);
if ((int)(end - f->buffer_offset) > (int)f->buffer_size)
f->buffer_size = end - f->buffer_offset;
}
return io_out(f,end,end - pos + (char *) o,len + pos - end);
}
/* Resets f->file_size to the actual size of the file.
Returns nonzero iff failed. */
static int checksize(struct io_file *f) {
struct stat buf;
if (unbuffer(f)) return -1;
if (fstat(f->fd,&buf)) {
perror("fstat");
return -1;
}
f->file_size = buf.st_size;
return 0;
}
int io_in(struct io_file *f,int pos,void *i,int len) {
int end = pos + len;
if (0 == len) return pos;
if (NULL == f || -1 == pos) return -1;
if (NULL == i) return pos + len;
if (remap(f,pos,len)) return -1;
if (unbuffer(f)) return -1;
if (pos >= f->file_size && checksize(f)) return -1;
if (pos >= f->file_size) {
/* TODO: fill with zeroes instead */
fputs("read: EOF\n",stderr);
return -1;
}
if (end > (int)(f->map_offset + f->map_size))
end = f->map_offset + f->map_size;
if (end > f->file_size)
end = f->file_size;
memcpy(i,pos - f->map_offset + (char *) f->map,end - pos);
return io_in(f,end,end - pos + (char *) i,len + pos - end);
}
void ScoredSeqFlipMinus::deepUnbuffer(){
unbuffer();
_innerSeq->deepUnbuffer();
}
virtual int_type
put (char_type c)
{
int_type result = traits_type::to_int_type (c);
try
{
bool defaulting = false;
if (!hold_.empty () && hold_.back () == '(')
{
// We don't need to hold it any more.
unbuffer ();
if (c == '\n')
indentation_.push (indentation_.top () + spaces_);
else
indentation_.push (position_);
}
switch (c)
{
case '\n':
{
hold_.push_back (c);
position_ = 0; // Starting a new line.
if (construct_ == JAVA_COMMENT)
{
//std::cerr << "end comment" << endl;
construct_ = OTHER;
}
break;
}
case '{':
{
ensure_new_line ();
output_indentation ();
result = write (c);
ensure_new_line ();
indentation_.push (indentation_.top () + spaces_);
break;
}
case '}':
{
if (indentation_.size () > 1)
indentation_.pop ();
// Reduce multiple newlines to one.
while (hold_.size () > 1)
{
typename Hold::reverse_iterator i = hold_.rbegin ();
if (*i == '\n' && *(i + 1) == '\n')
hold_.pop_back ();
else
break;
}
ensure_new_line ();
output_indentation ();
hold_.push_back (c);
// Add newline after '}'.
//
ensure_new_line ();
break;
}
case ';':
{
if (paren_balance_ != 0)
{
// We are inside for (;;) statement. Nothing to do here.
//
defaulting = true;
}
else if (construct_ != STRING_LITERAL && construct_ != CHAR_LITERAL)
{
output_indentation ();
result = write (c);
ensure_new_line ();
}
break;
}
case '\\':
{
if (construct_ != JAVA_COMMENT)
{
output_indentation ();
hold_.push_back (c);
position_++;
}
else
defaulting = true;
break;
}
case '\"':
{
if (construct_ != JAVA_COMMENT &&
(hold_.empty () || hold_.back () != '\\'))
{
// not escape sequence
if (construct_ == STRING_LITERAL) construct_ = OTHER;
else construct_ = STRING_LITERAL;
}
defaulting = true;
break;
}
case '\'':
{
if (construct_ != JAVA_COMMENT &&
(hold_.empty () || hold_.back () != '\\'))
{
// not escape sequence
if (construct_ == CHAR_LITERAL) construct_ = OTHER;
else
{
//std::cerr << "char literal" << endl;
construct_ = CHAR_LITERAL;
}
}
defaulting = true;
break;
}
case '(':
{
if (construct_ == OTHER)
{
// Hold it so that we can see what's coming next.
