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NCBI C++ ToolKit: include/objtools/align_format/tabular.hpp Source File

EFieldDelimiter delim = eTab,

parse_local_ids =

);

(

score,

bit_score,

evalue);

SetEndpoints(

q_start,

q_end,

s_start,

s_end);

SetCounts(

num_ident,

length,

gaps,

gap_opens,

positives =0,

query_frame = 1,

subject_frame = 1);

SetBTOP(

btop_string);

SetFields(

objects::CSeq_align& sal,

objects::CScope& scope,

x_SetFieldDelimiter(eCustom,customDelim);

(

);

PrintHeader(

& program,

objects::CBioseq& bioseq,

iteration =

objects::CSeq_align_set* align_set=0,

PrintNumProcessed(

num_queries);

list<string> GetAllFieldNames(

);

SetNoFetch(

nofetch);

PrintFieldNames(

=

);

PrintFieldSpecs(

);

x_AddDefaultFieldsToShow(

);

x_SetFieldsToShow(

&

);

x_ResetFields(

);

x_SetFieldDelimiter(EFieldDelimiter delim,

customDelim =

);

x_PrintQuerySeqId(

)

;

x_PrintQueryGi(

);

x_PrintQueryAccession(

);

x_PrintQueryAccessionVersion(

);

x_PrintQueryAndDbNames(

& program,

objects::CBioseq& bioseq,

iteration,

x_PrintSubjectSeqId(

);

x_PrintSubjectAllSeqIds(

);

x_PrintSubjectGi(

);

x_PrintSubjectAllGis(

);

x_PrintSubjectAccession(

);

x_PrintSubjectAccessionVersion(

);

x_PrintSubjectAllAccessions(

);

x_PrintQuerySeq(

);

x_PrintSubjectSeq(

);

x_PrintQueryStart(

);

x_PrintQueryEnd(

);

x_PrintSubjectStart(

);

x_PrintSubjectEnd(

);

x_PrintEvalue(

);

x_PrintBitScore(

);

x_PrintScore(

);

x_PrintAlignmentLength(

);

x_PrintPercentIdentical(

);

x_PrintNumIdentical(

);

x_PrintMismatches(

);

x_PrintNumPositives(

);

x_PrintGapOpenings(

);

x_PrintGaps(

);

x_PrintPercentPositives();

x_PrintFrames();

x_PrintQueryFrame();

x_PrintSubjectFrame();

x_PrintQueryLength();

x_PrintSubjectLength();

x_PrintSubjectTaxIds();

x_PrintSubjectSciNames();

x_PrintSubjectCommonNames();

x_PrintSubjectBlastNames();

x_PrintSubjectSuperKingdoms();

x_PrintSubjectTaxId();

x_PrintSubjectSciName();

x_PrintSubjectCommonName();

x_PrintSubjectBlastName();

x_PrintSubjectSuperKingdom();

x_PrintSubjectTitle();

x_PrintSubjectAllTitles();

x_PrintSubjectStrand();

x_PrintSeqalignCoverage();

x_PrintSubjectCoverage();

x_PrintUniqSubjectCoverage();

x_SetQueryCovSubject(

objects::CSeq_align & align);

x_SetQueryCovUniqSubject(

objects::CSeq_align & align);

x_SetQueryCovSeqalign(

& align,

query_len);

(m_CustomDelim ==

|| m_FieldDelimiter ==

);

perc_positives =

(

&

,

s,

e,

ss,

se):

name(

), start(s), end(e),

s_start(ss), s_end(se), length(0),

num_match(0), num_mismatch(0), num_gap(0) {};

(

,

s,

e) {

(

.substr(0,4) ==

) {

sid =

.substr(4,

.

