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NCBI C++ ToolKit: src/algo/blast/unit_tests/api/blastoptions_unit_test.cpp Source File

BOOST_CHECK(doc !=

);

kThresholdSentinel = -33;

threshold = kThresholdSentinel;

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(kThresholdSentinel, (

) threshold);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(11, (

) threshold);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(12, (

) threshold);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(13, (

) threshold);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(13, (

) threshold);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(16, (

) threshold);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(11, (

) threshold);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(0, (

) status);

existence=0, extension=0;

BOOST_CHECK_EQUAL(-1, (

) status);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(11, existence);

BOOST_CHECK_EQUAL(1, extension);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(10, existence);

BOOST_CHECK_EQUAL(1, extension);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(15, existence);

BOOST_CHECK_EQUAL(2, extension);

existence=-1, extension=-1;

reward=0, penalty=0;

BOOST_CHECK_EQUAL(-1, (

) status);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(0, existence);

BOOST_CHECK_EQUAL(0, extension);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(2, existence);

BOOST_CHECK_EQUAL(2, extension);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(4, existence);

BOOST_CHECK_EQUAL(4, extension);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK_EQUAL(2, existence);

BOOST_CHECK_EQUAL(2, extension);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK(filter_options);

BOOST_REQUIRE(filter_options ==

);

BOOST_CHECK_EQUAL(0, (

) status);

BOOST_CHECK(filter_options);

BOOST_REQUIRE(filter_options ==

);

BOOST_CHECK_EQUAL(1, (

) status);

i <= query_info->last_context;

++) {

lookup_wrap, sbp, query_info, subject_length, &word_params);

BOOST_REQUIRE(blast_seq_loc ==

);

BOOST_REQUIRE(lookup_wrap ==

);

BOOST_REQUIRE(lookup_options ==

);

BOOST_REQUIRE(query_options ==

);

kAvgSubjectLength = 335;

kSpecificSubjectLength = 186;

kDbLength = 703698559;

unique_ptr<SSeqLoc> qsl(

unique_ptr<SSeqLoc> ssl(

, strand_opt, &query_info);

query_info, &query_blk,

, strand_opt, blast_msg);

BOOST_CHECK(m->empty());

, -1, -1);

kBlastProgram, &sbp, 1.0, &blast_message,

query_info, sbp, word_options, kAvgSubjectLength, hit_params);

link_hsp_params, word_params,

kDbLength, kSpecificSubjectLength);

BOOST_REQUIRE(sbp ==

);

BOOST_REQUIRE(ext_options ==

);

BOOST_REQUIRE(scoring_options ==

);

BOOST_REQUIRE(hit_params ==

);

BOOST_REQUIRE(hit_options ==

);

BOOST_REQUIRE(word_params ==

);

BOOST_REQUIRE(word_options ==

);

BOOST_REQUIRE(query_info);

kbp_bad->

= -1.0;

sbp->

[0] = kbp_bad;

kbp_good->

= 0.1;

sbp->

[1] = kbp_good;

kAvgSubjectLength = 335;

kSpecificSubjectLength = 186;

kDbLength = 703698559;

kIsGapped =

;

link_hsp_params, &word_params,

kDbLength, kSpecificSubjectLength);

BOOST_REQUIRE(sbp ==

);

BOOST_REQUIRE(ext_options ==

);

BOOST_REQUIRE(hit_params ==

);

BOOST_REQUIRE(hit_options ==

);

kAvgSubjectLength = 316;

kSpecificSubjectLength = 21;

kDbLength = 1358990;

unique_ptr<SSeqLoc> qsl(

unique_ptr<SSeqLoc> ssl(

, strand_opt, &query_info);

query_info, &query_blk,

, strand_opt, blast_msg);

BOOST_CHECK(m->empty());

, -1, -1);

kBlastProgram, &sbp, 1.0, &blast_message,

query_info, sbp, word_options, kAvgSubjectLength, hit_params);

link_hsp_params, word_params,

kDbLength, kSpecificSubjectLength);

BOOST_REQUIRE(sbp ==

);

BOOST_REQUIRE(ext_options ==

);

BOOST_REQUIRE(scoring_options ==

);

BOOST_REQUIRE(hit_params ==

);

