NCBI C++ ToolKit
Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | List of all members
CGeneModelConfig Class Reference

Search Toolkit Book for CGeneModelConfig

#include <gui/widgets/seq_graphic/gene_model_config.hpp>

+ Inheritance diagram for CGeneModelConfig:
+ Collaboration diagram for CGeneModelConfig:

Public Types

enum  EMergeStyle { eMerge_No , eMerge_Pairs , eMerge_All , eMerge_OneLine }
 style on how to merge RNAs and CDSs. More...
 
enum  ERenderingOption {
  eOption_GeneOnly , eOption_MergeAll , eOption_MergePairs , eOption_ShowAllButGenes ,
  eOption_ShowAll , eOption_SingleLine , eOption_Default = eOption_MergeAll
}
 rendering options on how to render features overall. More...
 
- 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

 CGeneModelConfig ()
 
void LoadSettings (CConstRef< CSeqGraphicConfig > g_conf, const string &reg_path, const string &profile)
 
void LoadSettingsPartial (const string &reg_path, const string &profile)
 
void SaveSettings (CConstRef< CSeqGraphicConfig > g_conf, const string &reg_path, const string &profile) const
 
void UpdateSettings (const CSGConfigUtils::TKeyValuePairs &settings)
 
string SaveSettingsAsString (const string &preset_style) const
 
- 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 const stringStyleValueToStr (CGeneModelConfig::EMergeStyle style)
 
static EMergeStyle StyleStrToValue (const string &style)
 
static const stringOptionValueToStr (CGeneModelConfig::ERenderingOption option)
 
static ERenderingOption OptionStrToValue (const string &option)
 
- 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)
 

Public Attributes

int m_LandmarkFeatLimit
 
int m_OverviewFeatCutoff
 
int m_HighlightMode
 
bool m_HideNonCoding = false
 Hide transcripts without associated CDS. More...
 
bool m_HideModels = false
 Hide Model RefSeqs. More...
 
bool m_CCDSOnly = false
 Show only CCDS variants. More...
 
bool m_SelectOnly = false
 Show only Select/MANE variants. More...
 
CRef< CCdsConfigm_CdsConfig
 
CRef< CBoundaryParamsm_GeneBoxConfig
 
layout settings.
bool m_ShowLMGeneLabel
 landmark gene labels. More...
 
bool m_ShowGenes
 
bool m_ShowRNAs
 
bool m_ShowCDSs
 
bool m_ShowExons
 
bool m_ShowVDJCs
 show VDJ_segments and C_region More...
 
bool m_ShowGeneProducts
 feature histogram on a gene. More...
 
bool m_ShowCDSProductFeats
 CDS associated protein features. More...
 
bool m_ShowNtRuler
 Show nucleotide ruler. More...
 
bool m_ShowAaRuler
 Show protein ruler. More...
 
bool m_ShowHistogram
 show gene distribution histogram. More...
 
bool m_ShowLabel = true
 Show labels. More...
 
string m_CDSProfile
 cds setting profile More...
 
EMergeStyle m_MergeStyle
 the way on how to merge CDSs and RNAs. More...
 

Additional Inherited Members

- 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 46 of file gene_model_config.hpp.

Member Enumeration Documentation

◆ EMergeStyle

style on how to merge RNAs and CDSs.

Enumerator
eMerge_No 

show all feature individually

eMerge_Pairs 

merge each transcript and CDS pair

eMerge_All 

merge all transcripts and CDSs

eMerge_OneLine 

merge into one line

if there are transcripts and/or CDSs, show only transcripts and CDSs, and merge them into one bar (prefix the gene label to RNA and CDS label. If there is no RNA or CDS feature, show exon features only. If there is no exon feature, show gene bar.

Definition at line 50 of file gene_model_config.hpp.

◆ ERenderingOption

rendering options on how to render features overall.

each option corresponds to one or more settings.

Enumerator
eOption_GeneOnly 

show gene bar only

eOption_MergeAll 

merge all RNAs and CDSs, show exons, no gene bar

eOption_MergePairs 

merge each RNA and CDS pair, show exons, no gene bar

eOption_ShowAllButGenes 

show all RNAs, CDSs and exons, no gene bar

eOption_ShowAll 

show all features individually

eOption_SingleLine 

merge all RNAs and CDSs into one line

eOption_Default 

Definition at line 69 of file gene_model_config.hpp.

Constructor & Destructor Documentation

◆ CGeneModelConfig()

CGeneModelConfig::CGeneModelConfig ( )
inline

Definition at line 82 of file gene_model_config.hpp.

