/* Function: p7_filtermx_GrowTo()
* Synopsis: Resize filter DP matrix for new profile size.
*
* Purpose: Given an existing filter matrix structure <fx>,
* and the dimension <M> of a new profile that
* we're going to use (in consensus positions),
* assure that <fx> is large enough for such a
* profile; reallocate and reinitialize as needed.
*
* <p7_filtermx_Reuse(fx); p7_filtermx_GrowTo(fx, M)>
* is essentially equivalent to <p7_filtermx_Create(M)>,
* while minimizing reallocation.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEMEM> on allocation failure. The state of
* <fx> is now undefined, and it should not be used.
*/
int
p7_filtermx_GrowTo_neon64(P7_FILTERMX *fx, int allocM)
{
#ifdef HAVE_NEON64
int status;
/* Contract checks / argument validation */
ESL_DASSERT1( (allocM >= 1 && allocM <= 100000) );
if (allocM <= fx->allocM) return eslOK;
/* if not, grow it */
ESL_REALLOC(fx->dp_mem, (sizeof(esl_neon_128i_t) * (p7F_NSCELLS * P7_NVW(allocM))) + (p7_VALIGN-1));
fx->allocM = allocM;
fx->dp = (esl_neon_128i_t *) ( (unsigned long int) ( (char *) fx->dp_mem + (p7_VALIGN-1)) & p7_VALIMASK);
return eslOK;
ERROR:
return status;
#endif //HAVE_NEON64
#ifndef HAVE_NEON64
return eslENORESULT;
#endif
}
/* Function: p7_filtermx_MinSizeof()
* Synopsis: Calculate minimum size of a filter matrix, in bytes.
*
* Purpose: Calculate and return the minimum allocation size
* required for a one-row filter matrix for a query
* profile of <M> consensus positions.
*/
size_t
p7_filtermx_MinSizeof_neon64(int M)
{
size_t n = sizeof(P7_FILTERMX);
#ifdef HAVE_NEON64
n += (sizeof(esl_neon_128i_t) * p7F_NSCELLS * P7_NVW(M)) + (p7_VALIGN-1);
#endif
return n;
}
/* Function: p7_filtermx_Sizeof()
* Synopsis: Calculate and return the current size, in bytes.
*
* Purpose: Calculate and return the current allocated size
* of the filter matrix <fx>, in bytes.
*
* Used in diagnostics, benchmarking of memory usage.
*
* Returns: the allocation size.
*/
size_t
p7_filtermx_Sizeof_neon64(const P7_FILTERMX *fx)
{
size_t n = sizeof(P7_FILTERMX);
#ifdef HAVE_NEON64
n += (sizeof(esl_neon_128i_t) * p7F_NSCELLS * P7_NVW(fx->allocM)) + (p7_VALIGN-1);
#endif
return n;
}
/* Function: p7_filtermx_Create()
* Synopsis: Create a one-row DP matrix for MSV, VF.
*
* Purpose: Allocate a reusable, resizeable one-row <P7_FILTERMX>
* suitable for MSV and Viterbi filter calculations on
* query profiles of up to <allocM> consensus positions.
*
* <allocM> must be $\leq$ 100,000. This is an H3 design
* limit.
*
* Args: allocM - initial allocation size, in profile positions. (>=1, <=100000)
*
* Returns: ptr to new <P7_FILTERMX>
*
* Throws: <NULL> on allocation failure.
