NCBI C++ ToolKit
Classes | Macros | Enumerations | Functions
GUI Object Utility Classes and Modules

Utility and support routines for the GUI framework. More...

+ Collaboration diagram for GUI Object Utility Classes and Modules:

Classes

class  CTMSUtils
 
class  CAlignmentSmear
 
class  CTrackInfo
 Data structure for holding basic data track information. More...
 
class  CAnnotMetaData
 Data structure for holding meta information for an annotaion. More...
 
class  CBioTreeAttrReader
 Parser-reader for BKBTA - biotree attributes format. More...
 
class  CLayoutFeatLabel
 
class  CDataTrackUtils
 Utilities for data/track type discovery. More...
 
class  CNAUtils
 
class  CLayoutPWAlign
 
class  CLinkedFeature
 
class  ISeqTaskProgressCallback
 Task clients implement this callback interface. More...
 
class  CSeqUtils
 
class  CAlignGlyph
 
struct  CAlignGlyph::SDrawContext
 
class  CSwitchPointGlyph
 

Macros

#define __GUI_SEQ_UTILS_DEFINED__
 

Enumerations

enum  CAlignmentSmear::EAlignSmearStrand { CAlignmentSmear::eSmearStrand_Both, CAlignmentSmear::eSmearStrand_Pos, CAlignmentSmear::eSmearStrand_Neg }
 
enum  CAnnotMetaData::ELinksStatus { CAnnotMetaData::ELinksStatus_Undef, CAnnotMetaData::ELinksStatus_Present, CAnnotMetaData::ELinksStatus_Absent }
 
enum  CNAUtils::EEntrezDB { CNAUtils::EEDB_Undef, CNAUtils::EEDB_Nucleotide, CNAUtils::EEDB_Protein, CNAUtils::EEDB_All }
 eutils databases that can be used More...
 
enum  CNAUtils::EMetaDataSource {
  CNAUtils::EMetaDataSource_Undef, CNAUtils::EMetaDataSource_Cache, CNAUtils::EMetaDataSource_Mixed, CNAUtils::EMetaDataSource_Eutils,
  CNAUtils::EMetaDataSource_EmptyRequest, CNAUtils::EMetaDataSource_EmptyAfterFilteringRequest
}
 source of obtained NA metadata were internal caches hit, partially hit or totally missed during some cached operations More...
 
enum  CNAUtils::EUidsSource {
  CNAUtils::EUidsSource_Undef, CNAUtils::EUidsSource_Cache, CNAUtils::EUidsSource_Mixed, CNAUtils::EUidsSource_Eutils,
  CNAUtils::EUidsSource_EmptyRequest
}
 
enum  CSeqUtils::EAnnotationNameType { CSeqUtils::eAnnot_Unnamed, CSeqUtils::eAnnot_Named, CSeqUtils::eAnnot_All, CSeqUtils::eAnnot_Other }
 flags for classifying annotation names. More...
 
enum  { CSeqUtils::fFeature_LinkFeatures = 0x1, CSeqUtils::fFeature_Default = 0 }
 flags controlling feature retrieval More...
 
enum  { CSeqUtils::fAnnot_UnsetNamed = 0x01, CSeqUtils::fAnnot_UnsetDepth = 0x02 }
 flags controlling use of annotation selectors More...
 
enum  CAlignGlyph::EAlignSpacing { CAlignGlyph::eOne2One, CAlignGlyph::eOne2Three, CAlignGlyph::eThree2One }
 
enum  CAlignGlyph::ETail { CAlignGlyph::e5_Prime, CAlignGlyph::e3_Prime }
 

Functions

bool operator< (const CRef< CAnnotMetaData > &a1, const CRef< CAnnotMetaData > &a2)
 
CConstRef< objects::CBioseq > GetBioseqForSeqdesc (CRef< objects::CScope > scope, const objects::CSeqdesc &seq_desc)
 
objects::CBioseq_Handle GetBioseqForSeqFeat (const objects::CSeq_feat &f, objects::CScope &scope)
 
objects::CSeq_feat_Handle GetSeqFeatHandleForBadLocFeature (const objects::CSeq_feat &feat, objects::CScope &scope)
 
objects::CSeq_entry_Handle GetSeqEntryForSeqdesc (CRef< objects::CScope > scope, const objects::CSeqdesc &seq_desc)
 
objects::CSeq_entry_Handle GetSeqEntryForPubdesc (CRef< objects::CScope > scope, const objects::CPubdesc &pubdesc)
 
objects::CSeq_entry_Handle GetTopSeqEntryFromScopedObject (SConstScopedObject &obj)
 
vector< const objects::CFeatListItem * > GetSortedFeatList (objects::CSeq_entry_Handle seh, bool for_removal)
 
static bool CSeqUtils::IsUnnamed (const string &annot)
 check if a given annotation is a unnamed annotation. More...
 
static const stringCSeqUtils::GetUnnamedAnnot ()
 Get the commonly used symbol representing a unnnamed annotation. More...
 
const IAlnGraphicDataSourceCAlignGlyph::GetAlignMgr (void) const
 Inline methods. More...
 
const objects::CSeq_align & CAlignGlyph::GetAlignment (void) const
 
TAlnAnchorPair CAlignGlyph::GetAlnAnchorPair (void) const
 
int CAlignGlyph::GetOrigAnchor (void) const
 
const objects::CSeq_align_Handle & CAlignGlyph::GetOrigAlignment (void) const
 
TModelUnit CAlignGlyph::GetBarHeight () const
 
void CAlignGlyph::SetConfig (const CAlignmentConfig *conf)
 
void CAlignGlyph::SetScore (const ISGAlnScore &score)
 
bool CAlignGlyph::x_IsPWAlign () const
 
bool CAlignGlyph::IsNegative () const
 
void CAlignGlyph::SetShowScore ()
 
bool CAlignGlyph::IsSimplified () const
 

Detailed Description

Utility and support routines for the GUI framework.

