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CProSplignParams Class Reference

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#include <gui/packages/pkg_alignment/prosplign_params.hpp>

+ Inheritance diagram for CProSplignParams:
+ Collaboration diagram for CProSplignParams:

Public Member Functions

 CProSplignParams ()
 
 ~CProSplignParams ()
 
void Init ()
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 
CRef< CProSplignScoring > GetScoringParams () const
 
CRef< CProSplignOutputOptions > GetOutputOptions () const
 
IRegSettings interface implementation
virtual void SetRegistryPath (const string &reg_path)
 
virtual void LoadSettings ()
 
virtual void SaveSettings () const
 
- 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 Member Functions inherited from IRegSettings
virtual ~IRegSettings ()
 

Public Attributes

bool m_WithIntrons
 
int m_Strand
 
int m_GeneticCode
 
int m_FrameshiftCost
 
int m_GapOpenCost
 
int m_GapExtendCost
 
bool m_RefineAlignment
 
bool m_RemoveFlanks
 
bool m_RemoveNs
 
int m_FlankPositives
 
int m_TotalPositives
 
int m_MinGoodLength
 
int m_MinExonIdentity
 
int m_MinExonPositives
 
int m_MinFlankingExonLength
 

Private Attributes

string m_RegPath
 

Additional Inherited Members

- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 

Detailed Description

Definition at line 43 of file prosplign_params.hpp.

Constructor & Destructor Documentation

◆ CProSplignParams()

CProSplignParams::CProSplignParams ( )

Definition at line 40 of file prosplign_params.cpp.

References Init().

◆ ~CProSplignParams()

CProSplignParams::~CProSplignParams ( )
inline

Definition at line 48 of file prosplign_params.hpp.

Member Function Documentation

◆ DebugDump()

void CProSplignParams::DebugDump ( CDebugDumpContext  ddc,
unsigned int  depth 
) const
virtual

Implements CDebugDumpable.

Definition at line 170 of file prosplign_params.cpp.

References kFlankPosTag, kFrameshiftCostTag, kGapExtendCostTag, kGapOpenCostTag, kGeneticCodeTag, kMinExonIdTag, kMinExonPosTag, kMinFlankExonLenTag, kMinGoodLenTag, kNuclStrandTag, kRefineAlignTag, kRemoveFlanksTag, kRemoveNsTag, kTotalPosTag, kWithIntronsTag, CDebugDumpContext::Log(), m_FlankPositives, m_FrameshiftCost, m_GapExtendCost, m_GapOpenCost, m_GeneticCode, m_MinExonIdentity, m_MinExonPositives, m_MinFlankingExonLength, m_MinGoodLength, m_RefineAlignment, m_RemoveFlanks, m_RemoveNs, m_Strand, m_TotalPositives, m_WithIntrons, and CDebugDumpContext::SetFrame().

◆ GetOutputOptions()

CRef< CProSplignOutputOptions > CProSplignParams::GetOutputOptions ( ) const

Definition at line 78 of file prosplign_params.cpp.

References CProSplignOutputOptions::ePassThrough, m_FlankPositives, m_MinExonIdentity, m_MinExonPositives, m_MinFlankingExonLength, m_MinGoodLength, m_RefineAlignment, m_RemoveFlanks, m_RemoveNs, m_TotalPositives, Ref(), CProSplignOutputOptions::SetCutNs(), CProSplignOutputOptions::SetFillHoles(), CProSplignOutputOptions::SetFlankPositives(), CProSplignOutputOptions::SetMinExonId(), CProSplignOutputOptions::SetMinExonPos(), CProSplignOutputOptions::SetMinFlankingExonLen(), CProSplignOutputOptions::SetMinGoodLen(), and CProSplignOutputOptions::SetTotalPositives().

Referenced by CProSplignJob::x_RunProSplign().

◆ GetScoringParams()

CRef< CProSplignScoring > CProSplignParams::GetScoringParams ( ) const

Definition at line 69 of file prosplign_params.cpp.

References m_FrameshiftCost, m_GapExtendCost, m_GapOpenCost, CProSplignScoring::SetFrameshiftOpeningCost(), CProSplignScoring::SetGapExtensionCost(), and CProSplignScoring::SetGapOpeningCost().

Referenced by CProSplignJob::x_RunProSplign().

