NCBI C++ ToolKit
Classes | Enumerations | Functions | Variables
format_flags.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <corelib/ncbistl.hpp>
#include <string>
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Classes

struct  SFormatSpec
 Structure to store the format specification strings, their description and their corresponding enumeration. More...
 
struct  SSAMFormatSpec
 

Enumerations

enum  ETabularField {
  eQuerySeqId = 0 , eQueryGi , eQueryAccession , eQueryAccessionVersion ,
  eQueryLength , eSubjectSeqId , eSubjectAllSeqIds , eSubjectGi ,
  eSubjectAllGis , eSubjectAccession , eSubjAccessionVersion , eSubjectAllAccessions ,
  eSubjectLength , eQueryStart , eQueryEnd , eSubjectStart ,
  eSubjectEnd , eQuerySeq , eSubjectSeq , eEvalue ,
  eBitScore , eScore , eAlignmentLength , ePercentIdentical ,
  eNumIdentical , eMismatches , ePositives , eGapOpenings ,
  eGaps , ePercentPositives , eFrames , eQueryFrame ,
  eSubjFrame , eBTOP , eSubjectTaxIds , eSubjectSciNames ,
  eSubjectCommonNames , eSubjectBlastNames , eSubjectSuperKingdoms , eSubjectTitle ,
  eSubjectAllTitles , eSubjectStrand , eQueryCovSubject , eQueryCovSeqalign ,
  eQueryCovUniqSubject , eSubjectTaxId , eSubjectSciName , eSubjectCommonName ,
  eSubjectBlastName , eSubjectSuperKingdom , eMaxTabularField
}
 Enumeration for all fields that are supported in the tabular output. More...
 
enum  ESAMField { eSAM_SeqData = 0 , eSAM_SubjAsRefSeq }
 

Functions

string DescribeTabularOutputFormatSpecifiers (bool is_igblast=false)
 Returns a string documenting the available format specifiers. More...
 
string DescribeSAMOutputFormatSpecifiers ()
 Returns a string documenting the available format specifiers. More...
 

Variables

const string kArgOutputFormat
 Argument to select formatted output type. More...
 
const int kDfltArgOutputFormat
 Default value for formatted output type. More...
 
const string kArgShowGIs
 Argument to specify whether the GIs should be shown in the deflines in the traditional BLAST report. More...
 
const bool kDfltArgShowGIs
 Default value for the "show GIs" formatter option. More...
 
const string kArgNumDescriptions
 Argument to specify the number of one-line descriptions to show in the traditional BLAST report. More...
 
const size_t kDfltArgNumDescriptions
 Default number of one-line descriptions to display in the traditional BLAST report. More...
 
const string kArgNumAlignments
 Argument to specify the number of alignments to show in the traditional BLAST report. More...
 
const size_t kDfltArgNumAlignments
 Default number of alignments to display in the traditional BLAST report. More...
 
const string kArgProduceHtml
 Argument to specify whether to create output as HTML or not. More...
 
const bool kDfltArgProduceHtml
 Default value which specifies whether to create output as HTML or not. More...
 
string kDfltArgTabularOutputFmt
 Default value for tabular and comma-separated value output formats. More...
 
const string kDfltArgTabularOutputFmtTag
 Tag/keyword which is equivalent to using kDfltArgTabularOutputFmt. More...
 
const size_t kDfltLineLength
 
const string kArgAlignSeqList
 
const string kArgMetadata
 
const string kArgQueryIndex
 
const string kArgSortHits
 
const string kArgSortHSPs
 
const SFormatSpec sc_FormatSpecifiers []
 Array containing the supported output formats for tabular output. More...
 
const size_t kNumTabularOutputFormatSpecifiers
 Number of elements in the sc_FormatSpecifiers array. More...
 
const SSAMFormatSpec sc_SAMFormatSpecifiers []
 Array containing the supported output formats for SAM output. More...
 
const size_t kNumSAMOutputFormatSpecifiers
 Number of elements in the sc_SAMFormatSpecifiers array. More...
 

Enumeration Type Documentation

◆ ESAMField

enum ESAMField
Enumerator
eSAM_SeqData 

Include seq data.

eSAM_SubjAsRefSeq 

Subject as reference seqs.