BOOST_REQUIRE(hit_options ==

);

BOOST_REQUIRE(word_params ==

);

BOOST_REQUIRE(word_options ==

);

kAvgSubjectLength = 335;

kSpecificSubjectLength = 186;

kDbLength = 703698559;

unique_ptr<SSeqLoc> qsl(

unique_ptr<SSeqLoc> ssl(

, strand_opt, &query_info);

query_info, &query_blk,

, strand_opt, blast_msg);

BOOST_CHECK(m->empty());

, -1, -1);

kBlastProgram, &sbp, 1.0, &blast_message,

query_info, sbp, word_options, kAvgSubjectLength, hit_params);

link_hsp_params, word_params,

kDbLength, kSpecificSubjectLength);

BOOST_CHECK_EQUAL(5, (

) (10*link_hsp_params->

));

BOOST_REQUIRE(query_blk ==

);

BOOST_REQUIRE(sbp ==

);

BOOST_REQUIRE(scoring_options ==

);

BOOST_REQUIRE(ext_options ==

);

BOOST_REQUIRE(hit_params ==

);

BOOST_REQUIRE(hit_options ==

);

BOOST_REQUIRE(word_params ==

);

BOOST_REQUIRE(word_options ==

);

k_threshold = 0;

k_word_size = 100000;

k_is_megablast, k_threshold, k_word_size);

BOOST_CHECK_EQUAL(k_word_size, (

) lookup_options->

);

BOOST_REQUIRE(num > good_one);

(index=0; index<num; index++)

(index != good_one)

kbp_array[index] = kbp;

k_num_contexts=6;

query_info, &ext_params);

(

index=query_info->

; index<=query_info->last_context; index++)

BOOST_REQUIRE(ext_params ==

);

BOOST_REQUIRE(ext_options ==

);

(

index=0; index<num; index++)

kbp_array[index] = kbp;

k_num_contexts=6;

query_info, &ext_params);

BOOST_REQUIRE(ext_params ==

);

query_info, &ext_params);

(

index=query_info->

; index<=query_info->last_context; index++)

BOOST_REQUIRE(ext_params ==

);

BOOST_REQUIRE(ext_options ==

);

unique_ptr<SSeqLoc> qsl1(

unique_ptr<SSeqLoc> qsl2(

unique_ptr<SSeqLoc> qsl3(

query_v.push_back(*qsl1);

query_v.push_back(*qsl2);

query_v.push_back(*qsl3);

, strand_opt, blast_msg);

BOOST_CHECK(m->empty());

, -1, -1);

kBlastProgram, &sbp, 1.0, &blast_message,

BOOST_REQUIRE(scoring_options ==

);

BOOST_REQUIRE(hit_params ==

);

BOOST_REQUIRE(hit_options ==

);

BOOST_REQUIRE(ext_options ==

);

BOOST_REQUIRE(sbp ==

);

unique_ptr<SSeqLoc> qsl1(

query_v.push_back(*qsl1);

, strand_opt, blast_msg);

BOOST_CHECK(m->empty());

, -1, -1);

kBlastProgram, &sbp, 1.0, &blast_message,

k_avg_subject_length=128199245;

BOOST_REQUIRE(scoring_options ==

);

BOOST_REQUIRE(hit_params ==

);

BOOST_REQUIRE(hit_options ==

);

BOOST_REQUIRE(ext_options ==

);

BOOST_REQUIRE(sbp ==

);

unique_ptr<SSeqLoc> qsl1(

query_v.push_back(*qsl1);

, strand_opt, blast_msg);

BOOST_CHECK(m->empty());

, -1, -1);

kBlastProgram, &sbp, 1.0, &blast_message,

k_avg_subject_length=104833;

BOOST_REQUIRE(scoring_options ==

);

BOOST_REQUIRE(hit_params ==

);

BOOST_REQUIRE(hit_options ==

);

BOOST_REQUIRE(ext_options ==

);

BOOST_REQUIRE(sbp ==

);

unique_ptr<SSeqLoc> qsl1(

query_v.push_back(*qsl1);

, strand_opt, blast_msg);

BOOST_CHECK(m->empty());

, -1, -1);

kBlastProgram, &sbp, 1.0, &blast_message,

k_avg_subject_length=104833;