//
output_indentation ();
hold_.push_back (c);
position_++;
paren_balance_++;
}
else
defaulting = true;
break;
}
case ')':
{
if (construct_ == OTHER)
{
if (indentation_.size () > 1)
indentation_.pop ();
if (paren_balance_ > 0)
paren_balance_--;
}
defaulting = true;
break;
}
case '/':
{
if (construct_ == OTHER)
{
if (!hold_.empty () && hold_.back () == '/')
{
construct_ = JAVA_COMMENT;
//std::cerr << "start comment" << endl;
defaulting = true;
}
else
{
output_indentation ();
hold_.push_back (c);
position_++;
}
}
else
{
defaulting = true;
}
break;
}
default:
{
defaulting = true;
break;
}
}
if (defaulting)
{
output_indentation ();
result = write (c);
position_++;
}
}
catch (Full const&)
{
result = traits_type::eof ();
}
return result;
}
int enc_main(int argc, char **argv)
{
static char buf[128];
static const char magic[] = "Salted__";
BIO *in = NULL, *out = NULL, *b64 = NULL, *benc = NULL, *rbio =
NULL, *wbio = NULL;
EVP_CIPHER_CTX *ctx = NULL;
const EVP_CIPHER *cipher = NULL, *c;
const EVP_MD *dgst = NULL;
char *hkey = NULL, *hiv = NULL, *hsalt = NULL, *p;
char *infile = NULL, *outfile = NULL, *prog;
char *str = NULL, *passarg = NULL, *pass = NULL, *strbuf = NULL;
char mbuf[sizeof magic - 1];
OPTION_CHOICE o;
int bsize = BSIZE, verbose = 0, debug = 0, olb64 = 0, nosalt = 0;
int enc = 1, printkey = 0, i, k;
int base64 = 0, informat = FORMAT_BINARY, outformat = FORMAT_BINARY;
int ret = 1, inl, nopad = 0, non_fips_allow = 0;
unsigned char key[EVP_MAX_KEY_LENGTH], iv[EVP_MAX_IV_LENGTH];
unsigned char *buff = NULL, salt[PKCS5_SALT_LEN];
unsigned long n;
#ifdef ZLIB
int do_zlib = 0;
BIO *bzl = NULL;
#endif
/* first check the program name */
prog = opt_progname(argv[0]);
if (strcmp(prog, "base64") == 0)
base64 = 1;
#ifdef ZLIB
else if (strcmp(prog, "zlib") == 0)
do_zlib = 1;
#endif
else {
cipher = EVP_get_cipherbyname(prog);
if (cipher == NULL && strcmp(prog, "enc") != 0) {
BIO_printf(bio_err, "%s is not a known cipher\n", prog);
goto end;
}
}
prog = opt_init(argc, argv, enc_options);
while ((o = opt_next()) != OPT_EOF) {
switch (o) {
case OPT_EOF:
case OPT_ERR:
opthelp:
BIO_printf(bio_err, "%s: Use -help for summary.\n", prog);
goto end;
case OPT_HELP:
opt_help(enc_options);
ret = 0;
BIO_printf(bio_err, "Cipher Types\n");
OBJ_NAME_do_all_sorted(OBJ_NAME_TYPE_CIPHER_METH,
show_ciphers, bio_err);
BIO_printf(bio_err, "\n");
goto end;
case OPT_E:
enc = 1;
break;
case OPT_IN:
infile = opt_arg();
break;
case OPT_OUT:
outfile = opt_arg();
break;
case OPT_PASS:
passarg = opt_arg();
break;
case OPT_ENGINE:
(void)setup_engine(opt_arg(), 0);
break;
case OPT_D:
enc = 0;
break;
case OPT_P:
printkey = 1;
break;
case OPT_V:
verbose = 1;
break;
case OPT_NOPAD:
nopad = 1;
break;
case OPT_SALT:
nosalt = 0;
break;
case OPT_NOSALT:
nosalt = 1;
break;
case OPT_DEBUG:
debug = 1;
break;
case OPT_UPPER_P:
printkey = 2;
break;
case OPT_UPPER_A:
olb64 = 1;
break;
case OPT_A:
base64 = 1;
break;
case OPT_Z:
#ifdef ZLIB
do_zlib = 1;
#endif
break;
case OPT_BUFSIZE:
p = opt_arg();
i = (int)strlen(p) - 1;
k = i >= 1 && p[i] == 'k';
if (k)
p[i] = '\0';
if (!opt_ulong(opt_arg(), &n))
goto opthelp;
if (k)
n *= 1024;
bsize = (int)n;
break;
case OPT_K:
str = opt_arg();
break;
case OPT_KFILE:
