Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__format_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/format/blast_format.cpp Source File

blast::CLocalDbAdapter& db_adapter,

*matrix_name

,

use_sum_statistics

,

is_remote_search

,

dbfilt_algorithm

,

& custom_output_format

,

blast::CIgBlastOptions *ig_opts

,

blast::CLocalDbAdapter* domain_db_adapter

,

& cmdline

,

& subjectTag

)

: m_FormatType(format_type), m_IsHTML(is_html),

m_DbIsAA(db_adapter.IsProtein()), m_BelieveQuery(believe_query),

m_Outfile(

), m_NumSummary(num_summary),

m_NumAlignments(num_alignments), m_HitlistSize(options.GetHitlistSize()),

m_QueryGenCode(qgencode), m_DbGenCode(dbgencode),

m_ShowGi(show_gi), m_ShowLinkedSetSize(

),

m_IsUngappedSearch(!options.GetGappedMode()),

m_MatrixName(matrix_name),

m_SubjectTag(subjectTag),

m_IsRemoteSearch(is_remote_search),

m_QueriesFormatted(0),

m_Megablast(is_megablast),

m_IndexedMegablast(is_indexed),

m_CustomOutputFormatSpec(custom_output_format),

m_IgOptions(ig_opts),

m_IsIterative(

),

m_OrigExceptionMask(

.exceptions()),

= db_adapter.GetDatabaseName();

(!is_remote_search)

filteringAlgorithmId = db_adapter.GetFilteringAlgorithm();

(filteringAlgorithmId == -1) {

(db_Info && db_Info.

()) {

dbfilt_algorithm, is_remote_search);

options.GetMatchReward() == 0 &&

options.GetMismatchPenalty() == 0 )

(domain_db_adapter) {

domain_db_adapter->GetDatabaseName(),

, -1, is_remote_search);

vector< CBlastFormatUtil::SDbInfo >& dbinfo_list,

is_remote_search,

& custom_output_format,

& cmdline)

: m_FormatType(format_type),

m_BelieveQuery(believe_query),

m_NumSummary(num_summary),

m_NumAlignments(num_alignments),

m_HitlistSize(opts.GetHitlistSize()),

m_QueryGenCode(opts.GetQueryGeneticCode()),

m_DbGenCode(opts.GetDbGeneticCode()),

m_ShowLinkedSetSize(

),

m_IsUngappedSearch(!opts.GetGappedMode()),

m_MatrixName(opts.GetMatrixName()),

m_IsDbScan (

),

m_IsRemoteSearch(is_remote_search),

m_QueriesFormatted(0),

m_Megablast(opts.GetProgram() ==

||

m_IndexedMegablast(opts.GetMBIndexLoaded()),

m_CustomOutputFormatSpec(custom_output_format),

m_IsIterative(

),

m_OrigExceptionMask(

.exceptions()),

.assign(dbinfo_list.begin(), dbinfo_list.end());

vector< CBlastFormatUtil::SDbInfo >::const_iterator itInfo;

opts.GetMatchReward() == 0 &&

opts.GetMismatchPenalty() == 0 )

<<

;

<<

;

<<

;

<<

<<

;

? summary.GetPsiUngappedKarlinBlk()

: summary.GetUngappedKarlinBlk();

CBlastFormatUtil::PrintKAParameters(kbp_ungap->

,

kbp_ungap->

, kbp_ungap->

,

? summary.GetPsiGappedKarlinBlk()

: summary.GetGappedKarlinBlk();

CBlastFormatUtil::PrintKAParameters(kbp_gap->

,

kbp_gap->

, kbp_gap->

,

<<

<<

summary.GetSearchSpace() <<

;

retval =

;

skip_from,

skip_to,

index,

num_descriptions_to_show

)

(num_descriptions_to_show == 0)

blast::CPsiBlastIterationState::TSeqIds& prev_seqids)

( !prev_seqids.empty() );

= 0;

(prev_seqids.find(subj_id) != prev_seqids.end()) {

repeated_seqs.

().push_back(*alignment);

new_seqs.

().push_back(*alignment);

kIsGlobal = (seqalign_set->IsSet() && seqalign_set->CanGet() &&

seqalign_set->Get().front()->CanGetType() &&

itr_num,

blast::CPsiBlastIterationState::TSeqIds& prev_seqids,

!prev_seqids.empty()) {

repeated_seqs.

());

html,

showgi,

isbl2seq,

disableKAStats)

(program ==

) {

& db_title)

db_title =

.front().definition;

(

.HasAlignments()) {

(

.HasAlignments()) {

(query_id->

(*(*itr)->GetQueryId())) {

objects::CBlastOutput xml_output;

(

.HasAlignments()) {

itr_num)

(ncbi::NStr::ToLower(

) ==

(

))

strProgVersion =

(

.HasAlignments()) {

CBlastFormatUtil::PruneSeqalign(*aln_set, copy_aln_set,

);

ncbi::NStr::ToLower(

) ==

(

))

clone_info.

= seqid.substr(0, 45);

vector<CIgBlastTabularInfo::SIgDomain*>& domains = tabinfo.

();

(

=0;

<domains.size(); ++

) {

(domains[

]->length > 0) {

length += domains[

]->length;

num_match += domains[

]->num_match;

clone_info.