());

& program,

objects::CBioseq& bioseq,

& domain_sys,

iteration =

objects::CSeq_align_set* align_set=0,

SetMasterFields(

objects::CSeq_align& align,

objects::CScope& scope,

& chain_type,

& master_chain_type_to_show,

(

objects::CSeq_align& align,

objects::CScope& scope,

& chain_type,

& master_chain_type_to_show,

(

);

SetAirrFormatData(

& scope,

PrintAirrRearrangement(

& scope,

& program_version,

& domain_sys,

iteration,

print_airr_format_header,

m_IsMinusStrand =

;

s_start=-1,

s_end=-1) {

(start <0 || end <= start)

;

x_ComputeIgDomain(*domain);

m_IgDomains.push_back(domain);

(

&

,

s,

e) {

m_VGene.Set(

, s,e);

(

&

,

s,

e) {

m_DGene.Set(

, s,e);

(

&

,

s,

e) {

m_JGene.Set(

, s,e);

(

&

,

s,

e) {

m_CGene.Set(

, s,e);

& master_chain_to_show,

& productive)

{

master_chain_to_show = m_MasterChainTypeToShow;

cdr3_nuc = m_Cdr3Seq;

cdr3_aa = m_Cdr3SeqTrans;

productive = m_OtherInfo[4];

x_ResetIgFields();

x_PrintIgGenes(

isHtml=

,

& header=

)

;

x_ComputeIgDomain(SIgDomain &domain);

x_PrintIgDomain(

SIgDomain &domain)

;

x_PrintIgDomainHtml(

SIgDomain &domain)

;

x_PrintPartialQuery(

start,

end,

isHtml=

)

;

num_otherinfo = 5;

m_OtherInfo[num_otherinfo];

User-defined methods of the data storage class.

void SetScores(objects::CSeq_align &seq_align, objects::CScope &scope, const string &matrix_name="BLOSUM62")

Class containing information needed for tabular formatting of BLAST results.

void SetQueryGeneticCode(int q_gc)

ESeqIdType

In what form should the sequence identifiers be shown?

@ eAccession

Show only best accession.

@ eAccVersion

Show only best accession.version.

list< CRef< objects::CSeq_id > > m_QueryId

List of query ids for this HSP.

string m_BitScore

Bit score of this HSP, in appropriate format.

void SetParseSubjectDefline(bool val)

Should subject deflien be parsed for id or not?

void x_PrintSubjectSeq(void)

Print aligned part of subject sequence.

void x_PrintQueryLength()

Print the query sequence length.

void x_PrintNumIdentical(void)

Print number of identical matches.

map< string, ETabularField > m_FieldMap

Map of field enum values to field names.

void x_PrintSubjectEnd(void)

Print subject end.

pair< string, int > m_QueryCovUniqSubject

void SetQueryId(const objects::CBioseq_Handle &bh)

Set query id from a Bioseq handle.

void x_PrintGapOpenings(void)

Print number of gap openings.

set< string > m_SubjectSuperKingdoms

int m_AlignLength

Alignment length of this HSP.

set< string > m_SubjectBlastNames

bool m_ParseSubjectDefline

Parse subejct defline?

string m_SubjectBlastName

EFieldDelimiter

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

void SetCustomDelim(string customDelim)

int m_SubjectStart

Starting offset in subject.

void x_PrintPercentIdentical(void)

Print percent of identical matches.

void x_PrintScore(void)

Print raw score.

void x_PrintQueryStart(void)

Print query start.

void x_PrintBitScore(void)

Print bit score.

TSeqPos m_SubjectLength

Length of subject sequence.

void x_PrintGaps(void)

Print total number of gaps.

void x_PrintNumPositives(void)

Print number of positive matches.

int m_SubjectEnd

Ending offset in subject.

string m_SubjectSuperKingdom

string m_SubjectSeq

Aligned part of the subject sequence.

void SetQueryRange(TSeqRange &q_range)

Set query range.

void SetSubjectId(list< CRef< objects::CSeq_id > > &id)

Set subject id from a objects::CSeq_id.

CNcbiOstream & m_Ostream

Stream to write output to.

CRef< CBlast_def_line_set > m_SubjectDefline

void SetParseLocalIds(bool val)

Should local IDs be parsed or not?

void x_PrintSubjectStart(void)

Print subject start.

int m_QueryEnd

Ending offset in query.

int m_SubjectFrame

subject frame

int m_NumGapOpens

Number of gap openings in this HSP.

vector< string > m_SubjectCommonNames

void SetSubjectId(const objects::CBioseq_Handle &bh)

Set subject id from a Bioseq handle.

pair< string, int > m_QueryCovSubject

void x_PrintSubjectLength()

Print the subject sequence length.

list< ETabularField > m_FieldsToShow

Which fields to show?

