Int2
BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions* *options, Boolean gapped)
{
*options = (BlastExtensionOptions*)
calloc(1, sizeof(BlastExtensionOptions));
if (*options == NULL)
return BLASTERR_MEMORY;
if (program != eBlastTypeBlastn &&
program != eBlastTypePhiBlastn) /* protein-protein options. */
{
(*options)->gap_x_dropoff = BLAST_GAP_X_DROPOFF_PROT;
(*options)->gap_x_dropoff_final =
BLAST_GAP_X_DROPOFF_FINAL_PROT;
} else {
(*options)->gap_x_dropoff = BLAST_GAP_X_DROPOFF_NUCL;
(*options)->gap_x_dropoff_final = BLAST_GAP_X_DROPOFF_FINAL_NUCL;
}
(*options)->ePrelimGapExt = eDynProgScoreOnly;
(*options)->eTbackExt = eDynProgTbck;
(*options)->compositionBasedStats = eNoCompositionBasedStats;
/** @todo how to determine this for PSI-BLAST bootstrap run (i.e. when
* program is blastp? */
if (gapped && (Blast_QueryIsPssm(program) && ! Blast_SubjectIsTranslated(program))) {
(*options)->compositionBasedStats = eCompositionBasedStats;
}
(*options)->program_number = program;
return 0;
}
BlastHSPStream*
BlastHSPStreamNew(EBlastProgramType program,
const BlastExtensionOptions* extn_opts,
Boolean sort_on_read,
Int4 num_queries,
BlastHSPWriter *writer)
{
BlastHSPStream* hsp_stream =
(BlastHSPStream*) malloc(sizeof(BlastHSPStream));
hsp_stream->program = program;
hsp_stream->num_hsplists = 0;
hsp_stream->num_hsplists_alloc = 100;
hsp_stream->sorted_hsplists = (BlastHSPList **)malloc(
hsp_stream->num_hsplists_alloc *
sizeof(BlastHSPList *));
hsp_stream->results = Blast_HSPResultsNew(num_queries);
hsp_stream->results_sorted = FALSE;
/* This is needed to meet a pre-condition of the composition-based
* statistics code */
if ((Blast_QueryIsProtein(program) || Blast_QueryIsPssm(program)) &&
extn_opts->compositionBasedStats != 0) {
hsp_stream->sort_by_score =
(SSortByScoreStruct*)calloc(1, sizeof(SSortByScoreStruct));
hsp_stream->sort_by_score->sort_on_read = sort_on_read;
hsp_stream->sort_by_score->first_query_index = 0;
} else {
hsp_stream->sort_by_score = NULL;
}
hsp_stream->x_lock = NULL;
hsp_stream->writer = writer;
hsp_stream->writer_initialized = FALSE;
hsp_stream->writer_finalized = FALSE;
hsp_stream->pre_pipe = NULL;
hsp_stream->tback_pipe = NULL;
return hsp_stream;
}
/** Checks that the extension and scoring options are consistent with each other
* @param program_number identifies the program [in]
* @param ext_options the extension options [in]
* @param score_options the scoring options [in]
* @param blast_msg returns a message on errors. [in|out]
* @return zero on success, an error code otherwise.
*/
static Int2 s_BlastExtensionScoringOptionsValidate(EBlastProgramType program_number,
const BlastExtensionOptions* ext_options,
const BlastScoringOptions* score_options,
Blast_Message* *blast_msg)
{
if (ext_options == NULL || score_options == NULL)
return BLASTERR_INVALIDPARAM;
if (program_number == eBlastTypeBlastn)
{
if (score_options->gap_open == 0 && score_options->gap_extend == 0)
{
if (ext_options->ePrelimGapExt != eGreedyScoreOnly &&
ext_options->eTbackExt != eGreedyTbck)
{
Blast_MessageWrite(blast_msg, eBlastSevWarning, kBlastMessageNoContext,
"Greedy extension must be used if gap existence and extension options are zero");
return BLASTERR_OPTION_VALUE_INVALID;
}
}
}
if (ext_options->compositionBasedStats != eNoCompositionBasedStats)
{
if (!Blast_QueryIsPssm(program_number) && program_number != eBlastTypeTblastn &&
program_number != eBlastTypeBlastp) {
Blast_MessageWrite(blast_msg, eBlastSevWarning, kBlastMessageNoContext,
"Compositional adjustments are only supported with blastp or tblastn");
return BLASTERR_OPTION_VALUE_INVALID;
}
if (!score_options->gapped_calculation) {
Blast_MessageWrite(blast_msg, eBlastSevWarning, kBlastMessageNoContext,
"Compositional adjustments are only supported for gapped searches");
return BLASTERR_OPTION_VALUE_INVALID;
}
}
return 0;
}
Int2
BLAST_FillExtensionOptions(BlastExtensionOptions* options,
EBlastProgramType program, Int4 greedy, double x_dropoff,
double x_dropoff_final)
{
if (!options)
return BLASTERR_INVALIDPARAM;
if (program == eBlastTypeBlastn || program == eBlastTypePhiBlastn) {
if (greedy) {
options->gap_x_dropoff = BLAST_GAP_X_DROPOFF_GREEDY;
options->gap_x_dropoff_final = BLAST_GAP_X_DROPOFF_FINAL_NUCL;
options->ePrelimGapExt = eGreedyScoreOnly;
options->eTbackExt = eGreedyTbck;
} else {
options->gap_x_dropoff = BLAST_GAP_X_DROPOFF_NUCL;
options->gap_x_dropoff_final = BLAST_GAP_X_DROPOFF_FINAL_NUCL;
options->ePrelimGapExt = eDynProgScoreOnly;
options->eTbackExt = eDynProgTbck;
}
}
if (Blast_QueryIsPssm(program) && ! Blast_SubjectIsTranslated(program)) {
options->compositionBasedStats = eCompositionBasedStats;
}
if (x_dropoff)
options->gap_x_dropoff = x_dropoff;
if (x_dropoff_final) {
options->gap_x_dropoff_final = x_dropoff_final;
} else {
/* Final X-dropoff can't be smaller than preliminary X-dropoff */
options->gap_x_dropoff_final =
MAX(options->gap_x_dropoff_final, x_dropoff);
}
return 0;
}