= ((double)num_match)/length;

fill_clone_info)

strProgVersion =

(

.HasAlignments()) {

CSeq_align_set::Tdata::const_iterator itr = aln_set->

().begin();

(fill_clone_info) {

aln_set, subject_bioseq);

(; itr != aln_set->

().end(); ++itr) {

<<

;

fill_clone_info,

print_airr_format_header)

strProgVersion =

(

.HasAlignments()) {

annots =

.GetIgAnnotation();

(fill_clone_info) {

print_airr_format_header,

subj_index = 0;

list< CRef<CSeq_id> > ids =

->GetId(subj_index++);

(archive.

()) {

(outfmt.empty()) {

blast::CBlastOptionsHandle& options_handle,

num_iters,

seq_loc->SetWhole(*

);

query_vector->AddQuery(search_query);

(num_iters != 0) {

(

=0;

<

.size();

++) {

(

.size() > 0) {

archive->SetMessages() =

;

blast::CBlastOptionsHandle& options_handle,

num_iters,

(

.size() > 0) {

archive->SetMessages() =

;

delineFormatOption = 0;

deflines.

(delineFormatOption);

vector <CShowBlastDefline::SDeflineFormattingInfo *> sdlFortInfoVec = deflines.

();

(

= 0;

< sdlFortInfoVec.size();

++) {

obj.

(

,sdlFortInfoVec[

]->dfln_url);

obj.

(

,sdlFortInfoVec[

]->dfln_rid);

obj.

(

,sdlFortInfoVec[

]->dfln_gi);

obj.

(

,sdlFortInfoVec[

]->dfln_seqid);

obj.

(

,sdlFortInfoVec[

]->full_dfln_defline);

obj.

(

,sdlFortInfoVec[

]->dfln_defline);

obj.

(

,sdlFortInfoVec[

]->dfln_id);

obj.

(

,sdlFortInfoVec[

]->dflnFrm_id);

obj.

(

,sdlFortInfoVec[

]->dflnFASTA_id);

obj.

(

,sdlFortInfoVec[

]->dflnAccs);

obj.

(

,sdlFortInfoVec[

]->score_info);

obj.

(

,sdlFortInfoVec[

]->dfln_hspnum);

obj.

(

,sdlFortInfoVec[

]->dfln_alnLen);

obj.

(

,sdlFortInfoVec[

]->dfln_blast_rank);

obj.

(

,sdlFortInfoVec[

]->total_bit_string);

obj.

(

,sdlFortInfoVec[

]->percent_coverage);

obj.

(

,sdlFortInfoVec[

]->evalue_string);

obj.

(

,sdlFortInfoVec[

]->percent_identity);

delineFormatOption = 0;

deflines.

(delineFormatOption);

.GetMaskedQueryRegions(masklocs);

CBlastFormatUtil::PruneSeqalign(*aln_set, copy_aln_set,

);

blastAlignParamsTemplData = reg.

(

,

);

blastAlignParamsTag = (

==

) ?

:

;

blastAlignProtParamsTable = reg.

(

, blastAlignParamsTag);

AlignOption = 0;

molTypeString;

molTypeString =

;

molTypeString =

;

molTypeString =

;

molTypeString =

;

molTypeString =

;

molTypeString =

;

molTypeString;

queryID->

(&seqID,labelType);

seqDescr = CBlastFormatUtil::GetSeqDescrString(*bioseq);

seqDescr = seqDescr.empty() ?

: seqDescr;

obj.

(

,seqID);

obj.

(

,seqDescr);

obj.

(

,molType);

obj.

(

,dbTitle);

(

.HasWarnings()) {

itr_num

blast::CPsiBlastIterationState::TSeqIds prev_seqids

is_deltablast_domain_result

)

(

.HasWarnings()) {

reportCaption =

;

kIsTabularOutput =

;

(is_deltablast_domain_result) {

<<

<<

;

<<

<< itr_num <<

;

message =

+

.GetSeqId()->AsFastaString();

kBelieveSubject =

;

CBlastFormatUtil::AcknowledgeBlastSubject(*subject_bioseq,

( !

.HasAlignments() ) {

<<

<< CBlastFormatUtil::kNoHitsFound <<

<<

aln_set = CBlastFormatUtil::SortSeqalignForSortableFormat(

(

==

) ?

:

,

.GetMaskedQueryRegions(masklocs);

CBlastFormatUtil::PruneSeqalign(*aln_set, copy_aln_set,

);

kAlignToShow=2000000000;

.GetSubjectMasks(subj_masks);

fill_clone_info,

print_airr_format_header,

(

.HasWarnings()) {

(

.GetIgAnnotation()->m_MinusStrand) {

<<

<< endl;

reportCaption =

;

kIsTabularOutput =

;

( !

.HasAlignments() ) {

<<

<< CBlastFormatUtil::kNoHitsFound <<

<<

(

.HasAlignments()) {

CSeq_align_set::Tdata::const_iterator itr = aln_set->

().begin();

(fill_clone_info) {

<<

<<

->m_DomainSystem << endl << endl;

.GetMaskedQueryRegions(masklocs);

list < CRef<CDisplaySeqalign::DomainInfo> > domain;

kabat_domain_name[] = {

,

,

,

,

,

,

,

};

imgt_domain_name[] = {

,

,

,

,

,

,

,

};

domain_name_length = 8;

vector<string> domain_name;

(

= 0;

< domain_name_length;

++) {

domain_name.push_back(kabat_domain_name[

]);

(

= 0;

< domain_name_length;

++) {

domain_name.push_back(imgt_domain_name[

]);

(

=0;

<9;

=

+ 2) {

temp->is_subject_start_valid = subject_start > 0 ?