*/
P7_FILTERMX *
p7_filtermx_Create_neon64(int allocM)
{
#ifdef HAVE_NEON64
P7_FILTERMX *fx = NULL;
int status;
/* Contract checks / argument validation */
ESL_DASSERT1( (allocM >= 1 && allocM <= 100000) );
ESL_ALLOC(fx, sizeof(P7_FILTERMX));
fx->simd = NEON64;
fx->M = 0;
fx->dp = NULL;
fx->dp_mem = NULL;
fx->allocM = 0;
fx->type = p7F_NONE;
#ifdef p7_DEBUGGING
fx->do_dumping= FALSE;
fx->dfp = NULL;
#endif
// ISA we're using
/* 16B per vector * (MDI)states * ~M/4 vectors + alignment slop */
ESL_ALLOC(fx->dp_mem, (sizeof(esl_neon_128i_t) * p7F_NSCELLS * P7_NVW(allocM)) + (p7_VALIGN-1));
fx->allocM = allocM;
/* Manual memory alignment incantation: */
fx->dp = (esl_neon_128i_t *) ( (unsigned long int) ( (char *) fx->dp_mem + (p7_VALIGN-1) ) & p7_VALIMASK);
return fx;
ERROR:
p7_filtermx_Destroy(fx);
return NULL;
#endif //HAVE_NEON64
#ifndef HAVE_NEON64
return NULL;
#endif
}
/* Function: p7_filtermx_DumpVFRow()
* Synopsis: Dump current row of ViterbiFilter (int16) filter matrix.
*
* Purpose: Dump current row of ViterbiFilter (int16) filter DP
* matrix <fx> for diagnostics, and include the values of
* specials <xE>, etc. The index <rowi> for the current row
* is used as a row label.
*
* If <rowi> is 0, print a header first too.
*
* The output format is coordinated with <p7_refmx_Dump()> to
* facilitate comparison to a known answer.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEMEM> on allocation failure.
*/
int
p7_filtermx_DumpVFRow_neon64(const P7_FILTERMX *fx, int rowi, int16_t xE, int16_t xN, int16_t xJ, int16_t xB, int16_t xC)
{
#ifdef HAVE_NEON64
esl_neon_128i_t *dp = fx->dp; /* enable MMXf(q), DMXf(q), IMXf(q) macros */
int Q = P7_NVW(fx->M); /* number of vectors in the VF row */
int16_t *v = NULL; /* array of unstriped, uninterleaved scores */
int q,z,k;
union { esl_neon_128i_t v; int16_t i[8]; } tmp;
int status;
ESL_ALLOC(v, sizeof(int16_t) * ((Q*8)+1));
v[0] = 0;
/* Header (if we're on the 0th row)
*/
if (rowi == 0)
{
fprintf(fx->dfp, " ");
for (k = 0; k <= fx->M; k++) fprintf(fx->dfp, "%6d ", k);
fprintf(fx->dfp, "%6s %6s %6s %6s %6s\n", "E", "N", "J", "B", "C");
fprintf(fx->dfp, " ");
for (k = 0; k <= fx->M+5; k++) fprintf(fx->dfp, "%6s ", "------");
fprintf(fx->dfp, "\n");
}
/* Unpack and unstripe, then print M's. */
for (q = 0; q < Q; q++) {
tmp.v = MMXf(q);
for (z = 0; z < 8; z++) v[q+Q*z+1] = tmp.i[z];
}
fprintf(fx->dfp, "%4d M ", rowi);
for (k = 0; k <= fx->M; k++) fprintf(fx->dfp, "%6d ", v[k]);
/* The specials */
fprintf(fx->dfp, "%6d %6d %6d %6d %6d\n", xE, xN, xJ, xB, xC);
/* Unpack and unstripe, then print I's. */
for (q = 0; q < Q; q++) {
tmp.v = IMXf(q);
for (z = 0; z < 8; z++) v[q+Q*z+1] = tmp.i[z];
}
fprintf(fx->dfp, "%4d I ", rowi);
for (k = 0; k <= fx->M; k++) fprintf(fx->dfp, "%6d ", v[k]);
fprintf(fx->dfp, "\n");
/* Unpack, unstripe, then print D's. */
for (q = 0; q < Q; q++) {
tmp.v = DMXf(q);
for (z = 0; z < 8; z++) v[q+Q*z+1] = tmp.i[z];
}
fprintf(fx->dfp, "%4d D ", rowi);
for (k = 0; k <= fx->M; k++) fprintf(fx->dfp, "%6d ", v[k]);
fprintf(fx->dfp, "\n\n");
free(v);
return eslOK;
ERROR:
free(v);
return status;
#endif //HAVE_NEON64
#ifndef HAVE_NEON64
return eslENORESULT;
#endif
}
/* Function: p7_oprofile_Write()
* Synopsis: Write an optimized profile in two files.