Definition at line 170 of file format_flags.hpp.

◆ ETabularField

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

Enumerator
eQuerySeqId 

Query Seq-id(s)

eQueryGi 

Query gi.

eQueryAccession 

Query accession.

eQueryAccessionVersion 

Query accession.version.

eQueryLength 

Query sequence length.

eSubjectSeqId 

Subject Seq-id(s)

eSubjectAllSeqIds 

If multiple redundant sequences, all sets of subject Seq-ids, separated by ';'.

eSubjectGi 

Subject gi.

eSubjectAllGis 

All subject gis.

eSubjectAccession 

Subject accession.

eSubjAccessionVersion 

Subject accession.version.

eSubjectAllAccessions 

All subject accessions, separated by ';'.

eSubjectLength 

Subject sequence length.

eQueryStart 

Start of alignment in query.

eQueryEnd 

End of alignment in query.

eSubjectStart 

Start of alignment in subject.

eSubjectEnd 

End of alignment in subject.

eQuerySeq 

Aligned part of query sequence.

eSubjectSeq 

Aligned part of subject sequence.

eEvalue 

Expect value.

eBitScore 

Bit score.

eScore 

Raw score.

eAlignmentLength 

Alignment length.

ePercentIdentical 

Percentage of identical matches.

eNumIdentical 

Number of identical matches.

eMismatches 

Number of mismatches.

ePositives 

Number of positive-scoring matches.

eGapOpenings 

Number of gap openings.

eGaps 

Total number of gaps.

ePercentPositives 

Percentage of positive-scoring matches.

eFrames 

Query and subject frames separated by a '/'.

eQueryFrame 

Query frame.

eSubjFrame 

Subject frame.

eBTOP 

BLAST traceback operations.

eSubjectTaxIds 

Subject Tax IDs.

eSubjectSciNames 

Subject Scientific Names.

eSubjectCommonNames 

Subject Common Names.

eSubjectBlastNames 

Subject Blast Names.

eSubjectSuperKingdoms 

Subject Super Kingdoms.

eSubjectTitle 

Only the first subject defline.

eSubjectAllTitles 

All subject deflines.

eSubjectStrand 

Subject Strand.

eQueryCovSubject 

Query Coverage per Subject.

eQueryCovSeqalign 

Query Coverage per Seqalign.

eQueryCovUniqSubject 

Query Coverage per Subject.

eSubjectTaxId 

Subject Tax ID.

eSubjectSciName 

Subject Scientific Name.

eSubjectCommonName 

Subject Common Name.

eSubjectBlastName 

Subject Blast Name.

eSubjectSuperKingdom 

Subject Super Kingdom.

eMaxTabularField 

Sentinel value.

Definition at line 89 of file format_flags.hpp.

Function Documentation

◆ DescribeSAMOutputFormatSpecifiers()

string DescribeSAMOutputFormatSpecifiers ( )

Returns a string documenting the available format specifiers.

Definition at line 241 of file format_flags.cpp.

References SSAMFormatSpec::description, i, kNumSAMOutputFormatSpecifiers, SSAMFormatSpec::name, and sc_SAMFormatSpecifiers.

Referenced by CFormattingArgs::SetArgumentDescriptions().

◆ DescribeTabularOutputFormatSpecifiers()

string DescribeTabularOutputFormatSpecifiers ( bool  is_igblast = false)

Variable Documentation

◆ kArgAlignSeqList

const string kArgAlignSeqList
extern

◆ kArgMetadata

const string kArgMetadata
extern

◆ kArgNumAlignments

const string kArgNumAlignments
extern

Argument to specify the number of alignments to show in the traditional BLAST report.

Referenced by CFormattingArgs::ExtractAlgorithmOptions(), CFormattingArgs::SetArgumentDescriptions(), and CBlastAppArgs::x_IssueWarningsForIgnoredOptions().

◆ kArgNumDescriptions

const string kArgNumDescriptions
extern

Argument to specify the number of one-line descriptions to show in the traditional BLAST report.

Referenced by CFormattingArgs::ExtractAlgorithmOptions(), CFormattingArgs::SetArgumentDescriptions(), and CBlastAppArgs::x_IssueWarningsForIgnoredOptions().