:

;

temp->is_subject_stop_valid = subject_stop > 0 ?

:

;

temp->domain_name = domain_name[

/2];

domain.push_back(temp);

subject_start = -1;

subject_stop = -1;

temp->subject_seqloc =

(*id_holder,

temp->is_subject_start_valid = subject_start > 0 ?

:

;

temp->is_subject_stop_valid = subject_stop > 0 ?

:

;

temp->domain_name = domain_name[5];

domain.push_back(temp);

subject_start = -1;

subject_stop = -1;

temp->subject_seqloc =

(*id_holder,

temp->is_subject_start_valid = subject_start > 0 ?

:

;

temp->is_subject_stop_valid = subject_stop > 0 ?

:

;

temp->domain_name = domain_name[6];

domain.push_back(temp);

subject_start = -1;

subject_stop = -1;

temp->subject_seqloc =

(*id_holder,

temp->is_subject_start_valid = subject_start > 0 ?

:

;

temp->is_subject_stop_valid = subject_stop > 0 ?

:

;

temp->domain_name = domain_name[7];

domain.push_back(temp);

num_align_to_show =

.m_NumActualV +

.m_NumActualD +

vector<string> chain_type_list;

(*iter==

){

chain_type_list.push_back(*iter);

.GetSubjectMasks(subj_masks);

<<

(!

.HasAlignments()){

title = sequence::CDeflineGenerator().GenerateDefline(q_bh);

->SetTitle(

+ title);

->SetTitle(title);

align_set->

().push_back(new_align);

.SetSeqAlign().Reset(&*align_set);

(

=0;

<6;

+=2) {

(

=0;

<12; ++

) {

(

=0;

<3; ++

) {

itr_num

blast::CPsiBlastIterationState::TSeqIds prev_seqids

((**result).HasErrors()) {

<<

<< (**result).GetErrorStrings() <<

;

((**result).HasWarnings()) {

<<

<< (**result).GetWarningStrings() <<

;

reportCaption =

;

<<

<< itr_num <<

;

first_results.

());

reportCaption =

;

(

index=0; index<phi_query_info->

; index++)

CBlastFormatUtil::PrintPhiInfo(phi_query_info->

,

(phi_query_info->

),

<<

<< CBlastFormatUtil::kNoHitsFound <<

<<

(index=0; index<phi_query_info->

; index++)

list <CDisplaySeqalign::FeatureInfo*> phiblast_pattern;

(

) (occurrences[index].

+ occurrences[index].length - 1));

phiblast_pattern.push_back(feature_info);

<<

<< index+1

<<

<< 1+occurrences[index].

<<

;

result_set[index].GetMaskedQueryRegions(masklocs);

CBlastFormatUtil::PruneSeqalign(*aln_set, copy_aln_set,

);

(list<CDisplaySeqalign::FeatureInfo*>, itr, phiblast_pattern) {

<<

<<

<<

options.GetMatchReward() <<

<<

options.GetMismatchPenalty() <<

;

<<

<< options.GetMatrixName() <<

;

(options.GetGappedMode() ==

) {

gap_extension = (double) options.GetGapExtensionCost();

((

==

||

==

) && options.GetGapExtensionCost() == 0)

gap_extension = -2*options.GetMismatchPenalty() + options.GetMatchReward();

gap_extension /= 2.0;

<<

<< options.GetGapOpeningCost() <<

<< gap_extension <<

;

(options.GetWordThreshold()) {

<<

<<

options.GetWordThreshold() <<

;

(options.GetWindowSize()) {

<<

<<

options.GetWindowSize() <<

;

(

& baseFile,

isXML,

withPath)

(query_id->

(*(*itr)->GetQueryId())) {

(query_id->

(*(*itr)->GetQueryId())) {

(query_id->

(*(*itr)->GetQueryId())) {

<<

;

<<

;

total_subj_length = 0;

db_name =

.substr(dir.length());

(db_name.size() > 500) {

db_name.resize(500);

(

->GetNumGis()) {

(

->GetNumSis()){

(

->GetNumTaxIds()){

(

->GetNumPigs()) {

(

->GetNumGis()) {

(

->GetNumSis()){

(

->GetNumTaxIds()){

(

->GetNumPigs()) {

static CRef< CScope > m_Scope

Produce formatted blast output for command line applications.

Formatting of pairwise sequence alignments in XML form.

ESubjectMaskingType

Define the possible subject masking types.

bool s_SetCompBasedStats(EProgram program)

int s_SetFlags(string &program, blast::CFormattingArgs::EOutputFormat format_type, bool html, bool showgi, bool isbl2seq, bool disableKAStats)

static const string kHTML_Suffix

static string s_GetBaseName(const string &baseFile, bool isXML, bool withPath)

static void s_SetCloneInfo(const CIgBlastTabularInfo &tabinfo, const CBioseq_Handle &handle, CBlastFormat::SClone &clone_info)

static string s_GetMolType(const CBioseq_Handle &bioseqHandle)

static const string kHTML_Prefix

bool s_IsGlobalSeqAlign(CConstRef< objects::CSeq_align_set > seqalign_set)

static bool s_HasLocalIDs(CConstRef< CBlastQueryVector > queries)

Auxialiary function to determine if there are local IDs in the identifiers of the query sequences.

Boolean Blast_SubjectIsNucleotide(EBlastProgramType p)

Returns true if the subject is nucleotide.

Int4 BlastSeqSrcGetNumSeqs(const BlastSeqSrc *seq_src)

Get the number of sequences contained in the sequence source.