in = bio_open_default(opt_arg(), 'r', FORMAT_TEXT);
if (in == NULL)
goto opthelp;
i = BIO_gets(in, buf, sizeof buf);
BIO_free(in);
in = NULL;
if (i <= 0) {
BIO_printf(bio_err,
"%s Can't read key from %s\n", prog, opt_arg());
goto opthelp;
}
while (--i > 0 && (buf[i] == '\r' || buf[i] == '\n'))
buf[i] = '\0';
if (i <= 0) {
BIO_printf(bio_err, "%s: zero length password\n", prog);
goto opthelp;
}
str = buf;
break;
case OPT_UPPER_K:
hkey = opt_arg();
break;
case OPT_UPPER_S:
hsalt = opt_arg();
break;
case OPT_IV:
hiv = opt_arg();
break;
case OPT_MD:
if (!opt_md(opt_arg(), &dgst))
goto opthelp;
break;
case OPT_NON_FIPS_ALLOW:
non_fips_allow = 1;
break;
case OPT_CIPHER:
if (!opt_cipher(opt_unknown(), &c))
goto opthelp;
cipher = c;
break;
case OPT_NONE:
cipher = NULL;
break;
}
}
argc = opt_num_rest();
argv = opt_rest();
if (cipher && EVP_CIPHER_flags(cipher) & EVP_CIPH_FLAG_AEAD_CIPHER) {
BIO_printf(bio_err, "%s: AEAD ciphers not supported\n", prog);
goto end;
}
if (cipher && (EVP_CIPHER_mode(cipher) == EVP_CIPH_XTS_MODE)) {
BIO_printf(bio_err, "%s XTS ciphers not supported\n", prog);
goto end;
}
if (dgst == NULL)
dgst = EVP_sha256();
/* It must be large enough for a base64 encoded line */
if (base64 && bsize < 80)
bsize = 80;
if (verbose)
BIO_printf(bio_err, "bufsize=%d\n", bsize);
if (base64) {
if (enc)
outformat = FORMAT_BASE64;
else
informat = FORMAT_BASE64;
}
strbuf = app_malloc(SIZE, "strbuf");
buff = app_malloc(EVP_ENCODE_LENGTH(bsize), "evp buffer");
if (debug) {
BIO_set_callback(in, BIO_debug_callback);
BIO_set_callback(out, BIO_debug_callback);
BIO_set_callback_arg(in, (char *)bio_err);
BIO_set_callback_arg(out, (char *)bio_err);
}
if (infile == NULL) {
unbuffer(stdin);
in = dup_bio_in(informat);
} else
in = bio_open_default(infile, 'r', informat);
if (in == NULL)
goto end;
if (!str && passarg) {
if (!app_passwd(passarg, NULL, &pass, NULL)) {
BIO_printf(bio_err, "Error getting password\n");
goto end;
}
str = pass;
}
if ((str == NULL) && (cipher != NULL) && (hkey == NULL)) {
for (;;) {
char prompt[200];
BIO_snprintf(prompt, sizeof prompt, "enter %s %s password:"******"encryption" : "decryption");
strbuf[0] = '\0';
i = EVP_read_pw_string((char *)strbuf, SIZE, prompt, enc);
if (i == 0) {
if (strbuf[0] == '\0') {
ret = 1;
goto end;
}
str = strbuf;
break;
}
if (i < 0) {
BIO_printf(bio_err, "bad password read\n");
goto end;
}
}
}
out = bio_open_default(outfile, 'w', outformat);
if (out == NULL)
goto end;
rbio = in;
wbio = out;
#ifdef ZLIB
if (do_zlib) {
if ((bzl = BIO_new(BIO_f_zlib())) == NULL)
goto end;
if (enc)
wbio = BIO_push(bzl, wbio);
else
rbio = BIO_push(bzl, rbio);
}
#endif
if (base64) {
if ((b64 = BIO_new(BIO_f_base64())) == NULL)
goto end;
if (debug) {
BIO_set_callback(b64, BIO_debug_callback);
BIO_set_callback_arg(b64, (char *)bio_err);
}
if (olb64)
BIO_set_flags(b64, BIO_FLAGS_BASE64_NO_NL);
if (enc)
wbio = BIO_push(b64, wbio);
else
rbio = BIO_push(b64, rbio);
}
if (cipher != NULL) {
/*
* Note that str is NULL if a key was passed on the command line, so
* we get no salt in that case. Is this a bug?
*/
if (str != NULL) {
/*
* Salt handling: if encrypting generate a salt and write to
* output BIO. If decrypting read salt from input BIO.