*
* Purpose: Write the MSV filter part of <om> to open binary stream
* <ffp>, and the rest of the model to <pfp>. These two
* streams will typically be <.h3f> and <.h3p> files
* being created by hmmpress.
*
* Args: ffp - open binary stream for saving MSV filter part
* pfp - open binary stream for saving rest of profile
* om - optimized profile to save
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on any write failure, such as filling
* the disk.
*/
int
p7_oprofile_Write(FILE *ffp, FILE *pfp, P7_OPROFILE *om)
{
int Q4 = P7_NVF(om->M);
int Q8 = P7_NVW(om->M);
int Q16 = P7_NVB(om->M);
int Q16x = P7_NVB(om->M) + p7O_EXTRA_SB;
int n = strlen(om->name);
int x;
/* <ffp> is the part of the oprofile that MSVFilter() needs */
if (fwrite((char *) &(v3f_fmagic), sizeof(uint32_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->M), sizeof(int), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->abc->type), sizeof(int), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &n, sizeof(int), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->name, sizeof(char), n+1, ffp) != n+1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->max_length),sizeof(int), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->tbm_b), sizeof(uint8_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->tec_b), sizeof(uint8_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->tjb_b), sizeof(uint8_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->scale_b), sizeof(float), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->base_b), sizeof(uint8_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->bias_b), sizeof(uint8_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
for (x = 0; x < om->abc->Kp; x++)
if (fwrite( (char *) om->sbv[x], sizeof(__m128i), Q16x, ffp) != Q16x) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
for (x = 0; x < om->abc->Kp; x++)
if (fwrite( (char *) om->rbv[x], sizeof(__m128i), Q16, ffp) != Q16) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->evparam, sizeof(float), p7_NEVPARAM, ffp) != p7_NEVPARAM) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->offs, sizeof(off_t), p7_NOFFSETS, ffp) != p7_NOFFSETS) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->compo, sizeof(float), p7_MAXABET, ffp) != p7_MAXABET) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(v3f_fmagic), sizeof(uint32_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); /* sentinel */
/* <pfp> gets the rest of the oprofile */
if (fwrite((char *) &(v3f_pmagic), sizeof(uint32_t), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->M), sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->abc->type), sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &n, sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->name, sizeof(char), n+1, pfp) != n+1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (om->acc == NULL) {
n = 0;
if (fwrite((char *) &n, sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
} else {
n = strlen(om->acc);
if (fwrite((char *) &n, sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->acc, sizeof(char), n+1, pfp) != n+1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
}
if (om->desc == NULL) {
n = 0;
if (fwrite((char *) &n, sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
} else {
n = strlen(om->desc);
if (fwrite((char *) &n, sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->desc, sizeof(char), n+1, pfp) != n+1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
}
if (fwrite((char *) om->rf, sizeof(char), om->M+2, pfp) != om->M+2) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->mm, sizeof(char), om->M+2, pfp) != om->M+2) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->cs, sizeof(char), om->M+2, pfp) != om->M+2) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->consensus, sizeof(char), om->M+2, pfp) != om->M+2) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
/* ViterbiFilter part */
if (fwrite((char *) om->twv, sizeof(__m128i), 8*Q8, pfp) != 8*Q8) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
for (x = 0; x < om->abc->Kp; x++)
if (fwrite( (char *) om->rwv[x], sizeof(__m128i), Q8, pfp) != Q8) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
for (x = 0; x < p7O_NXSTATES; x++)
if (fwrite( (char *) om->xw[x], sizeof(int16_t), p7O_NXTRANS, pfp) != p7O_NXTRANS) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->scale_w), sizeof(float), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->base_w), sizeof(int16_t), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->ddbound_w), sizeof(int16_t), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->ncj_roundoff), sizeof(float), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
/* Forward/Backward part */
if (fwrite((char *) om->tfv, sizeof(__m128), 8*Q4, pfp) != 8*Q4) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
for (x = 0; x < om->abc->Kp; x++)
if (fwrite( (char *) om->rfv[x], sizeof(__m128), Q4, pfp) != Q4) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
for (x = 0; x < p7O_NXSTATES; x++)
if (fwrite( (char *) om->xf[x], sizeof(float), p7O_NXTRANS, pfp) != p7O_NXTRANS) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->cutoff, sizeof(float), p7_NCUTOFFS, pfp) != p7_NCUTOFFS) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->nj), sizeof(float), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->mode), sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->L) , sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(v3f_pmagic), sizeof(uint32_t), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); /* sentinel */
return eslOK;
}
/* Function: p7_oprofile_ReadRest()
* Synopsis: Read the rest of an optimized profile.