Int8 BlastSeqSrcGetTotLen(const BlastSeqSrc *seq_src)

Get the total length of all sequences in the sequence source.

Definitions and prototypes used by blast_stat.c to calculate BLAST statistics.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

@ eRPSBlast

protein-pssm (reverse-position-specific BLAST)

@ eBlastp

Protein-Protein.

@ eTblastn

Protein-Translated nucl.

@ eMegablast

Nucl-Nucl (traditional megablast)

@ eDeltaBlast

Delta Blast.

@ ePSITblastn

PSI Tblastn.

@ eDiscMegablast

Nucl-Nucl using discontiguous megablast.

@ eRPSTblastn

nucleotide-pssm (RPS blast with translated query)

@ eBlastx

Translated nucl-Protein.

build_archive declarations

static void GetAsciiProteinMatrix(const char *matrix_name, CNcbiMatrix< int > &retval)

Retrieve a scoring matrix for the provided matrix name.

@ eAddEOLAtLineEnd

add EOL at the beginning of the string

@ eAddEOLAtLineStart

add spaces at the end of the string

static string AddSpaces(string paramVal, size_t maxParamLength, int spacesFormatFlag=eSpacePosToCenter)

Calculate the number of spaces and add them to paramVal.

static string MapTemplate(string inpString, string tmplParamName, Int8 templParamVal)

Replace template tags by real data.

static void ExtractSeqAlignForSeqList(CRef< objects::CSeq_align_set > &all_aln_set, string alignSeqList)

extract seq_align_set coreesponding to seqid list

void LogBlastSearchInfo(blast::CBlastUsageReport &report)

void x_PrintOneQueryFooter(const blast::CBlastAncillaryData &summary)

Output the ancillary data for one query that was searched.

blast::CFormattingArgs::EOutputFormat m_FormatType

Format type.

string m_SubjectTag

Tag for subject sequences (e.g., name of input file)

void x_CreateDeflinesJson(CConstRef< CSeq_align_set > aln_set)

bool m_IsVdb

Flag indicate vdb search.

CConstRef< blast::CIgBlastOptions > m_IgOptions

Used by Igblast formatting.

string m_CustomOutputFormatSpec

The custom output format specification.

vector< CBlastFormatUtil::SDbInfo > m_DomainDbInfo

Information about DELTA-BLAST domain database.

void x_DisplayDeflinesWithTemplates(CConstRef< CSeq_align_set > aln_set)

bool m_IsUngappedSearch

true if the search was ungapped

void x_WriteXML2(CCmdLineBlastXML2ReportData &report_data)

void PrintOneResultSet(const blast::CSearchResults &results, CConstRef< blast::CBlastQueryVector > queries, unsigned int itr_num=numeric_limits< unsigned int >::max(), blast::CPsiBlastIterationState::TSeqIds prev_seqids=blast::CPsiBlastIterationState::TSeqIds(), bool is_deltablast_domain_result=false)

Print all alignment information for a single query sequence along with any errors or warnings (errors...

CRef< SBlastXMLIncremental > m_BlastXMLIncremental

Structure for incremental XML BLAST output.

CRef< blast::IBlastSeqInfoSrc > m_SeqInfoSrc

Used to retrieve subject sequence information.

CRef< blast::CSearchDatabase > m_SearchDb

CRef< CScope > m_Scope

Scope containing query and subject sequences.

bool m_IsBl2Seq

True if we are formatting for BLAST2Sequences.

void PrintReport(const blast::CSearchResults &results, CBlastFormat::DisplayOption displayOption)

Print Metadata in json format or descriptions in html format or alignments in html format app....

CConstRef< objects::CBioseq > x_CreateSubjectBioseq()

Creates a bioseq to be able to print the acknowledgement for the subject bioseq when formatting bl2se...

CRef< objects::CSeq_annot > x_WrapAlignmentInSeqAnnot(CConstRef< objects::CSeq_align_set > alnset, const string &db_title) const

Wrap the Seq-align-set to be printed in a Seq-annot (as the C toolkit binaries)

void x_ConfigCShowBlastDefline(align_format::CShowBlastDefline &showdef, int skip_from=-1, int skip_to=-1, int index=-1, int num_descriptions_to_show=-1)

Configure the CShowBlastDefline instance passed to it.

const char * m_MatrixName

name of scoring matrix

bool m_IsRemoteSearch

True if this object is formatting the results of a remote search.

void PrintEpilog(const blast::CBlastOptions &options)

Print the footer of the blast report.

void x_InitAlignTemplates(void)

void x_ReverseQuery(blast::CIgBlastResults &results)

Replace the query with its reversed-compliement.

CBlastFormat(const blast::CBlastOptions &opts, blast::CLocalDbAdapter &db_adapter, blast::CFormattingArgs::EOutputFormat format_type, bool believe_query, CNcbiOstream &outfile, int num_summary, int num_alignments, CScope &scope, const char *matrix_name=BLAST_DEFAULT_MATRIX, bool show_gi=false, bool is_html=false, int qgencode=BLAST_GENETIC_CODE, int dbgencode=BLAST_GENETIC_CODE, bool use_sum_statistics=false, bool is_remote_search=false, int dbfilt_algorithm=-1, const string &custom_output_format=kEmptyStr, bool is_megablast=false, bool is_indexed=false, const blast::CIgBlastOptions *ig_opts=NULL, const blast::CLocalDbAdapter *domain_db_adapter=NULL, const string &cmdline=kEmptyStr, const string &subjectTag=kEmptyStr)

