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CMapperFormattingArgs Class Reference

Search Toolkit Book for CMapperFormattingArgs

Formatting args for magicblast advertising only SAM and fast tabular formats. More...

#include <algo/blast/blastinput/blast_args.hpp>

+ Inheritance diagram for CMapperFormattingArgs:
+ Collaboration diagram for CMapperFormattingArgs:

Public Member Functions

 CMapperFormattingArgs (void)
 
virtual void SetArgumentDescriptions (CArgDescriptions &arg_desc)
 Interface method,. More...
 
virtual void ExtractAlgorithmOptions (const CArgs &args, CBlastOptions &opt)
 Interface method,. More...
 
virtual bool ArchiveFormatRequested (const CArgs &) const
 
bool TrimReadIds (void) const
 Should read ids be in SAM format be trimmed of .1 and .2 endings for paired mapping. More...
 
bool PrintUnaligned (void) const
 Should unaligned reads be reported. More...
 
bool NoDiscordant (void) const
 Should non-concordant pairs be filtered out of report. More...
 
bool SelectFwdRev (void) const
 Specify fwd/ref strands. More...
 
bool SelectRevFwd (void) const
 Specify rev/fwd strands. More...
 
bool SelectFwdOnly (void) const
 Specify fwd-only strands. More...
 
bool SelectRevOnly (void) const
 Specify rev-only strands. More...
 
bool SelectOnlyStrandSpecific (void) const
 Specify only-strand-specific. More...
 
bool PrintMdTag (void) const
 Should MD tag be included in SAM report. More...
 
EOutputFormat GetUnalignedOutputFormat (void) const
 Get format choice for unaligned reads. More...
 
const stringGetUserTag (void) const
 Get a user tag added to each alignment. More...
 
- Public Member Functions inherited from CFormattingArgs
 CFormattingArgs (bool isIgblast=false, EFormatFlags flag=eDefaultFlag)
 Default constructor. More...
 
virtual void ParseFormattingString (const CArgs &args, EOutputFormat &fmt_type, string &custom_fmt_spec, string &custom_delim) const
 Parses the output format command line option value, returns the requested output format type and any custom output formats (if any and applicable) More...
 
EOutputFormat GetFormattedOutputChoice () const
 Get the choice of formatted output. More...
 
bool HasStructuredOutputFormat () const
 Returns true if the desired output format is structured (needed to determine whether to print or not that a PSI-BLAST search has converged - this is not supported in structured formats) More...
 
bool ShowGis () const
 Display the NCBI GIs in formatted output? More...
 
TSeqPos GetNumDescriptions () const
 Number of one-line descriptions to show in traditional BLAST output. More...
 
TSeqPos GetNumAlignments () const
 Number of alignments to show in traditional BLAST output. More...
 
bool DisplayHtmlOutput () const
 Display HTML output? More...
 
string GetCustomOutputFormatSpec () const
 Retrieve for string that specifies the custom output format for tabular and comma-separated value. More...
 
size_t GetLineLength () const
 
int GetHitsSortOption () const
 
int GetHspsSortOption () const
 
string GetCustomDelimiter ()
 
- Public Member Functions inherited from IBlastCmdLineArgs
virtual ~IBlastCmdLineArgs ()
 Our virtual destructor. More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Private Attributes

bool m_TrimReadIds
 
bool m_PrintUnaligned
 
bool m_NoDiscordant
 
bool m_FwdRev
 
bool m_RevFwd
 
bool m_FwdOnly
 
bool m_RevOnly
 
bool m_OnlyStrandSpecific
 
bool m_PrintMdTag
 
EOutputFormat m_UnalignedOutputFormat
 
string m_UserTag
 

Additional Inherited Members

- Public Types inherited from CFormattingArgs
enum  EOutputFormat {
  ePairwise = 0 , eQueryAnchoredIdentities , eQueryAnchoredNoIdentities , eFlatQueryAnchoredIdentities ,
  eFlatQueryAnchoredNoIdentities , eXml , eTabular , eTabularWithComments ,
  eAsnText , eAsnBinary , eCommaSeparatedValues , eArchiveFormat ,
  eJsonSeqalign , eJson , eXml2 , eJson_S ,
  eXml2_S , eSAM , eTaxFormat , eAirrRearrangement ,
  eFasta , eEndValue
}
 Defines the output formats supported by our command line formatter. More...
 