*
* Purpose: Read the rest of an optimized profile <om> from
* the <.h3p> file associated with an open HMM
* file <hfp>.
*
* This is the second part of a two-part calling sequence.
* The <om> here must be the result of a previous
* successful <p7_oprofile_ReadMSV()> call on the same
* open <hfp>.
*
* Args: hfp - open HMM file, from which we've previously
* called <p7_oprofile_ReadMSV()>.
* om - optimized profile that was successfully
* returned by <p7_oprofile_ReadMSV()>.
*
* Returns: <eslOK> on success, and <om> is now a complete
* optimized profile.
*
* Returns <eslEFORMAT> if <hfp> has no <.h3p> file open,
* or on any parsing error, and set <hfp->errbuf> to
* an informative error message.
*
* Throws: <eslESYS> if an <fseek()> fails to reposition the
* binary <.h3p> file.
*
* <eslEMEM> on allocation error.
*/
int
p7_oprofile_ReadRest(P7_HMMFILE *hfp, P7_OPROFILE *om)
{
uint32_t magic;
int M, Q4, Q8;
int x,n;
char *name = NULL;
int alphatype;
int status;
#ifdef HMMER_THREADS
/* lock the mutex to prevent other threads from reading from the optimized
* profile at the same time.
*/
if (hfp->syncRead)
{
if (pthread_mutex_lock (&hfp->readMutex) != 0) ESL_EXCEPTION(eslESYS, "mutex lock failed");
}
#endif
hfp->errbuf[0] = '\0';
if (hfp->pfp == NULL) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "no MSV profile file; hmmpress probably wasn't run");
/* Position the <hfp->pfp> using offset stored in <om> */
if (fseeko(hfp->pfp, om->offs[p7_POFFSET], SEEK_SET) != 0) ESL_EXCEPTION(eslESYS, "fseeko() failed");
if (! fread( (char *) &magic, sizeof(uint32_t), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read magic");
if (magic == v3a_pmagic) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "binary auxfiles are in an outdated HMMER format (3/a); please hmmpress your HMM file again");
if (magic == v3b_pmagic) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "binary auxfiles are in an outdated HMMER format (3/b); please hmmpress your HMM file again");
if (magic == v3c_pmagic) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "binary auxfiles are in an outdated HMMER format (3/c); please hmmpress your HMM file again");
if (magic == v3d_pmagic) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "binary auxfiles are in an outdated HMMER format (3/d); please hmmpress your HMM file again");
if (magic == v3e_pmagic) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "binary auxfiles are in an outdated HMMER format (3/e); please hmmpress your HMM file again");
if (magic != v3f_pmagic) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "bad magic; not an HMM database file?");
if (! fread( (char *) &M, sizeof(int), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read model size M");
if (! fread( (char *) &alphatype, sizeof(int), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read alphabet type");
if (! fread( (char *) &n, sizeof(int), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read name length");
if (M != om->M) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "p/f model length mismatch");
if (alphatype != om->abc->type) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "p/f alphabet type mismatch");
ESL_ALLOC(name, sizeof(char) * (n+1));
if (! fread( (char *) name, sizeof(char), n+1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read name");
if (strcmp(name, om->name) != 0) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "p/f name mismatch");
if (! fread((char *) &n, sizeof(int), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read accession length");
if (n > 0) {
ESL_ALLOC(om->acc, sizeof(char) * (n+1));
if (! fread( (char *) om->acc, sizeof(char), n+1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read accession");