Constructor.

void x_DisplayAlignsWithTemplates(CConstRef< CSeq_align_set > aln_set, const blast::CSearchResults &results)

int m_DbGenCode

database genetic code

int m_NumAlignments

number of database sequences to present alignments for.

void ResetScopeHistory()

Resets the scope history for some output formats.

bool m_DbIsAA

true if database has protein sequences

void x_PrintStructuredReport(const blast::CSearchResults &results, CConstRef< blast::CBlastQueryVector > queries)

Prints XML and both species of ASN.1.

void x_DisplayDeflines(CConstRef< CSeq_align_set > aln_set, unsigned int itr_num, blast::CPsiBlastIterationState::TSeqIds &prev_seqids, int additional=0, int index=-1, int defline_length=-1)

Display the BLAST deflines in the traditional BLAST report.

void x_GenerateXML2MasterFile(void)

bool m_ShowGi

add GI number of database sequence IDs

CShowBlastDefline::SDeflineTemplates * m_DeflineTemplates

CConstRef< blast::CBlastOptions > m_Options

BLAST options.

DisplayOption

Display options for blast_report.

@ eDescriptionsWithTemplates

int m_HitlistSize

number of database sequences to save results for

string m_Program

blast program

int m_QueryGenCode

query genetic code

int m_QueriesFormatted

Used to count number of searches formatted.

void x_PrintXML2Report(const blast::CSearchResults &results, CConstRef< blast::CBlastQueryVector > queries)

CNcbiOstream & m_Outfile

stream to receive output

vector< CBlastFormatUtil::SDbInfo > m_DbInfo

internal representation of database information

bool x_IsVdbSearch() const

static void PrintArchive(CRef< objects::CBlast4_archive > archive, CNcbiOstream &out)

Auxiliary function to print the BLAST Archive in multiple output formats.

void WriteArchive(blast::IQueryFactory &queries, blast::CBlastOptionsHandle &options_handle, const blast::CSearchResultSet &results, unsigned int num_iters=0, const list< CRef< objects::CBlast4_error > > &msg=list< CRef< objects::CBlast4_error > >())

Writes out the query and results as an "archive" format.

~CBlastFormat()

Class destructor.

int m_NumSummary

number of 1-line summaries

bool m_IsHTML

true if HTML output desired

bool m_DisableKAStats

Modify format to accomodate results that do not contain KA stats such as bitscores and evalues.

bool m_Megablast

true if megablast was used.

CNcbiMatrix< int > m_ScoringMatrix

Scoring matrix instantiated from m_MatrixName.

CDisplaySeqalign::SAlignTemplates * m_AlignTemplates

void x_InitDeflineTemplates(void)

string m_DbName

name of blast database

bool m_IndexedMegablast

true if indexed megablast was used.

void x_PrintTaxReport(const blast::CSearchResults &results)

void x_GenerateJSONMasterFile(void)

bool m_LongSeqId

If true, print long sequence ids (database|accession)

void x_InitSAMFormatter()

CRef< blast::CBlastQueryVector > m_AccumulatedQueries

Queries are required for XML format only.

@ kMinTaxFormatLineLength

@ kFormatLineLength

The line length of pairwise blast output.

bool m_ShowLinkedSetSize

If the output format supports 1-line summaries, the search is ungapped and the alignments have had HS...

Int8 GetDbTotalLength()

Get total length of the database.

IOS_BASE::iostate m_OrigExceptionMask

bool m_BelieveQuery

true if query sequence IDs are parsed

void PrintProlog()

Print the header of the blast report.

void x_PrintAirrRearrangement(const blast::CIgBlastResults &results, SClone &clone_info, bool fill_clone_info, bool print_airr_format_header)

Prints AirrRearrangement format.

unique_ptr< CBlast_SAM_Formatter > m_SamFormatter

Pointer to the SAM formatting object.

bool m_IsDbScan

True if it is m_IsBl2Seq in dbscan mode.

void x_PrintIgTabularReport(const blast::CIgBlastResults &results, SClone &clone_info, bool fill_clone_info)

Prints IgTabular report for one query.

void x_SplitSeqAlign(CConstRef< CSeq_align_set > full_alignment, CSeq_align_set &repeated_seqs, CSeq_align_set &new_seqs, blast::CPsiBlastIterationState::TSeqIds &prev_seqids)

Split the full alignment into two sets of alignments: one for those seen in the previous iteration an...

blast::CSearchResultSet m_AccumulatedResults

Accumulated results to display in XML format.

void x_PrintTabularReport(const blast::CSearchResults &results, unsigned int itr_num)

Prints Tabular report for one query.

void x_SetAlignParameters(CDisplaySeqalign &cds)

void PrintPhiResult(const blast::CSearchResultSet &result_set, CConstRef< blast::CBlastQueryVector > queries, unsigned int itr_num=numeric_limits< unsigned int >::max(), blast::CPsiBlastIterationState::TSeqIds prev_seqids=blast::CPsiBlastIterationState::TSeqIds())

Print all alignment information for aa PHI-BLAST run.

Class containing information needed for tabular formatting of BLAST results.

void SetQueryGeneticCode(int q_gc)

void SetParseSubjectDefline(bool val)

Should subject deflien be parsed for id or not?

void PrintNumProcessed(int num_queries)

Prints number of queries processed.