enum  EFormatFlags {
  eDefaultFlag = 0 , eIsVDB = 0x01 , eIsSAM = 0x02 , eIsVDB_SAM = eIsVDB | eIsSAM ,
  eIsAirrRearrangement = 0x04
}
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 
- Protected Attributes inherited from CFormattingArgs
EOutputFormat m_OutputFormat
 Choice of formatting output. More...
 
bool m_ShowGis
 Display NCBI GIs? More...
 
TSeqPos m_NumDescriptions
 Number of 1-line descr. to show. More...
 
TSeqPos m_NumAlignments
 Number of alignments to show. More...
 
TSeqPos m_DfltNumDescriptions
 Default value for num descriptions. More...
 
TSeqPos m_DfltNumAlignments
 Default value for num alignments. More...
 
bool m_Html
 Display HTML output? More...
 
bool m_IsIgBlast
 IgBlast has a different default num_alignments. More...
 
string m_CustomOutputFormatSpec
 The format specification for custom output, e.g. More...
 
size_t m_LineLength
 
EFormatFlags m_FormatFlags
 
int m_HitsSortOption
 
int m_HspsSortOption
 
string m_CustomDelim
 

Detailed Description

Formatting args for magicblast advertising only SAM and fast tabular formats.

Definition at line 1209 of file blast_args.hpp.

Constructor & Destructor Documentation

◆ CMapperFormattingArgs()

CMapperFormattingArgs::CMapperFormattingArgs ( void  )
inline

Definition at line 1213 of file blast_args.hpp.

Member Function Documentation

◆ ArchiveFormatRequested()

virtual bool CMapperFormattingArgs::ArchiveFormatRequested ( const CArgs ) const
inlinevirtual

Reimplemented from CFormattingArgs.

Definition at line 1231 of file blast_args.hpp.

◆ ExtractAlgorithmOptions()

void CMapperFormattingArgs::ExtractAlgorithmOptions ( const CArgs args,
CBlastOptions opts 
)
virtual

◆ GetUnalignedOutputFormat()

EOutputFormat CMapperFormattingArgs::GetUnalignedOutputFormat ( void  ) const
inline

Get format choice for unaligned reads.

Definition at line 1264 of file blast_args.hpp.

References m_UnalignedOutputFormat.

Referenced by CMagicBlastThread::Main(), and CMagicBlastApp::Run().

◆ GetUserTag()

const string& CMapperFormattingArgs::GetUserTag ( void  ) const
inline

Get a user tag added to each alignment.

Definition at line 1268 of file blast_args.hpp.

References m_UserTag.

Referenced by CMagicBlastThread::Main(), and CMagicBlastApp::Run().

◆ NoDiscordant()

bool CMapperFormattingArgs::NoDiscordant ( void  ) const
inline

Should non-concordant pairs be filtered out of report.

Definition at line 1243 of file blast_args.hpp.

References m_NoDiscordant.

Referenced by CMagicBlastThread::Main().

◆ PrintMdTag()

bool CMapperFormattingArgs::PrintMdTag ( void  ) const
inline

Should MD tag be included in SAM report.

Definition at line 1261 of file blast_args.hpp.

References m_PrintMdTag.

Referenced by CMagicBlastThread::Main().

◆ PrintUnaligned()

bool CMapperFormattingArgs::PrintUnaligned ( void  ) const
inline

Should unaligned reads be reported.

