Search Toolkit Book for CTabularFormatter::IFormatter
#include <algo/align/util/tabular_fmt.hpp>
Inheritance diagram for CTabularFormatter::IFormatter:
Collaboration diagram for CTabularFormatter::IFormatter:
Public Member Functions | |
| virtual | ~IFormatter () |
| void | SetScoreLookup (objects::CScoreLookup *scores) |
| virtual void | SetGencoll (CConstRef< objects::CGC_Assembly >) |
| virtual void | PrintHelpText (CNcbiOstream &ostr) const =0 |
| virtual void | PrintHeader (CNcbiOstream &ostr) const =0 |
| virtual void | Print (CNcbiOstream &ostr, const objects::CSeq_align &align)=0 |
| Public Member Functions inherited from CObject | |
| CObject (void) | |
| Constructor. More... | |
| CObject (const CObject &src) | |
| Copy constructor. More... | |
| virtual | ~CObject (void) |
| Destructor. More... | |
| CObject & | operator= (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 |
Protected Attributes | |
| objects::CScoreLookup * | m_Scores |
Additional Inherited Members | |
| 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< Uint8 > | TCounter |
| 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... | |
Detailed Description
Definition at line 59 of file tabular_fmt.hpp.
Constructor & Destructor Documentation
◆ ~IFormatter()
|
inlinevirtual |
Definition at line 62 of file tabular_fmt.hpp.
Member Function Documentation
◆ Print()
|
pure virtual |
Implemented in CTabularFormatter_StopCodonChanges, CTabularFormatter_StartCodonChanges, CTabularFormatter_GeneSymbol, CTabularFormatter_Indels, CTabularFormatter_Traceback, CTabularFormatter_NearestGap, CTabularFormatter_PatchType, CTabularFormatter_AssemblyInfo, CTabularFormatter_Cigar, CTabularFormatter_AlignLengthRatio, CTabularFormatter_SegPercent, CTabularFormatter_Entropy, CTabularFormatter_FixedText, CTabularFormatter_DiscStrand, CTabularFormatter_Tech, CTabularFormatter_SeqClone, CTabularFormatter_SeqChrom, CTabularFormatter_BiggestGapBases, CTabularFormatter_ExonIntrons, CTabularFormatter_OrgName, CTabularFormatter_Comment, CTabularFormatter_TaxId, CTabularFormatter_ProtRef, CTabularFormatter_Defline, CTabularFormatter_BestPlacementGroup, CTabularFormatter_AlignId, CTabularFormatter_AnyScore, CTabularFormatter_Score, CTabularFormatter_BitScore, CTabularFormatter_EValue_Exponent, CTabularFormatter_EValue_Mantissa, CTabularFormatter_EValue, CTabularFormatter_GapBaseCount, CTabularFormatter_GapRanges, CTabularFormatter_MismatchPositions, CTabularFormatter_MismatchCount, CTabularFormatter_IdentityCount, CTabularFormatter_GapCount, CTabularFormatter_PercentCoverage, CTabularFormatter_PercentId, CTabularFormatter_AlignLengthUngap, CTabularFormatter_AlignLength, CTabularFormatter_SeqLength, CTabularFormatter_AlignStrand, CTabularFormatter_AlignEnd, CTabularFormatter_AlignStart, CTabularFormatter_SeqId, and CTabularFormatter_AllSeqIds.
◆ PrintHeader()
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pure virtual |
Implemented in CTabularFormatter_StopCodonChanges, CTabularFormatter_StartCodonChanges, CTabularFormatter_GeneSymbol, CTabularFormatter_Indels, CTabularFormatter_Traceback, CTabularFormatter_NearestGap, CTabularFormatter_PatchType, CTabularFormatter_AssemblyInfo, CTabularFormatter_Cigar, CTabularFormatter_AlignLengthRatio, CTabularFormatter_SegPercent, CTabularFormatter_Entropy, CTabularFormatter_FixedText, CTabularFormatter_DiscStrand, CTabularFormatter_Tech, CTabularFormatter_SeqClone, CTabularFormatter_SeqChrom, CTabularFormatter_BiggestGapBases, CTabularFormatter_ExonIntrons, CTabularFormatter_OrgName, CTabularFormatter_Comment, CTabularFormatter_TaxId, CTabularFormatter_ProtRef, CTabularFormatter_Defline, CTabularFormatter_BestPlacementGroup, CTabularFormatter_AlignId, CTabularFormatter_AnyScore, CTabularFormatter_Score, CTabularFormatter_BitScore, CTabularFormatter_EValue_Exponent, CTabularFormatter_EValue_Mantissa, CTabularFormatter_EValue, CTabularFormatter_GapBaseCount, CTabularFormatter_GapRanges, CTabularFormatter_MismatchPositions, CTabularFormatter_MismatchCount, CTabularFormatter_IdentityCount, CTabularFormatter_GapCount, CTabularFormatter_PercentCoverage, CTabularFormatter_PercentId, CTabularFormatter_AlignLengthUngap, CTabularFormatter_AlignLength, CTabularFormatter_SeqLength, CTabularFormatter_AlignStrand, CTabularFormatter_AlignEnd, CTabularFormatter_AlignStart, CTabularFormatter_SeqId, and CTabularFormatter_AllSeqIds.
