NCBI C++ ToolKit
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Classes | |
struct | SFormatSpec |
Structure to store the format specification strings, their description and their corresponding enumeration. More... | |
struct | SSAMFormatSpec |
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 char * | kArgOutputFormat |
Argument to select formatted output type. More... | |
const int | kDfltArgOutputFormat |
Default value for formatted output type. More... | |
const char * | 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 char * | 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 char * | 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 char * | 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... | |
const char * | kDfltArgTabularOutputFmt |
Default value for tabular and comma-separated value output formats. More... | |
const char * | kDfltArgTabularOutputFmtTag |
Tag/keyword which is equivalent to using kDfltArgTabularOutputFmt. More... | |
const size_t | kDfltLineLength |
const char * | kArgAlignSeqList |
const char * | kArgMetadata |
const char * | kArgQueryIndex |
const char * | kArgSortHits |
const char * | 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... | |
enum ESAMField |
Enumerator | |
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eSAM_SeqData | Include seq data. |
eSAM_SubjAsRefSeq | Subject as reference seqs. |
Definition at line 170 of file format_flags.hpp.
enum ETabularField |
Enumeration for all fields that are supported in the tabular output.
Definition at line 89 of file format_flags.hpp.
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().
Returns a string documenting the available format specifiers.
Definition at line 197 of file format_flags.cpp.
References SFormatSpec::description, i, kDfltArgTabularOutputFmt, kDfltArgTabularOutputFmtTag(), kNumTabularOutputFormatSpecifiers, SFormatSpec::name, and sc_FormatSpecifiers.
Referenced by CFormattingArgs::SetArgumentDescriptions().
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Argument to specify the number of alignments to show in the traditional BLAST report.
Referenced by CFormattingArgs::ExtractAlgorithmOptions(), CFormattingArgs::SetArgumentDescriptions(), and CBlastAppArgs::x_IssueWarningsForIgnoredOptions().
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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().
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Argument to select formatted output type.
Referenced by CMapperFormattingArgs::ExtractAlgorithmOptions(), CVecScreenApp::Init(), CFormattingArgs::ParseFormattingString(), PrintErrorArchive(), CVecScreenApp::Run(), CFormattingArgs::SetArgumentDescriptions(), CMapperFormattingArgs::SetArgumentDescriptions(), and CBlastAppArgs::x_IssueWarningsForIgnoredOptions().
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Argument to specify whether to create output as HTML or not.
Referenced by CFormattingArgs::ExtractAlgorithmOptions(), and CFormattingArgs::SetArgumentDescriptions().
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Argument to specify whether the GIs should be shown in the deflines in the traditional BLAST report.
Referenced by CFormattingArgs::ExtractAlgorithmOptions(), and CFormattingArgs::SetArgumentDescriptions().
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Referenced by CFormattingArgs::ExtractAlgorithmOptions(), and CFormattingArgs::SetArgumentDescriptions().
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Referenced by CFormattingArgs::ExtractAlgorithmOptions(), and CFormattingArgs::SetArgumentDescriptions().
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Default number of alignments to display in the traditional BLAST report.
Definition at line 221 of file format_flags.cpp.
Referenced by CFormattingArgs::CFormattingArgs().
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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().
Default value for formatted output type.
Definition at line 37 of file format_flags.cpp.
Referenced by CVecScreenApp::Init(), and CFormattingArgs::SetArgumentDescriptions().
Default value which specifies whether to create output as HTML or not.
Definition at line 223 of file format_flags.cpp.
Default value for the "show GIs" formatter option.
Definition at line 217 of file format_flags.cpp.
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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().
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Tag/keyword which is equivalent to using kDfltArgTabularOutputFmt.
Referenced by CBlastTabularInfo::x_SetFieldsToShow().
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Definition at line 224 of file format_flags.cpp.
Referenced by CFormattingArgs::SetArgumentDescriptions().
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Number of elements in the sc_SAMFormatSpecifiers array.
Definition at line 231 of file format_flags.cpp.
Referenced by DescribeSAMOutputFormatSpecifiers().
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Number of elements in the sc_FormatSpecifiers array.
Definition at line 43 of file format_flags.cpp.
Referenced by DescribeTabularOutputFormatSpecifiers(), and CBlastTabularInfo::x_SetFieldsToShow().
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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().
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Array containing the supported output formats for SAM output.
Definition at line 232 of file format_flags.cpp.
Referenced by DescribeSAMOutputFormatSpecifiers().