Definition at line 1240 of file blast_args.hpp.

References m_PrintUnaligned.

Referenced by CMagicBlastThread::Main().

◆ SelectFwdOnly()

bool CMapperFormattingArgs::SelectFwdOnly ( void  ) const
inline

Specify fwd-only strands.

Definition at line 1252 of file blast_args.hpp.

References m_FwdOnly.

◆ SelectFwdRev()

bool CMapperFormattingArgs::SelectFwdRev ( void  ) const
inline

Specify fwd/ref strands.

Definition at line 1246 of file blast_args.hpp.

References m_FwdRev.

Referenced by CMagicBlastThread::Main(), and CMagicBlastApp::Run().

◆ SelectOnlyStrandSpecific()

bool CMapperFormattingArgs::SelectOnlyStrandSpecific ( void  ) const
inline

Specify only-strand-specific.

Definition at line 1258 of file blast_args.hpp.

References m_OnlyStrandSpecific.

Referenced by CMagicBlastThread::Main(), and CMagicBlastApp::Run().

◆ SelectRevFwd()

bool CMapperFormattingArgs::SelectRevFwd ( void  ) const
inline

Specify rev/fwd strands.

Definition at line 1249 of file blast_args.hpp.

References m_RevFwd.

Referenced by CMagicBlastThread::Main(), and CMagicBlastApp::Run().

◆ SelectRevOnly()

bool CMapperFormattingArgs::SelectRevOnly ( void  ) const
inline

Specify rev-only strands.

Definition at line 1255 of file blast_args.hpp.

References m_RevOnly.

◆ SetArgumentDescriptions()

void CMapperFormattingArgs::SetArgumentDescriptions ( CArgDescriptions arg_desc)
virtual

◆ TrimReadIds()

bool CMapperFormattingArgs::TrimReadIds ( void  ) const
inline

Should read ids be in SAM format be trimmed of .1 and .2 endings for paired mapping.

Definition at line 1237 of file blast_args.hpp.

References m_TrimReadIds.

Referenced by CMagicBlastThread::Main().

Member Data Documentation

◆ m_FwdOnly

bool CMapperFormattingArgs::m_FwdOnly
private

Definition at line 1276 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and SelectFwdOnly().

◆ m_FwdRev

bool CMapperFormattingArgs::m_FwdRev
private

Definition at line 1274 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and SelectFwdRev().

◆ m_NoDiscordant

bool CMapperFormattingArgs::m_NoDiscordant
private

Definition at line 1273 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and NoDiscordant().

◆ m_OnlyStrandSpecific

bool CMapperFormattingArgs::m_OnlyStrandSpecific
private

Definition at line 1278 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and SelectOnlyStrandSpecific().

◆ m_PrintMdTag

bool CMapperFormattingArgs::m_PrintMdTag
private

Definition at line 1279 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and PrintMdTag().

◆ m_PrintUnaligned

bool CMapperFormattingArgs::m_PrintUnaligned
private

Definition at line 1272 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and PrintUnaligned().

◆ m_RevFwd

bool CMapperFormattingArgs::m_RevFwd
private

Definition at line 1275 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and SelectRevFwd().

◆ m_RevOnly

bool CMapperFormattingArgs::m_RevOnly
private

Definition at line 1277 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and SelectRevOnly().

◆ m_TrimReadIds

bool CMapperFormattingArgs::m_TrimReadIds
private

Definition at line 1271 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and TrimReadIds().

◆ m_UnalignedOutputFormat

EOutputFormat CMapperFormattingArgs::m_UnalignedOutputFormat
private

Definition at line 1280 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and GetUnalignedOutputFormat().

◆ m_UserTag

string CMapperFormattingArgs::m_UserTag
private

Definition at line 1281 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and GetUserTag().


The documentation for this class was generated from the following files:
Modified on Thu Jul 18 16:05:29 2024 by modify_doxy.py rev. 669887