BOOST_REQUIRE(scoring_options ==

);

BOOST_REQUIRE(hit_params ==

);

BOOST_REQUIRE(hit_options ==

);

BOOST_REQUIRE(ext_options ==

);

BOOST_REQUIRE(sbp ==

);

qid1(

);

unique_ptr<SSeqLoc> qsl1(

query_v.push_back(*qsl1);

, strand_opt, blast_msg);

BOOST_CHECK(m->empty());

, -1, -1);

kBlastProgram, &sbp, 1.0, &blast_message,

k_avg_subject_length=523;

BOOST_REQUIRE(scoring_options ==

);

BOOST_REQUIRE(hit_params ==

);

BOOST_REQUIRE(hit_options ==

);

BOOST_REQUIRE(ext_options ==

);

BOOST_REQUIRE(sbp ==

);

k_subject_length=10000;

unique_ptr<SSeqLoc> qsl1(

unique_ptr<SSeqLoc> qsl2(

unique_ptr<SSeqLoc> qsl3(

query_v.push_back(*qsl1);

query_v.push_back(*qsl2);

query_v.push_back(*qsl3);

, strand_opt, blast_msg);

BOOST_CHECK(m->empty());

, -1, -1);

kBlastProgram, &sbp, 1.0, &blast_message,

query_info, sbp, word_options, k_subject_length, hit_params);

BOOST_REQUIRE(scoring_options ==

);

BOOST_REQUIRE(hit_params ==

);

BOOST_REQUIRE(hit_options ==

);

BOOST_REQUIRE(word_params ==

);

BOOST_REQUIRE(word_options ==

);

BOOST_REQUIRE(ext_options ==

);

BOOST_REQUIRE(sbp ==

);

BOOST_CHECK_EQUAL(

, opts.

()->GetParamByName(

)->GetValue().GetBoolean());

BOOST_CHECK_EQUAL(

, opts.

()->GetParamByName(

)->GetValue().GetBoolean());

BOOST_CHECK_EQUAL(

, opts.

()->GetParamByName(

)->GetValue().GetBoolean());

BOOST_CHECK_EQUAL(

, opts.

()->GetParamByName(

)->GetValue().GetBoolean());

BOOST_CHECK_EQUAL(

, opts.

()->GetParamByName(

)->GetValue().GetBoolean());

BOOST_CHECK_EQUAL(

, opts.

()->GetParamByName(

)->GetValue().GetBoolean());

BOOST_CHECK_EQUAL(

, opts.

()->GetParamByName(

)->GetValue().GetBoolean());

BOOST_CHECK_EQUAL(

, opts.

()->GetParamByName(

)->GetValue().GetBoolean());

BOOST_CHECK_EQUAL(

, opts.

()->GetParamByName(

)->GetValue().GetBoolean());

BOOST_CHECK_EQUAL(

, opts.

()->GetParamByName(

)->GetValue().GetBoolean());

BOOST_CHECK_EQUAL(

, opts.

()->GetParamByName(

)->GetValue().GetBoolean());

BOOST_CHECK_EQUAL(

, opts.

()->GetParamByName(

)->GetValue().GetBoolean());

BOOST_CHECK_EQUAL(

(

),

(filter_string));

(filter_string);

BOOST_CHECK_EQUAL(

(

),

(filter_string));

(filter_string);

BOOST_REQUIRE(optsHandle.

());

optsHandle.

();

BOOST_CHECK_EQUAL(optsClone->

(), 10000);

BOOST_CHECK_EQUAL(

(optsClone->

()),

(

));

BOOST_CHECK_EQUAL(

(optsClone->

()),

(

));

optsClone = optsSnapshot;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Declares the CBl2Seq (BLAST 2 Sequences) class.

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

BlastSeqLoc * BlastSeqLocFree(BlastSeqLoc *loc)

Deallocate all BlastSeqLoc objects in a chain.

BlastSeqLoc * BlastSeqLocNew(BlastSeqLoc **head, Int4 from, Int4 to)

Create and initialize a new sequence interval.

#define BLASTERR_INVALIDPARAM

Invalid parameter: possible programmer error or pre-condition not met.

Definitions which are dependant on the NCBI C++ Object Manager.