}
if (! fread((char *) &n, sizeof(int), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read description length");
if (n > 0) {
ESL_ALLOC(om->desc, sizeof(char) * (n+1));
if (! fread( (char *) om->desc, sizeof(char), n+1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read description");
}
if (! fread((char *) om->rf, sizeof(char), M+2, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read rf annotation");
if (! fread((char *) om->mm, sizeof(char), M+2, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read mm annotation");
if (! fread((char *) om->cs, sizeof(char), M+2, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read cs annotation");
if (! fread((char *) om->consensus, sizeof(char), M+2, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read consensus annotation");
Q4 = P7_NVF(om->M);
Q8 = P7_NVW(om->M);
if (! fread((char *) om->twv, sizeof(__m128i), 8*Q8, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read <tu>, vitfilter transitions");
for (x = 0; x < om->abc->Kp; x++)
if (! fread( (char *) om->rwv[x], sizeof(__m128i), Q8, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read <ru>[%d], vitfilter emissions for sym %c", x, om->abc->sym[x]);
for (x = 0; x < p7O_NXSTATES; x++)
if (! fread( (char *) om->xw[x], sizeof(int16_t), p7O_NXTRANS, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read <xu>[%d], vitfilter special transitions", x);
if (! fread((char *) &(om->scale_w), sizeof(float), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read scale_w");
if (! fread((char *) &(om->base_w), sizeof(int16_t), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read base_w");
if (! fread((char *) &(om->ddbound_w), sizeof(int16_t), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read ddbound_w");
if (! fread((char *) &(om->ncj_roundoff), sizeof(float), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read ddbound_w");
if (! fread((char *) om->tfv, sizeof(__m128), 8*Q4, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read <tf> transitions");
for (x = 0; x < om->abc->Kp; x++)
if (! fread( (char *) om->rfv[x], sizeof(__m128), Q4, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read <rf>[%d] emissions for sym %c", x, om->abc->sym[x]);
for (x = 0; x < p7O_NXSTATES; x++)
if (! fread( (char *) om->xf[x], sizeof(float), p7O_NXTRANS, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read <xf>[%d] special transitions", x);
if (! fread((char *) om->cutoff, sizeof(float), p7_NCUTOFFS, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read Pfam score cutoffs");
if (! fread((char *) &(om->nj), sizeof(float), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read nj");
if (! fread((char *) &(om->mode), sizeof(int), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read mode");
if (! fread((char *) &(om->L) , sizeof(int), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "failed to read L");
/* record ends with magic sentinel, for detecting binary file corruption */
if (! fread( (char *) &magic, sizeof(uint32_t), 1, hfp->pfp)) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "no sentinel magic: .h3p file corrupted?");
if (magic != v3f_pmagic) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "bad sentinel magic; .h3p file corrupted?");
#ifdef HMMER_THREADS
if (hfp->syncRead)
{
if (pthread_mutex_unlock (&hfp->readMutex) != 0) ESL_EXCEPTION(eslESYS, "mutex unlock failed");
}
#endif
free(name);
return eslOK;
ERROR:
#ifdef HMMER_THREADS
if (hfp->syncRead)
{
if (pthread_mutex_unlock (&hfp->readMutex) != 0) ESL_EXCEPTION(eslESYS, "mutex unlock failed");
}
#endif
if (name != NULL) free(name);
return status;
}