*/
unsigned char *sptr;
if (nosalt)
sptr = NULL;
else {
if (enc) {
if (hsalt) {
if (!set_hex(hsalt, salt, sizeof salt)) {
BIO_printf(bio_err, "invalid hex salt value\n");
goto end;
}
} else if (RAND_bytes(salt, sizeof salt) <= 0)
goto end;
/*
* If -P option then don't bother writing
*/
if ((printkey != 2)
&& (BIO_write(wbio, magic,
sizeof magic - 1) != sizeof magic - 1
|| BIO_write(wbio,
(char *)salt,
sizeof salt) != sizeof salt)) {
BIO_printf(bio_err, "error writing output file\n");
goto end;
}
} else if (BIO_read(rbio, mbuf, sizeof mbuf) != sizeof mbuf
|| BIO_read(rbio,
(unsigned char *)salt,
sizeof salt) != sizeof salt) {
BIO_printf(bio_err, "error reading input file\n");
goto end;
} else if (memcmp(mbuf, magic, sizeof magic - 1)) {
BIO_printf(bio_err, "bad magic number\n");
goto end;
}
sptr = salt;
}
if (!EVP_BytesToKey(cipher, dgst, sptr,
(unsigned char *)str,
strlen(str), 1, key, iv)) {
BIO_printf(bio_err, "EVP_BytesToKey failed\n");
goto end;
}
/*
* zero the complete buffer or the string passed from the command
* line bug picked up by Larry J. Hughes Jr. <*****@*****.**>
*/
if (str == strbuf)
OPENSSL_cleanse(str, SIZE);
else
OPENSSL_cleanse(str, strlen(str));
}
if (hiv != NULL) {
int siz = EVP_CIPHER_iv_length(cipher);
if (siz == 0) {
BIO_printf(bio_err, "warning: iv not use by this cipher\n");
} else if (!set_hex(hiv, iv, sizeof iv)) {
BIO_printf(bio_err, "invalid hex iv value\n");
goto end;
}
}
if ((hiv == NULL) && (str == NULL)
&& EVP_CIPHER_iv_length(cipher) != 0) {
/*
* No IV was explicitly set and no IV was generated during
* EVP_BytesToKey. Hence the IV is undefined, making correct
* decryption impossible.
*/
BIO_printf(bio_err, "iv undefined\n");
goto end;
}
if ((hkey != NULL) && !set_hex(hkey, key, EVP_CIPHER_key_length(cipher))) {
BIO_printf(bio_err, "invalid hex key value\n");
goto end;
}
if ((benc = BIO_new(BIO_f_cipher())) == NULL)
goto end;
/*
* Since we may be changing parameters work on the encryption context
* rather than calling BIO_set_cipher().
*/
BIO_get_cipher_ctx(benc, &ctx);
if (non_fips_allow)
EVP_CIPHER_CTX_set_flags(ctx, EVP_CIPH_FLAG_NON_FIPS_ALLOW);
if (!EVP_CipherInit_ex(ctx, cipher, NULL, NULL, NULL, enc)) {
BIO_printf(bio_err, "Error setting cipher %s\n",
EVP_CIPHER_name(cipher));
ERR_print_errors(bio_err);
goto end;
}
if (nopad)
EVP_CIPHER_CTX_set_padding(ctx, 0);
if (!EVP_CipherInit_ex(ctx, NULL, NULL, key, iv, enc)) {
BIO_printf(bio_err, "Error setting cipher %s\n",
EVP_CIPHER_name(cipher));
ERR_print_errors(bio_err);
goto end;
}
if (debug) {
BIO_set_callback(benc, BIO_debug_callback);
BIO_set_callback_arg(benc, (char *)bio_err);
}
if (printkey) {
if (!nosalt) {
printf("salt=");
for (i = 0; i < (int)sizeof(salt); i++)
printf("%02X", salt[i]);
printf("\n");
}
if (cipher->key_len > 0) {
printf("key=");
for (i = 0; i < cipher->key_len; i++)
printf("%02X", key[i]);
printf("\n");
}
if (cipher->iv_len > 0) {
printf("iv =");
for (i = 0; i < cipher->iv_len; i++)
printf("%02X", iv[i]);
printf("\n");
}
if (printkey == 2) {
ret = 0;
goto end;
}
}
}
/* Only encrypt/decrypt as we write the file */
if (benc != NULL)
wbio = BIO_push(benc, wbio);
for (;;) {
inl = BIO_read(rbio, (char *)buff, bsize);
if (inl <= 0)
break;
if (BIO_write(wbio, (char *)buff, inl) != inl) {
BIO_printf(bio_err, "error writing output file\n");
goto end;
}
}
if (!BIO_flush(wbio)) {
BIO_printf(bio_err, "bad decrypt\n");
goto end;
}
ret = 0;
if (verbose) {
BIO_printf(bio_err, "bytes read :%8"PRIu64"\n", BIO_number_read(in));
BIO_printf(bio_err, "bytes written:%8"PRIu64"\n", BIO_number_written(out));
}
end:
ERR_print_errors(bio_err);
OPENSSL_free(strbuf);
OPENSSL_free(buff);
BIO_free(in);
BIO_free_all(out);
BIO_free(benc);
BIO_free(b64);
#ifdef ZLIB
BIO_free(bzl);
#endif
OPENSSL_free(pass);
return (ret);
}
ScoredSeqSubseq::~ScoredSeqSubseq(){
//_readCount--;
unbuffer();
}
void ScoredSeqSubseq::deepUnbuffer(){
unbuffer();
_innerSeq->deepUnbuffer();
}
