/* Function: p7_bg_Create()
* Incept: SRE, Fri Jan 12 13:32:51 2007 [Janelia]
*
* Purpose: Allocate a <P7_BG> object for digital alphabet <abc>,
* initializes it to appropriate default values, and
* returns a pointer to it.
*
* For protein models, default iid background frequencies
* are set (by <p7_AminoFrequencies()>) to average
* SwissProt residue composition. For DNA, RNA and other
* alphabets, default frequencies are set to a uniform
* distribution.
*
* The model composition <bg->mcomp[]> is not initialized
* here; neither is the filter null model <bg->fhmm>. To
* use the filter null model, caller will want to
* initialize these fields by calling
* <p7_bg_SetFilterByHMM()>.
*
* Throws: <NULL> on allocation failure.
*
* Xref: STL11/125.
*/
P7_BG *
p7_bg_Create(const ESL_ALPHABET *abc)
{
P7_BG *bg = NULL;
int status;
ESL_ALLOC(bg, sizeof(P7_BG));
bg->f = NULL;
bg->fhmm = NULL;
ESL_ALLOC(bg->f, sizeof(float) * abc->K);
if ((bg->fhmm = esl_hmm_Create(abc, 2)) == NULL) goto ERROR;
if (abc->type == eslAMINO)
{
if (p7_AminoFrequencies(bg->f) != eslOK) goto ERROR;
}
else
esl_vec_FSet(bg->f, abc->K, 1. / (float) abc->K);
bg->p1 = 350./351.;
bg->omega = 1./256.;
bg->abc = abc;
return bg;
ERROR:
p7_bg_Destroy(bg);
return NULL;
}
/* Function: p7_bg_Create()
* Synopsis: Create a <P7_BG> null model object.
*
* Purpose: Allocate a <P7_BG> object for digital alphabet <abc>,
* initializes it to appropriate default values, and
* returns a pointer to it.
*
* For protein models, default iid background frequencies
* are set (by <p7_AminoFrequencies()>) to average
* Swiss-Prot residue composition. For DNA, RNA and other
* alphabets, default frequencies are set to a uniform
* distribution.
*
* The model composition <bg->mcomp[]> is not initialized
* here; neither is the filter null model <bg->fhmm>. To
* use the filter null model, caller will want to
* initialize these fields by calling
* <p7_bg_SetFilter()>.
*
* Throws: <NULL> on allocation failure.
*
* Xref: STL11/125.
*/
P7_BG *
p7_bg_Create(const ESL_ALPHABET *abc)
{
P7_BG *bg = NULL;
int status;
ESL_ALLOC(bg, sizeof(P7_BG));
bg->f = NULL;
bg->fhmm = NULL;
// this is not hard-coded for alphabet size...
ESL_ALLOC(bg->f, sizeof(float) * abc->K);
if ((bg->fhmm = esl_hmm_Create(abc, 2)) == NULL) goto ERROR;
if (abc->type == eslAMINO)
{
if (p7_AminoFrequencies(bg->f) != eslOK) goto ERROR;
}
// adding in background probabilities for music intervals
else if (abc->type == eslMUSIC)
{
if (p7_MusicFrequencies(bg->f) != eslOK) goto ERROR;
}
else
esl_vec_FSet(bg->f, abc->K, 1. / (float) abc->K);
bg->p1 = 350./351.;
bg->omega = 1./256.;
bg->abc = abc;
return bg;
ERROR:
p7_bg_Destroy(bg);
return NULL;
}