PSIBlastOptions * PSIBlastOptionsFree(PSIBlastOptions *psi_options)

Deallocate PSI BLAST options.

BlastHitSavingOptions * BlastHitSavingOptionsFree(BlastHitSavingOptions *options)

Deallocate memory for BlastHitSavingOptions.

Int2 BlastQuerySetUpOptionsNew(QuerySetUpOptions **options)

Allocate memory for QuerySetUpOptions and fill with default values.

Int2 BLAST_GetSuggestedThreshold(EBlastProgramType program_number, const char *matrixName, double *threshold)

Get thresholds for word-finding suggested by Stephen Altschul.

Int2 BLAST_GetSuggestedWindowSize(EBlastProgramType program_number, const char *matrixName, Int4 *window_size)

Get window sizes for two hit algorithm suggested by Stephen Altschul.

Int2 BLAST_FillScoringOptions(BlastScoringOptions *options, EBlastProgramType program, Boolean greedy_extension, Int4 penalty, Int4 reward, const char *matrix, Int4 gap_open, Int4 gap_extend)

Fill non-default values in the BlastScoringOptions structure.

BlastInitialWordOptions * BlastInitialWordOptionsFree(BlastInitialWordOptions *options)

Deallocate memory for BlastInitialWordOptions.

Int2 BlastScoringOptionsNew(EBlastProgramType program, BlastScoringOptions **options)

Allocate memory for BlastScoringOptions and fill with default values.

BlastEffectiveLengthsOptions * BlastEffectiveLengthsOptionsFree(BlastEffectiveLengthsOptions *options)

Deallocate memory for BlastEffectiveLengthsOptions*.

SBlastFilterOptions * SBlastFilterOptionsFree(SBlastFilterOptions *filter_options)

Frees SBlastFilterOptions and all subservient structures.

Int2 BLAST_FillLookupTableOptions(LookupTableOptions *options, EBlastProgramType program, Boolean is_megablast, double threshold, Int4 word_size)

Allocate memory for lookup table options and fill with default values.

Int2 LookupTableOptionsNew(EBlastProgramType program, LookupTableOptions **options)

Allocate memory for lookup table options and fill with default values.

BlastExtensionOptions * BlastExtensionOptionsFree(BlastExtensionOptions *options)

Deallocate memory for BlastExtensionOptions.

Int2 BlastHitSavingOptionsNew(EBlastProgramType program, BlastHitSavingOptions **options, Boolean gapped_calculation)

Allocate memory for BlastHitSavingOptions.

BlastDatabaseOptions * BlastDatabaseOptionsFree(BlastDatabaseOptions *db_options)

Deallocate database options.

@ eDust

low-complexity for nucleotides.

@ eSeg

low-complexity for proteins.

Int2 SBlastFilterOptionsNew(SBlastFilterOptions **filter_options, EFilterOptions type)

Allocates memory for SBlastFilterOptions and.

Int2 BlastInitialWordOptionsNew(EBlastProgramType program, BlastInitialWordOptions **options)

Allocate memory for BlastInitialWordOptions and fill with default values.

BlastScoringOptions * BlastScoringOptionsFree(BlastScoringOptions *options)

Deallocate memory for BlastScoringOptions.

LookupTableOptions * LookupTableOptionsFree(LookupTableOptions *options)

Deallocates memory for LookupTableOptions*.

QuerySetUpOptions * BlastQuerySetUpOptionsFree(QuerySetUpOptions *options)

Deallocate memory for QuerySetUpOptions.

Int2 BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions **options, Boolean gapped)

Allocate memory for BlastExtensionOptions and fill with default values.

BlastHitSavingParameters * BlastHitSavingParametersFree(BlastHitSavingParameters *parameters)

Deallocate memory for BlastHitSavingOptions*.

Int2 BlastExtensionParametersNew(EBlastProgramType blast_program, const BlastExtensionOptions *options, BlastScoreBlk *sbp, BlastQueryInfo *query_info, BlastExtensionParameters **parameters)

Calculate the raw values for the X-dropoff parameters.

BlastInitialWordParameters * BlastInitialWordParametersFree(BlastInitialWordParameters *parameters)

Deallocate memory for BlastInitialWordParameters.

