NCBI C++ ToolKit
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CGenomeAnnotComment Class Reference

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#include <objtools/format/items/comment_item.hpp>

+ Inheritance diagram for CGenomeAnnotComment:
+ Collaboration diagram for CGenomeAnnotComment:

Public Member Functions

 CGenomeAnnotComment (CBioseqContext &ctx, const string &build_num=kEmptyStr)
- Public Member Functions inherited from CCommentItem
 CCommentItem (const string &comment, CBioseqContext &ctx, const CSerialObject *obj=0)
 CCommentItem (const CSeqdesc &desc, CBioseqContext &ctx)
 CCommentItem (const CSeq_feat &feat, CBioseqContext &ctx)
 CCommentItem (const CUser_object &userObject, CBioseqContext &ctx)
void Format (IFormatter &formatter, IFlatTextOStream &text_os) const override
const string GetComment (void) const
const list< string > & GetCommentList (void) const
bool IsFirst (void) const
void SetFirst (bool val)
int GetCommentInternalIndent (void) const
bool NeedPeriod (void) const
void SetNeedPeriod (bool val)
void AddPeriod (void)
void RemoveExcessNewlines (const CCommentItem &next_comment)
void RemovePeriodAfterURL (void)
EItem GetItemType () const override
- Public Member Functions inherited from CFlatItem
bool IsSetObject (void) const
const CSerialObjectGetObject (void) const
CBioseqContextGetContext (void)
CBioseqContextGetContext (void) const
bool Skip (void) const
bool IsExternal (void) const
 ~CFlatItem (void)
- Public Member Functions inherited from IFlatItem
virtual ~IFlatItem (void)
- 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

Static Public Member Functions

static string GetGenomeBuildNumber (const CBioseq_Handle &bsh)
static string GetGenomeBuildNumber (const CUser_object &uo)
- Static Public Member Functions inherited from CCommentItem
static const stringGetNsAreGapsStr (void)
static string GetStringForTPA (const CUser_object &uo, CBioseqContext &ctx)
static string GetStringForBankIt (const CUser_object &uo, bool dump_mode)
static string GetStringForRefTrack (const CBioseqContext &ctx, const CUser_object &uo, const CBioseq_Handle &seq, EGenomeBuildComment eGenomeBuildComment=eGenomeBuildComment_Yes)
static string GetStringForRefSeqGenome (const CUser_object &uo)
static string GetStringForWGS (CBioseqContext &ctx)
static string GetStringForTSA (CBioseqContext &ctx)
static string GetStringForTLS (CBioseqContext &ctx)
static string GetStringForMolinfo (const CMolInfo &mi, CBioseqContext &ctx)
static string GetStringForHTGS (CBioseqContext &ctx)
static string GetStringForUnordered (CBioseqContext &ctx)
static string GetStringForModelEvidance (const CBioseqContext &ctx, const SModelEvidance &me)
static TRefTrackStatus GetRefTrackStatus (const CUser_object &uo, string *st=0)
static string GetStringForEncode (CBioseqContext &ctx)
static string GetStringForAuthorizedAccess (CBioseqContext &ctx)
static string GetStringForOpticalMap (CBioseqContext &ctx)
static string GetStringForBaseMod (CBioseqContext &ctx)
static string GetStringForUnique (CBioseqContext &ctx)
- 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)

Private Member Functions

void x_GatherInfo (CBioseqContext &ctx)

Private Attributes

string m_GenomeBuildNumber

Additional Inherited Members

- Public Types inherited from CCommentItem
enum  EType { eGenomeAnnotation , eModel , eUser }
enum  ERefTrackStatus {
  eRefTrackStatus_Unknown , eRefTrackStatus_Inferred , eRefTrackStatus_Pipeline , eRefTrackStatus_Provisional ,
  eRefTrackStatus_Predicted , eRefTrackStatus_Validated , eRefTrackStatus_Reviewed , eRefTrackStatus_Model ,
  eRefTrackStatus_WGS , eRefTrackStatus_TSA
enum  ECommentFormat { eFormat_Text , eFormat_Html }
enum  EGenomeBuildComment { eGenomeBuildComment_No = 0 , eGenomeBuildComment_Yes }
typedef EType TType
typedef ERefTrackStatus TRefTrackStatus
- Public Types inherited from IFlatItem
enum  EItem {
  eItem_None = 0 , eItem_StartSection , eItem_StartItem , eItem_HtmlAnchor ,
  eItem_Head , eItem_Locus , eItem_Date , eItem_Defline ,
  eItem_Accession , eItem_Version , eItem_Project , eItem_GenomeProject ,
  eItem_DbSource , eItem_Keywords , eItem_Segment , eItem_Source ,
  eItem_Reference , eItem_Cache , eItem_Comment , eItem_Primary ,
  eItem_FeatHeader , eItem_SourceFeat , eItem_Feature , eItem_Gap ,
  eItem_BaseCount , eItem_Origin , eItem_Sequence , eItem_Contig ,
  eItem_Wgs , eItem_Tsa , eItem_Alignment , eItem_EndItem ,
  eItem_EndSection , eItem_Slash
- 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 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 Types inherited from CCommentItem
enum  EPeriod { ePeriod_Add , ePeriod_NoAdd }
- Protected Member Functions inherited from CCommentItem
 CCommentItem (CBioseqContext &ctx, bool need_period=true)
void x_GatherDescInfo (const CSeqdesc &desc, CBioseqContext &ctx)
void x_GatherFeatInfo (const CSeq_feat &feat, CBioseqContext &ctx)
void x_GatherUserObjInfo (const CUser_object &userObject)
void x_SetComment (const string &comment)
void x_SetComment (const string &comment, CBioseqContext &ctx)
void x_SetCommentWithURLlinks (const string &prefix, const string &str, const string &suffix, CBioseqContext &ctx, EPeriod can_add_period=ePeriod_Add)
list< string > & x_GetComment (void)
void x_SetSkip (void)
- Protected Member Functions inherited from CFlatItem
 CFlatItem (CBioseqContext *ctx=0)
void x_SetObject (const CSerialObject &obj)
void x_SetContext (CBioseqContext &ctx)
void x_SetSkip (void)
void x_SetExternal (void)
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...

Detailed Description

Definition at line 202 of file comment_item.hpp.

Constructor & Destructor Documentation

◆ CGenomeAnnotComment()

CGenomeAnnotComment::CGenomeAnnotComment ( CBioseqContext ctx,
const string build_num = kEmptyStr 

Definition at line 2047 of file comment_item.cpp.

References ctx, and x_GatherInfo().

Member Function Documentation

◆ GetGenomeBuildNumber() [1/2]

string CGenomeAnnotComment::GetGenomeBuildNumber ( const CBioseq_Handle bsh)

◆ GetGenomeBuildNumber() [2/2]

string CGenomeAnnotComment::GetGenomeBuildNumber ( const CUser_object uo)

◆ x_GatherInfo()

void CGenomeAnnotComment::x_GatherInfo ( CBioseqContext ctx)

Member Data Documentation

◆ m_GenomeBuildNumber

string CGenomeAnnotComment::m_GenomeBuildNumber

Definition at line 215 of file comment_item.hpp.

Referenced by x_GatherInfo().

The documentation for this class was generated from the following files:
Modified on Mon Feb 26 04:04:12 2024 by rev. 669887