EFieldDelimiter

What delimiter to use between fields in each row of the tabular output.

void SetCustomDelim(string customDelim)

void PrintFieldSpecs(void)

Print field specifiers of all requested fields.

void SetQueryRange(TSeqRange &q_range)

Set query range.

void SetParseLocalIds(bool val)

Should local IDs be parsed or not?

virtual void Print(void)

Print one line of tabular output.

int SetFields(const objects::CSeq_align &sal, objects::CScope &scope, CNcbiMatrix< int > *matrix=0)

Set all member fields, given a Seq-align.

void SetNoFetch(bool nofetch)

Avoid fetching sequence (if possible) If the sequence is needed (e.g., will be formatted,...

void SetDbGeneticCode(int db_gc)

void PrintHeader(const string &program, const objects::CBioseq &bioseq, const string &dbname, const string &rid=kEmptyStr, unsigned int iteration=numeric_limits< unsigned int >::max(), const objects::CSeq_align_set *align_set=0, CConstRef< objects::CBioseq > subj_bioseq=CConstRef< objects::CBioseq >(), bool is_csv=false)

Print the tabular output header.

void AddParam(EUsageParams p, int val)

Strategy class to gather the data for generating BLAST XML output.

Strategy class to gather the data for generating BLAST XML output.

Class for computing sequences' titles ("definitions").

@ eShowSequencePropertyLabel

@ eTranslateNucToNucAlignment

@ eShowInfoOnMouseOverSeqid

@ eShowTranslationForLocalSeq

@ eShowAlignStatsForMultiAlignView

void SetLineLen(size_t len)

number of bases or amino acids per line

TranslatedFrameForLocalSeq

void SetQueryNumber(int number)

for linking to mapviewer

void SetSeqLocColor(SeqLocColorOption option=eBlack)

color for seqloc display such as masked region

void SetMasterDomain(list< CRef< DomainInfo > > *domain)

void SetMiddleLineStyle(MiddleLineStyle option=eBar)

set middle line style

void SetSeqLocChar(SeqLocCharOption option=eX)

character style for seqloc display such as masked region

void SetAlignOption(int option)

Set functions.

void SetTranslatedFrameForLocalSeq(TranslatedFrameForLocalSeq frame)

void DisplaySeqalign(CNcbiOstream &out)

call this to display seqalign

void SetDbType(bool is_na)

database type.

void SetResultPositionIndex(int index)

void SetDbName(string name)

set blast database name

void SetSequencePropertyLabel(const vector< string > *SequencePropertyLabel, EOwnership ownership=eNoOwnership)

void SetAlignType(AlignType type)

Needed only if you want to display positives and strand.

static CRef< objects::CSeq_align_set > PrepareBlastUngappedSeqalign(const objects::CSeq_align_set &alnset)

static functions Need to call this if the seqalign is stdseg or dendiag for ungapped blast alignment ...

void SetMasterGeneticCode(int code)

Set genetic code for master sequence.

void SetSlaveGeneticCode(int code)

Set Genetic cod for slaves.

void SetNumAlignToShow(int num)

Display top num seqalign Note this only limit the number of seqalign regardless of the seqids.

void SetSubjectMasks(const TSeqLocInfoVector &masks)

Sets the masks and the masking algorithm used for the subject sequences.

void UseLongSequenceIds(void)

Sets usage of long sequence ids (database|accession)

void SetAlignTemplates(SAlignTemplates *alignTemplates)

@ eJsonSeqalign

JSON seq-align.

@ eTabular

Tabular output.

@ eCommaSeparatedValues

Comma-separated values.

@ eCommaSeparatedValuesWithHeader

Comma-separated values with a header.

@ eAsnText

ASN.1 text output.

@ eAirrRearrangement

igblast AIRR rearrangement, 19

@ eXml2_S

XML2 single file.

@ eJson_S

JSON2 single file.

@ eAsnBinary

ASN.1 binary output.

@ eFlatQueryAnchoredNoIdentities

@ eFlatQueryAnchoredIdentities

Flat query anchored no identities.

@ eQueryAnchoredNoIdentities

Flat query anchored showing identities.

@ eQueryAnchoredIdentities

Query anchored no identities.

@ eTabularWithComments

Tabular output with comments.

Class containing information needed for tabular formatting of BLAST results.

void PrintMasterAlign(const CConstRef< blast::CIgBlastOptions > &ig_opts, const string &header="# ") const

Print domain information.

int SetFields(const objects::CSeq_align &align, objects::CScope &scope, const string &chain_type, const string &master_chain_type_to_show, CNcbiMatrix< int > *matrix=0)

Set fields for all other alignments.

const vector< SIgDomain * > & GetIgDomains() const

Get Ig domain.

void PrintHeader(const CConstRef< blast::CIgBlastOptions > &ig_opts, const string &program, const objects::CBioseq &bioseq, const string &dbname, const string &domain_sys, const string &rid=kEmptyStr, unsigned int iteration=numeric_limits< unsigned int >::max(), const objects::CSeq_align_set *align_set=0, CConstRef< objects::CBioseq > subj_bioseq=CConstRef< objects::CBioseq >())

virtual void Print(void)

Override the print method.

void SetIgAnnotation(const CRef< blast::CIgAnnotation > &annot, const CConstRef< blast::CIgBlastOptions > &ig_opts, CConstRef< CSeq_align_set > &align_result, CScope &scope)

One method to set all annotation information.

int SetMasterFields(const objects::CSeq_align &align, objects::CScope &scope, const string &chain_type, const string &master_chain_type_to_show, CNcbiMatrix< int > *matrix=0)

Set fields for master alignment.