BlastExtensionParameters * BlastExtensionParametersFree(BlastExtensionParameters *parameters)

Deallocate memory for BlastExtensionParameters.

Int2 BlastInitialWordParametersNew(EBlastProgramType program_number, const BlastInitialWordOptions *word_options, const BlastHitSavingParameters *hit_params, const LookupTableWrap *lookup_wrap, const BlastScoreBlk *sbp, BlastQueryInfo *query_info, Uint4 subject_length, BlastInitialWordParameters **parameters)

Allocate memory for BlastInitialWordParameters and set x_dropoff.

Int2 BlastHitSavingParametersNew(EBlastProgramType program_number, const BlastHitSavingOptions *options, const BlastScoreBlk *sbp, const BlastQueryInfo *query_info, Int4 avg_subject_length, Int4 compositionBasedStats, BlastHitSavingParameters **parameters)

Allocate memory and initialize the BlastHitSavingParameters structure.

Int2 BlastHitSavingParametersUpdate(EBlastProgramType program_number, const BlastScoreBlk *sbp, const BlastQueryInfo *query_info, Int4 avg_subject_length, Int4 compositionBasedStats, BlastHitSavingParameters *parameters)

Updates cutoff scores in hit saving parameters.

void CalculateLinkHSPCutoffs(EBlastProgramType program, BlastQueryInfo *query_info, const BlastScoreBlk *sbp, BlastLinkHSPParameters *link_hsp_params, const BlastInitialWordParameters *word_params, Int8 db_length, Int4 subject_length)

Calculates cutoff scores and returns them.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

BlastQueryInfo * BlastQueryInfoNew(EBlastProgramType program, int num_queries)

Allocate memory for query information structure.

Utilities initialize/setup BLAST.

Int2 BlastSetup_ScoreBlkInit(BLAST_SequenceBlk *query_blk, const BlastQueryInfo *query_info, const BlastScoringOptions *scoring_options, EBlastProgramType program_number, BlastScoreBlk **sbpp, double scale_factor, Blast_Message **blast_message, GET_MATRIX_PATH get_path)

Initializes the score block structure.

Internal auxiliary setup classes/functions for C++ BLAST APIs.

BlastScoreBlk * BlastScoreBlkFree(BlastScoreBlk *sbp)

Deallocates BlastScoreBlk as well as all associated structures.

Int2 BLAST_GetProteinGapExistenceExtendParams(const char *matrixName, Int4 *gap_existence, Int4 *gap_extension)

Extract the recommended gap existence and extension values.

Blast_KarlinBlk * Blast_KarlinBlkNew(void)

Callocs a Blast_KarlinBlk.

Blast_KarlinBlk * Blast_KarlinBlkFree(Blast_KarlinBlk *kbp)

Deallocates the KarlinBlk.

Int2 BLAST_GetNucleotideGapExistenceExtendParams(Int4 reward, Int4 penalty, Int4 *gap_existence, Int4 *gap_extension)

Extract the recommended gap existence and extension values.

BlastScoreBlk * BlastScoreBlkNew(Uint1 alphabet, Int4 number_of_contexts)

Allocates and initializes BlastScoreBlk.

@ eBlastNotSet

Not yet set.

@ eTblastx

Translated nucl-Translated nucl.

@ eBlastn

Nucl-Nucl (traditional blastn)

@ eBlastp

Protein-Protein.

@ eTblastn

Protein-Translated nucl.

@ eBlastx

Translated nucl-Protein.

BLAST_SequenceBlk * BlastSequenceBlkFree(BLAST_SequenceBlk *seq_blk)

Deallocate memory for a sequence block.

BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &bioseq)

static BlastScoreBlk * s_FillScoreBlkWithBadKbp(BlastQueryInfo *query_info)

static void MakeSomeInvalidKBP(Blast_KarlinBlk **kbp_array, Int4 num, Int4 good_one, BlastQueryInfo *query_info)

static void s_FillSearchSpace(BlastQueryInfo *query_info, Int8 searchsp)

BOOST_AUTO_TEST_CASE(TestTasksDefinitionsAndDocumentation)

static BlastInitialWordParameters * s_GetInitialWordParameters(EBlastProgramType program_number, BLAST_SequenceBlk *query_blk, BlastQueryInfo *query_info, BlastScoreBlk *sbp, const BlastInitialWordOptions *word_options, int subject_length, const BlastHitSavingParameters *hit_params)

static void MakeSomeValidKBP(Blast_KarlinBlk **kbp_array, Int4 num, BlastQueryInfo *query_info)

Wrapper class for BLAST_SequenceBlk .