◆ Init()

void CProSplignParams::Init ( void  )

Definition at line 45 of file prosplign_params.cpp.

References CProSplignOutputOptions::default_cut_ns, CProSplignOutputOptions::default_fill_holes, CProSplignOutputOptions::default_flank_positives, CProSplignScoring::default_frameshift_opening, CProSplignScoring::default_gap_extension, CProSplignScoring::default_gap_opening, CProSplignOutputOptions::default_min_exon_id, CProSplignOutputOptions::default_min_exon_pos, CProSplignOutputOptions::default_min_flanking_exon_len, CProSplignOutputOptions::default_min_good_len, CProSplignOutputOptions::default_total_positives, m_FlankPositives, m_FrameshiftCost, m_GapExtendCost, m_GapOpenCost, m_GeneticCode, m_MinExonIdentity, m_MinExonPositives, m_MinFlankingExonLength, m_MinGoodLength, m_RefineAlignment, m_RemoveFlanks, m_RemoveNs, m_Strand, m_TotalPositives, and m_WithIntrons.

Referenced by CProSplignParams(), and CProSplignPanel::RestoreDefaults().

◆ LoadSettings()

void CProSplignParams::LoadSettings ( )
virtual

Implements IRegSettings.

Definition at line 145 of file prosplign_params.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CGuiRegistry::GetReadView(), kFlankPosTag, kFrameshiftCostTag, kGapExtendCostTag, kGapOpenCostTag, kGeneticCodeTag, kMinExonIdTag, kMinExonPosTag, kMinFlankExonLenTag, kMinGoodLenTag, kNuclStrandTag, kRefineAlignTag, kRemoveFlanksTag, kRemoveNsTag, kTotalPosTag, kWithIntronsTag, m_FlankPositives, m_FrameshiftCost, m_GapExtendCost, m_GapOpenCost, m_GeneticCode, m_MinExonIdentity, m_MinExonPositives, m_MinFlankingExonLength, m_MinGoodLength, m_RefineAlignment, m_RegPath, m_RemoveFlanks, m_RemoveNs, m_Strand, m_TotalPositives, and m_WithIntrons.

◆ SaveSettings()

void CProSplignParams::SaveSettings ( ) const
virtual

Implements IRegSettings.

Definition at line 121 of file prosplign_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kFlankPosTag, kFrameshiftCostTag, kGapExtendCostTag, kGapOpenCostTag, kGeneticCodeTag, kMinExonIdTag, kMinExonPosTag, kMinFlankExonLenTag, kMinGoodLenTag, kNuclStrandTag, kRefineAlignTag, kRemoveFlanksTag, kRemoveNsTag, kTotalPosTag, kWithIntronsTag, m_FlankPositives, m_FrameshiftCost, m_GapExtendCost, m_GapOpenCost, m_GeneticCode, m_MinExonIdentity, m_MinExonPositives, m_MinFlankingExonLength, m_MinGoodLength, m_RefineAlignment, m_RegPath, m_RemoveFlanks, m_RemoveNs, m_Strand, m_TotalPositives, m_WithIntrons, and CRegistryWriteView::Set().

◆ SetRegistryPath()

void CProSplignParams::SetRegistryPath ( const string &  reg_path)
virtual

Implements IRegSettings.

Definition at line 99 of file prosplign_params.cpp.

References m_RegPath.

Member Data Documentation

◆ m_FlankPositives

int CProSplignParams::m_FlankPositives

Definition at line 79 of file prosplign_params.hpp.

Referenced by DebugDump(), GetOutputOptions(), Init(), LoadSettings(), SaveSettings(), CProSplignPanel::TransferDataFromWindow(), and CProSplignPanel::TransferDataToWindow().

◆ m_FrameshiftCost

int CProSplignParams::m_FrameshiftCost

Definition at line 72 of file prosplign_params.hpp.

Referenced by DebugDump(), GetScoringParams(), Init(), LoadSettings(), SaveSettings(), CProSplignPanel::TransferDataFromWindow(), and CProSplignPanel::TransferDataToWindow().

◆ m_GapExtendCost

int CProSplignParams::m_GapExtendCost

Definition at line 74 of file prosplign_params.hpp.

Referenced by DebugDump(), GetScoringParams(), Init(), LoadSettings(), SaveSettings(), CProSplignPanel::TransferDataFromWindow(), and CProSplignPanel::TransferDataToWindow().