void PrintHtmlSummary(const CConstRef< blast::CIgBlastOptions > &ig_opts) const

Print Html style summary.

void SetAirrFormatData(CScope &scope, const CRef< blast::CIgAnnotation > &annot, const CBioseq_Handle &query_handle, CConstRef< CSeq_align_set > align_result, const CConstRef< blast::CIgBlastOptions > &ig_opts)

void GetIgInfo(string &v, string &d, string &j, string &c, string &master_chain_to_show, string &cdr3_nuc, string &cdr3_aa, string &productive) const

Getter.

void PrintAirrRearrangement(CScope &scope, const CRef< blast::CIgAnnotation > &annot, const string &program_version, const CBioseq &query_bioseq, const string &dbname, const string &domain_sys, const string &rid, unsigned int iteration, const CSeq_align_set *align_set, CConstRef< CBioseq > subj_bioseq, CNcbiMatrix< int > *matrix, bool print_airr_format_header, const CConstRef< blast::CIgBlastOptions > &ig_opts)

CJson_Object push_back_object(void)

Add object type element to the end of the array.

bool Write(std::ostream &out, TJson_Write_Flags flags=fJson_Write_IndentWithSpace, unsigned int indent_char_count=4) const

Write JSON data into a stream.

CJson_Object SetObject(void)

Get JSON object contents of the node.

CJson_Array insert_array(const CJson_Node::TKeyType &name)

Insert array type element into the object.

void insert(const CJson_Node::TKeyType &name)

Insert null element into the object.

static CNcbiApplication * Instance(void)

Singleton method.

NCBI C++ Object Manager dependant implementation of IQueryFactory.

Search Results for All Queries.

Search Results for One Query.

string GetTitle() const

Returns the database title.

Tdata::size_type Size() const

This class displays the defline for BLAST result.

void SetDeflineTemplates(SDeflineTemplates *deflineTemplates)

Set this if defline tempaltes are used Param deflineTemplates: struct containg defline templates info...

void SetDbType(bool is_na)

Set this for constructing seqid url.

void DisplayBlastDefline(CNcbiOstream &out)

Display defline.

void SetResultPosIndex(int index)

set and add result position index to <name=seqid> in score quick link for multiple result case

void SetOption(int option)

options per DisplayOption

void SetupPsiblast(TIdString2SeqStatus *seq_status=NULL, PsiblastStatus status=eFirstPass)

Set psiblast specific options.

void Init(void)

Initialize defline params.

void SetQueryNumber(int number)

Set this for linking to mapviewer.

vector< CShowBlastDefline::SDeflineFormattingInfo * > GetFormattingInfo(void)

Get deflines formatting info.

void SetSkipRange(int from, int to)

Skip certain seqaligns (only used in Igblast)

void Display(CNcbiOstream &out)

Display defline.

@ eNewPass

Sequences are newly found in current pass.

@ eRepeatPass

Sequences were found in previous pass.

void SetDbName(string database)

Set this for constructing seqid url.

void DisplayOrgReport(CNcbiOstream &out)

Displays Organism Report.

Collection of masked regions for a single query sequence.

void Print(const CCompactSAMApplication::AlignInfo &ai)

API (CDeflineGenerator) for computing sequences' titles ("definitions").

Implementation of interface class to produce data required for generating BLAST XML2 output.

Implementation of interface class to produce data required for generating BLAST XML output.

std::ofstream out("events_result.xml")

main entry point for tests

const size_t kDfltLineLength

static void des(const char *src, const char *out)

CRef< objects::CBlast4_archive > BlastBuildArchive(blast::IQueryFactory &queries, blast::CBlastOptionsHandle &options_handle, const CSearchResultSet &results, CRef< CSearchDatabase > search_db, unsigned int num_iters=0)

Returns a blast archive object.

vector< string > m_ChainType

string GetRID() const

Returns the RID for these results (if applicable), otherwise returns an empty string.

CRef< CBlastAncillaryData > GetAncillaryData() const

Accessor for the query's search ancillary.

bool IsLocalId(const objects::CSeq_id *seqid)

Returns true if the CSeq_id is a local id.

const SPHIQueryInfo * GetPhiQueryInfo() const

Retrieves PHI-BLAST information about pattern on query.

set< objects::CSeq_id_Handle > TSeqIds

List of CSeq_ids.

ESubjectMaskingType GetMaskType() const

string Blast_ProgramNameFromType(EBlastProgramType program)

Returns a string program name, given a blast::EBlastProgramType enumeration.

CConstRef< objects::CSeq_id > GetSeqId() const

Accessor for the query's sequence identifier.

EProgram ProgramNameToEnum(const std::string &program_name)

Map a string into an element of the ncbi::blast::EProgram enumeration (except eBlastProgramMax).

void SetFilteringAlgorithm(int filt_algorithm_id)

Temporary fix for backwards compatibility with other 6.0 SCs.

EMoleculeType

Molecule of the BLAST database.

bool HasAlignments() const

Return true if there are any alignments for this query.