Runs the BLAST algorithm between 2 sequences.

Defines BLAST error codes (user errors included)

Wrapper class for BlastInitialWordOptions .

Encapsulates ALL the BLAST algorithm's options.

@ eRemote

To be used when running BLAST remotely.

Wrapper class for BlastQueryInfo .

Wrapper class for LookupTableOptions .

static CTestObjMgr & Instance()

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

void SetPHIPattern(const char *pattern, bool is_dna)

BlastQueryInfo * Get() const

const CBlastOptionsHandle & GetOptionsHandle() const

Retrieve the options handle.

void SetQueryCovHspPerc(double p)

Sets QueryCovHspPerc.

void SetDbLength(Int8 len)

Sets DbLength.

void SetQueryCovHspPerc(double p)

const char * GetPHIPattern() const

static string GetDocumentation(const string &task_name)

Return the documentation for the provided task.

double GetBestHitOverhang() const

void SetupQueries(TSeqLocVector &queries, BlastQueryInfo *qinfo, BLAST_SequenceBlk **seqblk, EBlastProgramType prog, objects::ENa_strand strand_opt, TSearchMessages &messages)

Populates BLAST_SequenceBlk with sequence data for use in CORE BLAST.

objects::ENa_strand GetStrandOption() const

void SetRepeatFilteringDB(const char *db)

Sets the repeat filtering database to use.

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested program,...

double GetQueryCovHspPerc() const

CBlastOptions & SetOptions()

Returns a reference to the internal options class which this object is a handle for.

void SetUnifiedP(int u=0)

void SetProgram(EProgram p)

Sets the task this object is best suited for.

#define BLASTAA_SEQ_CODE

== Seq_code_ncbistdaa

void SetMaxHspsPerSubject(int m)

Sets MaxHspPerSubjectQueryPair.

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

void SetBestHitOverhang(double overhang)

static set< string > GetTasks(ETaskSets choice=eAll)

Retrieve the set of supported tasks.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

CRef< CBlastOptions > Clone() const

Explicit deep copy of the Blast options object.

char * GetFilterString() const

Return the filtering string used.

void SetFilterString(const char *f, bool clear=true)

char * BlastFindMatrixPath(const char *matrix_name, Boolean is_prot)

Returns the path to a specified matrix.

const TSeqLocVector & GetQueries() const

Retrieve a vector of query sequences.

void SetupQueryInfo(TSeqLocVector &queries, EBlastProgramType prog, objects::ENa_strand strand_opt, BlastQueryInfo **qinfo)

Allocates the query information structure and fills the context offsets, in case of multiple queries,...

double GetQueryCovHspPerc() const

Returns QueryCovHspPerc.

void SetFilterString(const char *f, bool clear=true)

Sets FilterString.

void SetMaskAtHash(bool val=true)

void SetBestHitScoreEdge(double score_edge)

void SetDustFiltering(bool val=true)

void SetSegFiltering(bool val=true)

double GetBestHitScoreEdge() const

TBlast4Opts * GetBlast4AlgoOpts()

char * GetFilterString() const

Returns FilterString.

static CBlastOptionsHandle * CreateTask(string task, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested task,...

int GetMaxHspsPerSubject() const

Returns MaxHspsPerSubjectQueryPair.

void SetRepeatFiltering(bool val=true)

Turns on repeat filtering using the default repeat database, namely kDefaultRepeatFilterDb.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

ENa_strand

strand of nucleic acid

@ eNa_strand_both

in forward orientation

Implementation of a number of BlastHSPWriters to save hits from a BLAST search, and subsequently retu...

#define kBestHit_ScoreEdgeDflt

Default value for score_edge.

#define kBestHit_OverhangDflt

The "best hit" writer.

LookupTableWrap * LookupTableWrapFree(LookupTableWrap *lookup)

Deallocate memory for the lookup table.

