NCBI C++ ToolKit
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CAlnUserOptions Class Reference

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Options for different alignment manager operations. More...

#include <objtools/alnmgr/aln_user_options.hpp>

+ Inheritance diagram for CAlnUserOptions:
+ Collaboration diagram for CAlnUserOptions:

Public Types

enum  EDirection { eBothDirections = 0 , eDirect = 1 , eReverse = 2 , eDefaultDirection = eBothDirections }
 Row direction flags. More...
 
enum  EMergeAlgo { eMergeAllSeqs = 0 , eQuerySeqMergeOnly = 1 , ePreserveRows = 2 , eDefaultMergeAlgo = eMergeAllSeqs }
 Alignment merging algorithm. More...
 
enum  EMergeFlags {
  fTruncateOverlaps = 1 << 0 , fAllowMixedStrand = 1 << 1 , fAllowTranslocation = 1 << 2 , fSkipSortByScore = 1 << 3 ,
  fUseAnchorAsAlnSeq = 1 << 4 , fAnchorRowFirst = 1 << 5 , fIgnoreInsertions = 1 << 6
}
 Additional merge flags. More...
 
enum  EShowUnalignedOption { eHideUnaligned , eShowFlankingN , eShowAllUnaligned }
 
typedef CPairwiseAln::TPos TPos
 
typedef int TMergeFlags
 
- 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...
 

Public Member Functions

 CAlnUserOptions (void)
 
void SetAnchorId (const TAlnSeqIdIRef &anchor_id)
 Set anchor id. More...
 
const TAlnSeqIdIRefGetAnchorId (void) const
 Get anchor id. More...
 
void SetMergeFlags (TMergeFlags flags, bool set)
 Set/clear merge flags. 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
 

Public Attributes

EDirection m_Direction
 
EMergeAlgo m_MergeAlgo
 
TMergeFlags m_MergeFlags
 
bool m_ClipAlignment
 
objects::CBioseq_Handle m_ClipSeq
 
TPos m_ClipStart
 
TPos m_ClipEnd
 
bool m_ExtendAlignment
 
TPos m_Extension
 
EShowUnalignedOption m_UnalignedOption
 
TPos m_ShowUnalignedN
 
objects::CBioseq_Handle m_Anchor
 Anchor bioseq - if null then a multiple alignment shall be built. More...
 

Private Attributes

TAlnSeqIdIRef m_AnchorId
 

Additional Inherited Members

- 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

Options for different alignment manager operations.

Definition at line 48 of file aln_user_options.hpp.

Member Typedef Documentation

◆ TMergeFlags

Definition at line 118 of file aln_user_options.hpp.

◆ TPos

Definition at line 51 of file aln_user_options.hpp.

Member Enumeration Documentation

◆ EDirection

Row direction flags.

NOTE: in most cases directions are relative to the anchor row.

Enumerator
eBothDirections 

No filtering: use both direct and reverse sequences.

eDirect 

Use only sequences whose strand is the same as that of the anchor.

eReverse 

Use only sequences whose strand is opposite to that of the anchor.

eDefaultDirection 

By default don't filter by direction.

Definition at line 55 of file aln_user_options.hpp.

◆ EMergeAlgo

Alignment merging algorithm.

Enumerator
eMergeAllSeqs 

Merge all sequences (greedy algo).

eQuerySeqMergeOnly 

Only put the query seq on same row (input order is not significant).

ePreserveRows 

Preserve all rows as they were in the input (e.g.

self-align a sequence). Greedy algo.

eDefaultMergeAlgo 

Definition at line 71 of file aln_user_options.hpp.

◆ EMergeFlags

Additional merge flags.

Enumerator
fTruncateOverlaps 

Truncate overlapping ranges.

If not set, the overlaps are put on separate rows.

fAllowMixedStrand 

Allow mixed strands on the same row.

Experimental feature, not supported for all alignment types.

fAllowTranslocation 

Allow translocations on the same row.

fSkipSortByScore 

In greedy algos, skip sorting input alignments by score thus allowing for user-defined sort order.

fUseAnchorAsAlnSeq 

Use the anchor sequence as the alignment sequence.

