/* Function: p7_Forward()
* Synopsis: The Forward algorithm, full matrix fill version.
* Incept: SRE, Fri Aug 15 18:59:43 2008 [Casa de Gatos]
*
* Purpose: Calculates the Forward algorithm for sequence <dsq> of
* length <L> residues, using optimized profile <om>, and a
* preallocated DP matrix <ox>. Upon successful return, <ox>
* contains the filled Forward matrix, and <*opt_sc>
* optionally contains the raw Forward score in nats.
*
* This calculation requires $O(ML)$ memory and time.
* The caller must provide a suitably allocated full <ox>
* by calling <ox = p7_omx_Create(M, L, L)> or
* <p7_omx_GrowTo(ox, M, L, L)>.
*
* The model <om> must be configured in local alignment
* mode. The sparse rescaling method used to keep
* probability values within single-precision floating
* point dynamic range cannot be safely applied to models in
* glocal or global mode.
*
* Args: dsq - digital target sequence, 1..L
* L - length of dsq in residues
* om - optimized profile
* ox - RETURN: Forward DP matrix
* opt_sc - RETURN: Forward score (in nats)
*
* Returns: <eslOK> on success.
*
* Throws: <eslEINVAL> if <ox> allocation is too small, or if the profile
* isn't in local alignment mode.
* <eslERANGE> if the score exceeds the limited range of
* a probability-space odds ratio.
* In either case, <*opt_sc> is undefined.
*/
int
p7_Forward(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *opt_sc)
{
#ifdef p7_DEBUGGING
if (om->M > ox->allocQ4*4) ESL_EXCEPTION(eslEINVAL, "DP matrix allocated too small (too few columns)");
if (L >= ox->validR) ESL_EXCEPTION(eslEINVAL, "DP matrix allocated too small (too few MDI rows)");
if (L >= ox->allocXR) ESL_EXCEPTION(eslEINVAL, "DP matrix allocated too small (too few X rows)");
if (! p7_oprofile_IsLocal(om)) ESL_EXCEPTION(eslEINVAL, "Forward implementation makes assumptions that only work for local alignment");
#endif
return forward_engine(TRUE, dsq, L, om, ox, opt_sc);
}
/* Function: p7_BackwardParser()
* Synopsis: The Backward algorithm, linear memory parsing version.
* Incept: SRE, Sat Aug 16 08:34:13 2008 [Janelia]
*
* Purpose: Same as <p7_Backward()> except that the full matrix isn't
* kept. Instead, a linear $O(M+L)$ memory algorithm is
* used, keeping only the DP matrix values for the special
* (BENCJ) states. These are sufficient to do posterior
* decoding to identify high-probability regions where
* domains are.
*
* The caller must provide a suitably allocated "parsing"
* <bck> by calling <bck = p7_omx_Create(M, 0, L)> or
* <p7_omx_GrowTo(bck, M, 0, L)>.
*
* Args: dsq - digital target sequence, 1..L
* L - length of dsq in residues
* om - optimized profile
* fwd - filled Forward DP matrix, for scale factors
* bck - RETURN: filled Backward matrix
* opt_sc - optRETURN: Backward score (in nats)
*
* Returns: <eslOK> on success.
*
* Throws: <eslEINVAL> if <ox> allocation is too small, or if the profile
* isn't in local alignment mode.
* <eslERANGE> if the score exceeds the limited range of
* a probability-space odds ratio.
* In either case, <*opt_sc> is undefined.
*/
int
p7_BackwardParser(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P7_OMX *bck, float *opt_sc)
{
#ifdef p7_DEBUGGING
if (om->M > bck->allocQ4*4) ESL_EXCEPTION(eslEINVAL, "DP matrix allocated too small (too few columns)");
if (bck->validR < 1) ESL_EXCEPTION(eslEINVAL, "DP matrix allocated too small (too few MDI rows)");
if (L >= bck->allocXR) ESL_EXCEPTION(eslEINVAL, "DP matrix allocated too small (too few X rows)");
if (L != fwd->L) ESL_EXCEPTION(eslEINVAL, "fwd matrix size doesn't agree with length L");
if (! p7_oprofile_IsLocal(om)) ESL_EXCEPTION(eslEINVAL, "Forward implementation makes assumptions that only work for local alignment");
#endif
return backward_engine(FALSE, dsq, L, om, fwd, bck, opt_sc);
}