Int2 LookupTableWrapInit(BLAST_SequenceBlk *query, const LookupTableOptions *lookup_options, const QuerySetUpOptions *query_options, BlastSeqLoc *lookup_segments, BlastScoreBlk *sbp, LookupTableWrap **lookup_wrap_ptr, const BlastRPSInfo *rps_info, Blast_Message **error_msg, BlastSeqSrc *seqsrc)

Create the lookup table for all query words.

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

BOOST_AUTO_TEST_SUITE(psiblast_iteration)

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Structure to hold a sequence.

The context related information.

Int4 query_length

Length of this query, strand or frame.

Boolean is_valid

Determine if this context is valid or not.

Int4 query_offset

Offset of this query, strand or frame in the concatenated super-query.

Int8 eff_searchsp

Effective search space for this context.

Options used for gapped extension These include: a.

double gap_x_dropoff_final

X-dropoff value for the final gapped extension (in bits)

double gap_x_dropoff

X-dropoff value for gapped extension (in bits)

Computed values used as parameters for gapped alignments.

Int4 gap_x_dropoff_final

X-dropoff value for the final gapped extension (raw)

Int4 gap_x_dropoff

X-dropoff value for gapped extension (raw)

Int4 cutoff_score

Raw cutoff score corresponding to the e-value provided by the user if no sum stats,...

Int4 cutoff_score_max

Raw cutoff score corresponding to the e-value provided by user, cutoff_score must be <= this.

Options used when evaluating and saving hits These include: a.

Int4 max_hsps_per_subject

Queries are paired reads, for mapping.

Boolean do_sum_stats

Force sum statistics to be used to combine HSPs, TRUE by default for all ungapped searches and transl...

double query_cov_hsp_perc

Min query coverage hsp percentage.

Parameter block that contains a pointer to BlastHitSavingOptions and the values derived from it.

BlastGappedCutoffs * cutoffs

per-context gapped cutoff information

Int4 cutoff_score_min

smallest cutoff score across all contexts

double prelim_evalue

evalue for preliminary search (may be higher for CBS).

BlastLinkHSPParameters * link_hsp_params

Parameters for linking HSPs with sum statistics; linking is not done if NULL.

Options needed for initial word finding and processing.

double x_dropoff

X-dropoff value (in bits) for the ungapped extension.

Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it.

Int4 cutoff_score_min

smallest cutoff score across all contexts

Int4 x_dropoff_max

largest X-drop cutoff across all contexts

Parameter block for linking HSPs with sum statistics.

double gap_decay_rate

Decay rate for linking HSPs and calculating cutoff scores.

double gap_prob

Probability of decay for linking HSPs.

Int4 cutoff_big_gap

Cutoff sum score for linked HSPs with big gaps.

Int4 cutoff_small_gap

Cutoff sum score for linked HSPs with small gaps.

The query related information.

Int4 first_context

Index of the first element of the context array.

BlastContextInfo * contexts

Information per context.

Int4 last_context

Index of the last element of the context array.

Structure used for scoring calculations.

Blast_KarlinBlk ** kbp

Karlin-Altschul parameters.

Boolean matrix_only_scoring

Score ungapped/gapped alignment only using the matrix parameters and with raw scores.

double scale_factor

multiplier for all cutoff and dropoff scores

Blast_KarlinBlk ** kbp_gap

K-A parameters for gapped alignments.

Blast_KarlinBlk ** kbp_std

K-A parameters for ungapped alignments.

Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lo...

Boolean gapped_calculation

gap-free search if FALSE

Used to hold a set of positions, mostly used for filtering.

Structure to hold the Karlin-Altschul parameters.

double K

K value used in statistics.

double Lambda

Lambda value used in statistics.

double H

H value used in statistics.

double logK

natural log of K value used in statistics

Structure to hold the a message from the core of the BLAST engine.

Options needed to construct a lookup table Also needed: query sequence and query length.

Int4 word_size

Determines the size of the lookup table.

Wrapper structure for different types of BLAST lookup tables.

Options required for setting up the query sequence.

SSegOptions * segOptions

low-complexity filtering for proteins sequences (includes translated nucleotides).

SDustOptions * dustOptions

low-complexity filtering for nucleotides.

Utility stuff for more convenient using of Boost.Test library.

voidp calloc(uInt items, uInt size)

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