Member Function Documentation

◆ LoadSettings()

void CGeneModelConfig::LoadSettings ( CConstRef< CSeqGraphicConfig g_conf,
const string reg_path,
const string profile 
)

◆ LoadSettingsPartial()

void CGeneModelConfig::LoadSettingsPartial ( const string reg_path,
const string profile 
)

◆ OptionStrToValue()

CGeneModelConfig::ERenderingOption CGeneModelConfig::OptionStrToValue ( const string option)
static

Definition at line 115 of file gene_model_config.cpp.

References NCBI_THROW, and option.

Referenced by UpdateSettings().

◆ OptionValueToStr()

const string & CGeneModelConfig::OptionValueToStr ( CGeneModelConfig::ERenderingOption  option)
static

Definition at line 103 of file gene_model_config.cpp.

References kEmptyStr, and option.

Referenced by CGeneModelFactory::GetSettings().

◆ SaveSettings()

void CGeneModelConfig::SaveSettings ( CConstRef< CSeqGraphicConfig g_conf,
const string reg_path,
const string profile 
) const

◆ SaveSettingsAsString()

string CGeneModelConfig::SaveSettingsAsString ( const string preset_style) const

◆ StyleStrToValue()

CGeneModelConfig::EMergeStyle CGeneModelConfig::StyleStrToValue ( const string style)
static

Definition at line 65 of file gene_model_config.cpp.

References NCBI_THROW.

Referenced by LoadSettings(), LoadSettingsPartial(), and UpdateSettings().

◆ StyleValueToStr()

const string & CGeneModelConfig::StyleValueToStr ( CGeneModelConfig::EMergeStyle  style)
static

Definition at line 76 of file gene_model_config.cpp.

References kEmptyStr.

Referenced by SaveSettings(), and SaveSettingsAsString().

◆ UpdateSettings()

void CGeneModelConfig::UpdateSettings ( const CSGConfigUtils::TKeyValuePairs settings)

Member Data Documentation

◆ m_CCDSOnly

bool CGeneModelConfig::m_CCDSOnly = false

◆ m_CdsConfig

CRef<CCdsConfig> CGeneModelConfig::m_CdsConfig

◆ m_CDSProfile

string CGeneModelConfig::m_CDSProfile

cds setting profile

Definition at line 127 of file gene_model_config.hpp.

Referenced by LoadSettings(), LoadSettingsPartial(), and SaveSettings().

◆ m_GeneBoxConfig

CRef<CBoundaryParams> CGeneModelConfig::m_GeneBoxConfig

◆ m_HideModels

bool CGeneModelConfig::m_HideModels = false

◆ m_HideNonCoding

bool CGeneModelConfig::m_HideNonCoding = false

◆ m_HighlightMode

int CGeneModelConfig::m_HighlightMode

◆ m_LandmarkFeatLimit

int CGeneModelConfig::m_LandmarkFeatLimit

◆ m_MergeStyle

EMergeStyle CGeneModelConfig::m_MergeStyle

◆ m_OverviewFeatCutoff

int CGeneModelConfig::m_OverviewFeatCutoff

◆ m_SelectOnly

bool CGeneModelConfig::m_SelectOnly = false

◆ m_ShowAaRuler

bool CGeneModelConfig::m_ShowAaRuler

◆ m_ShowCDSProductFeats

bool CGeneModelConfig::m_ShowCDSProductFeats

◆ m_ShowCDSs

bool CGeneModelConfig::m_ShowCDSs

◆ m_ShowExons

bool CGeneModelConfig::m_ShowExons

◆ m_ShowGeneProducts

bool CGeneModelConfig::m_ShowGeneProducts

feature histogram on a gene.

Definition at line 121 of file gene_model_config.hpp.

Referenced by LoadSettings(), LoadSettingsPartial(), and SaveSettings().

◆ m_ShowGenes

bool CGeneModelConfig::m_ShowGenes

◆ m_ShowHistogram

bool CGeneModelConfig::m_ShowHistogram

◆ m_ShowLabel

bool CGeneModelConfig::m_ShowLabel = true

◆ m_ShowLMGeneLabel

bool CGeneModelConfig::m_ShowLMGeneLabel

landmark gene labels.

Definition at line 115 of file gene_model_config.hpp.

Referenced by LoadSettings(), LoadSettingsPartial(), SaveSettings(), SaveSettingsAsString(), and UpdateSettings().

◆ m_ShowNtRuler

bool CGeneModelConfig::m_ShowNtRuler

◆ m_ShowRNAs

bool CGeneModelConfig::m_ShowRNAs

◆ m_ShowVDJCs

bool CGeneModelConfig::m_ShowVDJCs

The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:09:10 2024 by modify_doxy.py rev. 669887