◆ m_GapOpenCost

int CProSplignParams::m_GapOpenCost

Definition at line 73 of file prosplign_params.hpp.

Referenced by DebugDump(), GetScoringParams(), Init(), LoadSettings(), SaveSettings(), CProSplignPanel::TransferDataFromWindow(), and CProSplignPanel::TransferDataToWindow().

◆ m_GeneticCode

int CProSplignParams::m_GeneticCode

Definition at line 70 of file prosplign_params.hpp.

Referenced by CProSplignPanel::CreateControls(), DebugDump(), Init(), LoadSettings(), SaveSettings(), and CProSplignJob::x_RunProSplign().

◆ m_MinExonIdentity

int CProSplignParams::m_MinExonIdentity

Definition at line 82 of file prosplign_params.hpp.

Referenced by DebugDump(), GetOutputOptions(), Init(), LoadSettings(), SaveSettings(), CProSplignPanel::TransferDataFromWindow(), and CProSplignPanel::TransferDataToWindow().

◆ m_MinExonPositives

int CProSplignParams::m_MinExonPositives

Definition at line 83 of file prosplign_params.hpp.

Referenced by DebugDump(), GetOutputOptions(), Init(), LoadSettings(), SaveSettings(), CProSplignPanel::TransferDataFromWindow(), and CProSplignPanel::TransferDataToWindow().

◆ m_MinFlankingExonLength

int CProSplignParams::m_MinFlankingExonLength

Definition at line 84 of file prosplign_params.hpp.

Referenced by DebugDump(), GetOutputOptions(), Init(), LoadSettings(), SaveSettings(), CProSplignPanel::TransferDataFromWindow(), and CProSplignPanel::TransferDataToWindow().

◆ m_MinGoodLength

int CProSplignParams::m_MinGoodLength

Definition at line 81 of file prosplign_params.hpp.

Referenced by DebugDump(), GetOutputOptions(), Init(), LoadSettings(), SaveSettings(), CProSplignPanel::TransferDataFromWindow(), and CProSplignPanel::TransferDataToWindow().

◆ m_RefineAlignment

bool CProSplignParams::m_RefineAlignment

Definition at line 76 of file prosplign_params.hpp.

Referenced by CProSplignPanel::CreateControls(), DebugDump(), GetOutputOptions(), Init(), LoadSettings(), SaveSettings(), and CProSplignPanel::TransferDataToWindow().

◆ m_RegPath

string CProSplignParams::m_RegPath
private

Definition at line 65 of file prosplign_params.hpp.

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

◆ m_RemoveFlanks

bool CProSplignParams::m_RemoveFlanks

Definition at line 77 of file prosplign_params.hpp.

Referenced by CProSplignPanel::CreateControls(), DebugDump(), GetOutputOptions(), Init(), LoadSettings(), and SaveSettings().

◆ m_RemoveNs

bool CProSplignParams::m_RemoveNs

Definition at line 78 of file prosplign_params.hpp.

Referenced by CProSplignPanel::CreateControls(), DebugDump(), GetOutputOptions(), Init(), LoadSettings(), and SaveSettings().

◆ m_Strand

int CProSplignParams::m_Strand

Definition at line 69 of file prosplign_params.hpp.

Referenced by CProSplignPanel::CreateControls(), DebugDump(), Init(), LoadSettings(), SaveSettings(), and CProSplignJob::x_CreateProjectItems().

◆ m_TotalPositives

int CProSplignParams::m_TotalPositives

Definition at line 80 of file prosplign_params.hpp.

Referenced by DebugDump(), GetOutputOptions(), Init(), LoadSettings(), SaveSettings(), CProSplignPanel::TransferDataFromWindow(), and CProSplignPanel::TransferDataToWindow().

◆ m_WithIntrons

bool CProSplignParams::m_WithIntrons

Definition at line 68 of file prosplign_params.hpp.

Referenced by CProSplignPanel::CreateControls(), DebugDump(), Init(), LoadSettings(), SaveSettings(), and CProSplignJob::x_RunProSplign().

The documentation for this class was generated from the following files:
Generated by doxygen 1.9.0
Modified on Fri Sep 20 14:58:03 2024 by modify_doxy.py rev. 669887