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.

bool m_ParseLocalIds

Should the query deflines be parsed for local IDs?

void x_PrintEvalue(void)

Print e-value.

void x_PrintMismatches(void)

Print number of mismatches.

void SetNoFetch(bool nofetch)

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

bool m_NoFetch

program as a string

void SetDbGeneticCode(int db_gc)

void x_PrintPercentPositives()

Print percent positives.

vector< list< CRef< objects::CSeq_id > > > m_SubjectIds

All subject sequence ids for this HSP.

string m_FieldDelimiter

Delimiter character for fields to print.

bool GetNoFetch()

Avoid fetch of sequence if true returned.

const list< CRef< CSeq_id > > & GetQueryId() const

Get query seqid list.

set< TTaxId > m_SubjectTaxIds

Blast-traceback-operations.

bool x_IsFieldRequested(ETabularField field)

int m_NumPositives

Number of positives in this HSP.

bool x_IsCsv() const

Convenience method to determine if this object is dealing with CSV output formats.

int m_QueryStart

Starting offset in query.

void SetQueryId(list< CRef< objects::CSeq_id > > &id)

Set query id from a objects::CSeq_id.

void x_PrintQuerySeq(void)

Print aligned part of query sequence.

void x_PrintSubjectFrame()

void x_PrintFrames()

Print frames.

void x_PrintAlignmentLength(void)

Print alignment length.

int m_Score

Raw score of this HSP.

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.

vector< string > m_SubjectSciNames

int m_QueryFrame

query frame

list< CRef< objects::CSeq_id > > m_SubjectId

string m_SubjectCommonName

void x_PrintQueryEnd(void)

Print query end.

int m_NumGaps

Total number of gaps in this HSP.

int m_NumIdent

Number of identities in this HSP.

string m_QuerySeq

Aligned part of the query sequence.

string m_Evalue

E-value of this HSP, in appropriate format.

TSeqPos m_QueryLength

Length of query sequence.

Class containing information needed for tabular formatting of BLAST results.

void SetMinusStrand(bool minus=true)

Set strand information.

vector< SIgDomain * > m_IgDomains

~CIgBlastTabularInfo()

Destructor.

map< string, string > m_AirrData

CIgBlastTabularInfo(CNcbiOstream &ostr, const string &format=kDfltArgTabularOutputFmt, EFieldDelimiter delim=eTab)

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

CRef< CSeq_align > m_TopAlign_V

void SetSeqType(bool isNucl)

Set sequence type.

void SetJGene(const string &id, int s, int e)

Set gene info.

const vector< SIgDomain * > & GetIgDomains() const

Get Ig domain.

void SetDGene(const string &id, int s, int e)

Set gene info.

void AddIgDomain(const string &name, int start, int end, int s_start=-1, int s_end=-1)

Set domain info.

void SetFrame(const string &frame="N/A")

Set out-of-frame information.

void SetCGene(const string &id, int s, int e)

Set gene info.

CRef< CSeq_align > m_TopAlign_J

CRef< CSeq_align > m_TopAlign_D

CRef< CSeq_align > m_TopAlign_C

void SetVGene(const string &id, int s, int e)

Set gene info.

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.

string m_AirrCdr3SeqTrans

string m_MasterChainTypeToShow

void Print(const CCompactSAMApplication::AlignInfo &ai)

ETabularField

Enumeration for all fields that are supported in the tabular output.

const char * kDfltArgTabularOutputFmt

Default value for tabular and comma-separated value output formats.

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

#define NCBI_ALIGN_FORMAT_EXPORT

char * dbname(DBPROCESS *dbproc)

Get name of current database.

Declares CIgBlast, the C++ API for the IG-BLAST engine.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

const struct ncbi::grid::netcache::search::fields::SIZE size

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

Defines BLAST database access classes.

struct containing annotated domain information

SIgDomain(const string &n, int s, int e, int ss, int se)

struct containing annotated gene information

void Set(const string id, int s, int e)

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