◆ PrintHelpText()
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pure virtual |
Implemented in CTabularFormatter_StopCodonChanges, CTabularFormatter_StartCodonChanges, CTabularFormatter_GeneSymbol, CTabularFormatter_Indels, CTabularFormatter_Traceback, CTabularFormatter_NearestGap, CTabularFormatter_PatchType, CTabularFormatter_AssemblyInfo, CTabularFormatter_Cigar, CTabularFormatter_AlignLengthRatio, CTabularFormatter_SegPercent, CTabularFormatter_Entropy, CTabularFormatter_FixedText, CTabularFormatter_DiscStrand, CTabularFormatter_Tech, CTabularFormatter_SeqClone, CTabularFormatter_SeqChrom, CTabularFormatter_BiggestGapBases, CTabularFormatter_ExonIntrons, CTabularFormatter_OrgName, CTabularFormatter_Comment, CTabularFormatter_TaxId, CTabularFormatter_ProtRef, CTabularFormatter_Defline, CTabularFormatter_BestPlacementGroup, CTabularFormatter_AlignId, CTabularFormatter_AnyScore, CTabularFormatter_Score, CTabularFormatter_BitScore, CTabularFormatter_EValue_Exponent, CTabularFormatter_EValue_Mantissa, CTabularFormatter_EValue, CTabularFormatter_GapBaseCount, CTabularFormatter_GapRanges, CTabularFormatter_MismatchPositions, CTabularFormatter_MismatchCount, CTabularFormatter_IdentityCount, CTabularFormatter_GapCount, CTabularFormatter_PercentCoverage, CTabularFormatter_PercentId, CTabularFormatter_AlignLengthUngap, CTabularFormatter_AlignLength, CTabularFormatter_SeqLength, CTabularFormatter_AlignStrand, CTabularFormatter_AlignEnd, CTabularFormatter_AlignStart, CTabularFormatter_SeqId, and CTabularFormatter_AllSeqIds.
◆ SetGencoll()
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inlinevirtual |
Reimplemented in CTabularFormatter_AssemblyInfo.
Definition at line 65 of file tabular_fmt.hpp.
◆ SetScoreLookup()
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inline |
Definition at line 63 of file tabular_fmt.hpp.
Member Data Documentation
◆ m_Scores
|
protected |
Definition at line 73 of file tabular_fmt.hpp.
Referenced by CTabularFormatter_AllSeqIds::Print(), CTabularFormatter_SeqId::Print(), CTabularFormatter_SeqLength::Print(), CTabularFormatter_AlignLength::Print(), CTabularFormatter_AlignLengthUngap::Print(), CTabularFormatter_PercentId::Print(), CTabularFormatter_PercentCoverage::Print(), CTabularFormatter_IdentityCount::Print(), CTabularFormatter_MismatchCount::Print(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_EValue::Print(), CTabularFormatter_EValue_Mantissa::Print(), CTabularFormatter_EValue_Exponent::Print(), CTabularFormatter_BitScore::Print(), CTabularFormatter_Score::Print(), CTabularFormatter_AnyScore::Print(), CTabularFormatter_Defline::Print(), CTabularFormatter_ProtRef::Print(), CTabularFormatter_TaxId::Print(), CTabularFormatter_Comment::Print(), CTabularFormatter_OrgName::Print(), CTabularFormatter_SeqChrom::Print(), CTabularFormatter_SeqClone::Print(), CTabularFormatter_Tech::Print(), CTabularFormatter_Entropy::Print(), CTabularFormatter_SegPercent::Print(), CTabularFormatter_Traceback::Print(), CTabularFormatter_Indels::Print(), CTabularFormatter_GeneSymbol::Print(), CTabularFormatter_StartCodonChanges::Print(), CTabularFormatter_StopCodonChanges::Print(), and CTabularFormatter_AnyScore::PrintHelpText().
The documentation for this class was generated from the following file:
- include/algo/align/util/tabular_fmt.hpp
