void
CBlastAncillaryData::do_copy(const CBlastAncillaryData& other)
{
if (this != &other) {
m_UngappedKarlinBlk = m_GappedKarlinBlk = NULL;
m_SearchSpace = other.m_SearchSpace;
if (other.m_UngappedKarlinBlk) {
m_UngappedKarlinBlk = Blast_KarlinBlkNew();
Blast_KarlinBlkCopy(m_UngappedKarlinBlk,
other.m_UngappedKarlinBlk);
}
if (other.m_GappedKarlinBlk) {
m_GappedKarlinBlk = Blast_KarlinBlkNew();
Blast_KarlinBlkCopy(m_GappedKarlinBlk, other.m_GappedKarlinBlk);
}
if (other.m_PsiUngappedKarlinBlk) {
m_PsiUngappedKarlinBlk = Blast_KarlinBlkNew();
Blast_KarlinBlkCopy(m_PsiUngappedKarlinBlk,
other.m_PsiUngappedKarlinBlk);
}
if (other.m_PsiGappedKarlinBlk) {
m_PsiGappedKarlinBlk = Blast_KarlinBlkNew();
Blast_KarlinBlkCopy(m_PsiGappedKarlinBlk,
other.m_PsiGappedKarlinBlk);
}
if (other.m_GumbelBlk) {
s_InitializeGumbelBlk(other.m_GumbelBlk, &m_GumbelBlk);
}
}
}
static void
s_InitializeKarlinBlk(Blast_KarlinBlk* src, Blast_KarlinBlk** dest)
{
_ASSERT(dest);
if (src && src->Lambda >= 0) {
*dest = Blast_KarlinBlkNew();
Blast_KarlinBlkCopy(*dest, src);
}
}
/**
* Read a checkpoint file and set the necessary structures in a
* BlastScoreBlk: the psi_matrix, kbp_psi[0], and kbp_gap_psi[0].
*
* @param sbp a BlastScoreBlk to receive a PSSM [in/out]
* @param query query sequence data
* @param psi_matrix_file checkpoint file to read
* @pcore_msg a pointer to receive error and warning messages
*/
static int
s_SetupScoreBlkPssmFromChkpt(BlastScoreBlk * sbp,
BLAST_SequenceBlk * query,
Blast_PsiCheckpointLoc * psi_checkpoint,
Blast_Message* *pcore_msg)
{
int status = 0;
/* An intermediate representation of the PSSM data that is used
in PSIBlast routines */
PSIMatrix * pssm = NULL;
/* The actual PSSM that is saved in the BlastScoreBlk */
SPsiBlastScoreMatrix * psi_matrix = NULL;
size_t i, j;
psi_matrix = SPsiBlastScoreMatrixNew(query->length);
if (!psi_matrix) {
ErrPostEx(SEV_FATAL, 1, 0,
"Out-of-memory: cannot allocate a PSSM of length %d.\n",
query->length);
status = -1;
goto error_return;
}
status = Blast_PosReadCheckpoint(psi_matrix->freq_ratios,
query->length, query->sequence,
psi_checkpoint,
pcore_msg);
if (status != 0) {
goto error_return;
}
Blast_KarlinBlkCopy(psi_matrix->kbp, sbp->kbp_gap_std[0]);
status = PSICreatePssmFromFrequencyRatios(query->sequence,
query->length, sbp,
psi_matrix->freq_ratios,
kPSSM_NoImpalaScaling,
&pssm);
if (0 != status) {
goto error_return;
}
for (i = 0; i < psi_matrix->pssm->ncols; i++) {
for (j = 0; j < psi_matrix->pssm->nrows; j++) {
psi_matrix->pssm->data[i][j] = pssm->pssm[i][j];
}
}
PSIMatrixFree(pssm);
sbp->psi_matrix = psi_matrix;
return 0;
error_return:
if (psi_matrix)
SPsiBlastScoreMatrixFree(psi_matrix);
return status;
}