@ eCompBasedStats

2001 NAR paper

@ eIndexedMegablast

2008 Bioinformatics on indexed megablast

@ eMegaBlast

2000 J Compt Biol paper

@ eDeltaBlast

2012 Biology Direct on DeltaBLAST

@ eCompAdjustedMatrices

submitted for publication

@ eBlastDbIsNucleotide

nucleotide

@ eBlastDbIsProtein

protein

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

static void BlastPrintVersionInfo(const string program, bool html, CNcbiOstream &out)

Print out blast engine version.

static void BlastPrintReference(bool html, size_t line_len, CNcbiOstream &out, blast::CReference::EPublication publication=blast::CReference::eGappedBlast, bool is_psiblast=false)

Print out blast reference.

static void InsertSubjectScores(objects::CSeq_align_set &org_align_set, const objects::CBioseq_Handle &query_handle, TSeqRange query_range=TSeqRange(), ESubjectScores score_type=eQueryCovPerSubj)

string m_SerialXmlEnd

tag to be printed at end.

static CRef< objects::CSeq_annot > CreateSeqAnnotFromSeqAlignSet(const objects::CSeq_align_set &alnset, blast::EProgram program, const string &db_name, const string &db_title, bool vdb_search=false)

void BlastXML2_FormatReport(const IBlastXML2ReportData *data, CNcbiOstream *out_stream)

Fills all fields in the XML BLAST v2 output object.

void BlastJSON_FormatReport(const IBlastXML2ReportData *data, string file_name)

void BlastXML2_PrintHeader(CNcbiOstream *out_stream)

void BlastXML_FormatReport(objects::CBlastOutput &bxmlout, const IBlastXMLReportData *data, CNcbiOstream *out_stream=NULL, SBlastXMLIncremental *incremental_struct=NULL)

Fills all fields in the XML BLAST output object.

void BlastJSON_PrintHeader(CNcbiOstream *out_stream)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

const string & Get(const string &name, bool *found=NULL) const

Get environment value by name.

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void Warning(CExceptionArgs_Base &args)

static void SplitPath(const string &path, string *dir=0, string *base=0, string *ext=0)

Split a path string into its basic components.

#define MSerial_AsnBinary

#define MSerial_AsnText

I/O stream manipulators –.

string m_Name

PN - program name.

const string AsFastaString(void) const

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static int WorstRank(const CRef< CSeq_id > &id)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

static int BestRank(const CRef< CSeq_id > &id)

ELabelType

return the label for a given string

@ eContent

Untagged human-readable accession or the like.

@ eDefault

default is to show type + content

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

string GenerateDefline(const CBioseq_Handle &bsh, TUserFlags flags=0)

Main method.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void ResetDataAndHistory(void)

Clear all information in the scope except added data loaders.

CBioseq_EditHandle GetBioseqEditHandle(const CBioseq &bioseq)

Get edit handle for the specified object Throw an exception if object is not found,...

@ eGetBioseq_All

Search bioseq, load if not loaded yet.

void SetDescr(TDescr &v) const

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

TMol GetBioseqMolType(void) const

Get some values from core:

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

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.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

bool IsEnabled(void)

Indicates whether application usage statistics collection is enabled for a current reporter instance.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

@ eTrunc_End

Truncate trailing whitespace only.

@ eNocase

Case insensitive compare.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsLocal(void) const

Check if variant Local is selected.

const TInst & GetInst(void) const

Get the Inst member data.

bool CanGetLength(void) const

Check if it is safe to call GetLength method.

const TId & GetId(void) const

Get the Id member data.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TLength GetLength(void) const

Get the Length member data.

@ eMol_not_set

> cdna = rna

@ eMol_na

just a nucleic acid

char * dbname(DBPROCESS *dbproc)

Get name of current database.

unsigned int

A callback function used to compare two keys in a database.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

Useful/utility classes and methods.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

static PCRE2_SIZE * offsets

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Defines BLAST database access classes.

vector< TMaskedQueryRegions > TSeqLocInfoVector

Collection of masked regions for all queries in a BLAST search.

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Definition of SSeqLoc structure.

Complete type definition of Blast Sequence Source ADT.

Structure to hold the Gumbel parameters (for FSC).

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.

structure for showing domains on the master sequence

structure for store feature display info

CConstRef< objects::CSeq_loc > seqloc

string alignRowTmpl

Template for displayin actual pairwise alignment - BLAST_ALIGN_ROWS.

string alnTitlesTmpl

Template for displaying multiple defline titles.

string alignFeatureLinkTmpl

Template for displaying align features link -ALN_FEATURES_LINK.

string alnSeqInfoTmpl

Template for displaying sequnce link in defline.

string alnTitlesLinkTmpl

Template for displaying link for more defline titles.

string alignFeatureTmpl

Template for displaying align features -ALN_FEATURES.

string sortInfoTmpl

Template for displaying Sort by header - SORT_ALIGNS_SEQ.

string alnDefLineTmpl

Template for displaying one defline ALN_DEFLINE_ROW.

string alignInfoTmpl

Template for displaying singe align params - BLAST_ALIGN_PARAMS_NUC,BLAST_ALIGN_PARAMS_PROT.

string alignHeaderTmpl

Template for displaying header,deflines and gene info - BLAST_ALIGN_HEADER.

string alignRowTmplLast

Template for displayin actual last pairwise alignment - BLAST_ALIGN_ROWS_LST.

string scoreInfoTmpl

score info template

string seqInfoTmpl

sequence infor template

string defLineTmpl

whole defilne template

Structure to hold data for incremental XML formatting.

Information about a single pattern occurence in the query.

Int4 offset

Starting offset of this pattern occurrence.

In PHI BLAST, structure containing information about all pattern occurrences in query.

char * pattern

Pattern used, saved here for formatting purposes.

double probability

Estimated probability of the pattern.

Int4 num_patterns

Number of pattern occurrences in query.

SPHIPatternInfo * occurrences

Array of pattern occurrence information structures.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4