◆ kArgOutputFormat

const string kArgOutputFormat
extern

◆ kArgProduceHtml

const string kArgProduceHtml
extern

Argument to specify whether to create output as HTML or not.

Referenced by CFormattingArgs::ExtractAlgorithmOptions(), and CFormattingArgs::SetArgumentDescriptions().

◆ kArgQueryIndex

const string kArgQueryIndex
extern

◆ kArgShowGIs

const string kArgShowGIs
extern

Argument to specify whether the GIs should be shown in the deflines in the traditional BLAST report.

Referenced by CFormattingArgs::ExtractAlgorithmOptions(), and CFormattingArgs::SetArgumentDescriptions().

◆ kArgSortHits

const string kArgSortHits
extern

◆ kArgSortHSPs

const string kArgSortHSPs
extern

◆ kDfltArgNumAlignments

const size_t kDfltArgNumAlignments
extern

Default number of alignments to display in the traditional BLAST report.

Definition at line 221 of file format_flags.cpp.

Referenced by CFormattingArgs::CFormattingArgs().

◆ kDfltArgNumDescriptions

const size_t kDfltArgNumDescriptions
extern

Default number of one-line descriptions to display in the traditional BLAST report.

Definition at line 219 of file format_flags.cpp.

Referenced by CFormattingArgs::CFormattingArgs().

◆ kDfltArgOutputFormat

const int kDfltArgOutputFormat
extern

Default value for formatted output type.

Definition at line 37 of file format_flags.cpp.

Referenced by CVecScreenApp::Init(), and CFormattingArgs::SetArgumentDescriptions().

◆ kDfltArgProduceHtml

const bool kDfltArgProduceHtml
extern

Default value which specifies whether to create output as HTML or not.

Definition at line 223 of file format_flags.cpp.

◆ kDfltArgShowGIs

const bool kDfltArgShowGIs
extern

Default value for the "show GIs" formatter option.

Definition at line 217 of file format_flags.cpp.

◆ kDfltArgTabularOutputFmt

string kDfltArgTabularOutputFmt
extern

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

Definition at line 38 of file format_flags.cpp.

Referenced by DescribeTabularOutputFormatSpecifiers(), and CBlastTabularInfo::x_AddDefaultFieldsToShow().

◆ kDfltArgTabularOutputFmtTag

const string kDfltArgTabularOutputFmtTag
extern

Tag/keyword which is equivalent to using kDfltArgTabularOutputFmt.

Referenced by CBlastTabularInfo::x_SetFieldsToShow().

◆ kDfltLineLength

const size_t kDfltLineLength
extern

Definition at line 224 of file format_flags.cpp.

Referenced by CFormattingArgs::SetArgumentDescriptions().

◆ kNumSAMOutputFormatSpecifiers

const size_t kNumSAMOutputFormatSpecifiers
extern

Number of elements in the sc_SAMFormatSpecifiers array.

Definition at line 231 of file format_flags.cpp.

Referenced by DescribeSAMOutputFormatSpecifiers().

◆ kNumTabularOutputFormatSpecifiers

const size_t kNumTabularOutputFormatSpecifiers
extern

Number of elements in the sc_FormatSpecifiers array.

Definition at line 43 of file format_flags.cpp.

Referenced by DescribeTabularOutputFormatSpecifiers(), and CBlastTabularInfo::x_SetFieldsToShow().

◆ sc_FormatSpecifiers

const SFormatSpec sc_FormatSpecifiers[]
extern

Array containing the supported output formats for tabular output.

Definition at line 44 of file format_flags.cpp.

Referenced by DescribeTabularOutputFormatSpecifiers(), and CBlastTabularInfo::x_SetFieldsToShow().

◆ sc_SAMFormatSpecifiers

const SSAMFormatSpec sc_SAMFormatSpecifiers[]
extern

Array containing the supported output formats for SAM output.

Definition at line 232 of file format_flags.cpp.

Referenced by DescribeSAMOutputFormatSpecifiers().

Modified on Sat Feb 24 07:48:17 2024 by modify_doxy.py rev. 669887