These routines make use of the object manager and associated tools.

Macro Definition Documentation

#define __GUI_SEQ_UTILS_DEFINED__

Definition at line 109 of file utils.hpp.

Enumeration Type Documentation

anonymous enum

flags controlling feature retrieval

Enumerator
fFeature_LinkFeatures 
fFeature_Default 

Definition at line 136 of file utils.hpp.

anonymous enum

flags controlling use of annotation selectors

Enumerator
fAnnot_UnsetNamed 
fAnnot_UnsetDepth 

Definition at line 143 of file utils.hpp.

Enumerator
eSmearStrand_Both 
eSmearStrand_Pos 
eSmearStrand_Neg 

Definition at line 61 of file alignment_smear.hpp.

Enumerator
eOne2One 
eOne2Three 
eThree2One 

Definition at line 68 of file alignment_glyph.hpp.

flags for classifying annotation names.

Enumerator
eAnnot_Unnamed 

unnamed annotation

eAnnot_Named 

all named annotations

eAnnot_All 

all annotations

eAnnot_Other 

any given named annots

Definition at line 122 of file utils.hpp.

eutils databases that can be used

Enumerator
EEDB_Undef 
EEDB_Nucleotide 
EEDB_Protein 
EEDB_All 

try both nucleotide and protein databases, merge results

Definition at line 125 of file na_utils.hpp.

Enumerator
ELinksStatus_Undef 
ELinksStatus_Present 
ELinksStatus_Absent 

Definition at line 87 of file annot_info.hpp.

source of obtained NA metadata were internal caches hit, partially hit or totally missed during some cached operations

Enumerator
EMetaDataSource_Undef 
EMetaDataSource_Cache 
EMetaDataSource_Mixed 
EMetaDataSource_Eutils 
EMetaDataSource_EmptyRequest 
EMetaDataSource_EmptyAfterFilteringRequest 

Definition at line 133 of file na_utils.hpp.

enum CAlignGlyph::ETail
private
Enumerator
e5_Prime 
e3_Prime 

Definition at line 127 of file alignment_glyph.hpp.

Enumerator
EUidsSource_Undef 
EUidsSource_Cache 
EUidsSource_Mixed 
EUidsSource_Eutils 
EUidsSource_EmptyRequest 

Definition at line 142 of file na_utils.hpp.

Function Documentation

const objects::CSeq_align & CAlignGlyph::GetAlignment ( void  ) const
inline
const IAlnGraphicDataSource & CAlignGlyph::GetAlignMgr ( void  ) const
inline
CAlignGlyph::TAlnAnchorPair CAlignGlyph::GetAlnAnchorPair ( void  ) const
inline
TModelUnit CAlignGlyph::GetBarHeight ( ) const
inline
CConstRef<objects::CBioseq> GetBioseqForSeqdesc ( CRef< objects::CScope >  scope,
const objects::CSeqdesc &  seq_desc 
)
objects::CBioseq_Handle GetBioseqForSeqFeat ( const objects::CSeq_feat &  f,
objects::CScope &  scope 
)
const objects::CSeq_align_Handle & CAlignGlyph::GetOrigAlignment ( void  ) const
inline
int CAlignGlyph::GetOrigAnchor ( void  ) const
inline
objects::CSeq_entry_Handle GetSeqEntryForPubdesc ( CRef< objects::CScope >  scope,
const objects::CPubdesc &  pubdesc 
)
objects::CSeq_entry_Handle GetSeqEntryForSeqdesc ( CRef< objects::CScope >  scope,
const objects::CSeqdesc &  seq_desc 
)
objects::CSeq_feat_Handle GetSeqFeatHandleForBadLocFeature ( const objects::CSeq_feat &  feat,
objects::CScope &  scope 
)
vector<const objects::CFeatListItem *> GetSortedFeatList ( objects::CSeq_entry_Handle  seh,
bool  for_removal 
)
objects::CSeq_entry_Handle GetTopSeqEntryFromScopedObject ( SConstScopedObject obj)
const string & CSeqUtils::GetUnnamedAnnot ( )
inlinestatic
bool CAlignGlyph::IsNegative ( ) const
inline
bool CAlignGlyph::IsSimplified ( ) const
inline
bool CSeqUtils::IsUnnamed ( const string annot)
inlinestatic
bool operator< ( const CRef< CAnnotMetaData > &  a1,
const CRef< CAnnotMetaData > &  a2 
)
inline

Definition at line 125 of file annot_info.hpp.

void CAlignGlyph::SetConfig ( const CAlignmentConfig conf)
inline
void CAlignGlyph::SetScore ( const ISGAlnScore score)
inline
void CAlignGlyph::SetShowScore ( )
inline

Definition at line 294 of file alignment_glyph.hpp.

References CAlignGlyph::m_ShowScore.

Referenced by CAlignmentTrack::x_AddAlignmentLayout().

bool CAlignGlyph::x_IsPWAlign ( ) const
inlineprivate
Modified on Sun Jun 25 17:49:42 2017 by modify_doxy.py rev. 533848