Otherwise (by default) a pseudo sequence is created whose coordinates are the alignment coordinates. NOTE: Setting this flag is not recommended. Using it will make all CSparseAln::*AlnPos* methods inconsistent with CAlnVec::*AlnPos* methods.

fAnchorRowFirst 

Store anchor row in the first pairwise alignment (by default it's stored in the last one).

fIgnoreInsertions 

Do not collect and store insertions (gaps on the anchor).

Definition at line 87 of file aln_user_options.hpp.

◆ EShowUnalignedOption

Enumerator
eHideUnaligned 
eShowFlankingN 
eShowAllUnaligned 

Definition at line 129 of file aln_user_options.hpp.

Constructor & Destructor Documentation

◆ CAlnUserOptions()

CAlnUserOptions::CAlnUserOptions ( void  )
inline

Definition at line 138 of file aln_user_options.hpp.

Member Function Documentation

◆ GetAnchorId()

const TAlnSeqIdIRef& CAlnUserOptions::GetAnchorId ( void  ) const
inline

Get anchor id.

Definition at line 158 of file aln_user_options.hpp.

References m_AnchorId.

Referenced by CreateAnchoredAlnFromAln(), and CAlnBuildApp::Run().

◆ SetAnchorId()

void CAlnUserOptions::SetAnchorId ( const TAlnSeqIdIRef anchor_id)
inline

Set anchor id.

Definition at line 152 of file aln_user_options.hpp.

References m_AnchorId.

Referenced by BOOST_AUTO_TEST_CASE(), CAlnBuildApp::Run(), and CAlnTestApp::Run().

◆ SetMergeFlags()

void CAlnUserOptions::SetMergeFlags ( TMergeFlags  flags,
bool  set 
)
inline

Member Data Documentation

◆ m_Anchor

objects::CBioseq_Handle CAlnUserOptions::m_Anchor

Anchor bioseq - if null then a multiple alignment shall be built.

Definition at line 175 of file aln_user_options.hpp.

◆ m_AnchorId

TAlnSeqIdIRef CAlnUserOptions::m_AnchorId
private

Definition at line 178 of file aln_user_options.hpp.

Referenced by GetAnchorId(), and SetAnchorId().

◆ m_ClipAlignment

bool CAlnUserOptions::m_ClipAlignment

Definition at line 121 of file aln_user_options.hpp.

Referenced by CBuildOptionsDlg::SetParams().

◆ m_ClipEnd

TPos CAlnUserOptions::m_ClipEnd

Definition at line 124 of file aln_user_options.hpp.

◆ m_ClipSeq

objects::CBioseq_Handle CAlnUserOptions::m_ClipSeq

Definition at line 122 of file aln_user_options.hpp.

◆ m_ClipStart

TPos CAlnUserOptions::m_ClipStart

Definition at line 123 of file aln_user_options.hpp.

◆ m_Direction

EDirection CAlnUserOptions::m_Direction

◆ m_ExtendAlignment

bool CAlnUserOptions::m_ExtendAlignment

Definition at line 126 of file aln_user_options.hpp.

Referenced by CBuildOptionsDlg::SetParams().

◆ m_Extension

TPos CAlnUserOptions::m_Extension

Definition at line 127 of file aln_user_options.hpp.

◆ m_MergeAlgo

EMergeAlgo CAlnUserOptions::m_MergeAlgo

◆ m_MergeFlags

TMergeFlags CAlnUserOptions::m_MergeFlags

◆ m_ShowUnalignedN

TPos CAlnUserOptions::m_ShowUnalignedN

Definition at line 136 of file aln_user_options.hpp.

◆ m_UnalignedOption

EShowUnalignedOption CAlnUserOptions::m_UnalignedOption

Definition at line 135 of file aln_user_options.hpp.


The documentation for this class was generated from the following file:
Modified on Fri Jul 12 16:21:55 2024 by modify_doxy.py rev. 669887