Search Toolkit Book for CProSplignOutputOptions

Output filtering parameters. More...

#include <algo/align/prosplign/prosplign.hpp>

Inheritance diagram for CProSplignOutputOptions:

Collaboration diagram for CProSplignOutputOptions:

Public Types
enum	EMode { eWithHoles , ePassThrough }

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< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CProSplignOutputOptions (EMode mode=eWithHoles)

	CProSplignOutputOptions (const CArgs &args)

bool	IsPassThrough () const

CProSplignOutputOptions &	SetCutFlanksWithPositDrop (bool)
	cut flanks if drop of positives is more than a dropoff in comparison to positives in a window next to a flank More...

bool	GetCutFlanksWithPositDrop () const

CProSplignOutputOptions &	SetCutFlanksWithPositDropoff (int)

int	GetCutFlanksWithPositDropoff () const

CProSplignOutputOptions &	SetCutFlanksWithPositWindow (int)
	window size More...

int	GetCutFlanksWithPositWindow () const

CProSplignOutputOptions &	SetCutFlanksWithPositMaxLen (int)
	max flank size to cut More...

int	GetCutFlanksWithPositMaxLen () const

CProSplignOutputOptions &	SetCutFlanksWithPositGapRatio (int)
	count gaps as 1+1/gap_ratio, gap_ratio = 1 - standart behaviour. More...

int	GetCutFlanksWithPositGapRatio () const

CProSplignOutputOptions &	SetCutFlankPartialCodons (bool)
	cut partial codons and adjecent at the beginning and at the end good pieces called at the end of post processing More...

bool	GetCutFlankPartialCodons () const

CProSplignOutputOptions &	SetFillHoles (bool)
	fill back holes between good pieces. More...

bool	GetFillHoles () const

CProSplignOutputOptions &	SetMinHoleLen (int)
	fill back small holes between good pieces holes with both unaligned protein and nucleotide portions less than min_hole_len will be filled back 0 - don't fill. More...

int	GetMinHoleLen () const

CProSplignOutputOptions &	SetCutNs (bool)
	cut trailing Ns at the ends of good pieces. More...

bool	GetCutNs () const

CProSplignOutputOptions &	SetFlankPositives (int)
	any length flank of a good piece should not be worse than this percentage threshold More...

int	GetFlankPositives () const

CProSplignOutputOptions &	SetTotalPositives (int)
	good piece total percentage threshold More...

int	GetTotalPositives () const

CProSplignOutputOptions &	SetMaxBadLen (int)
	any part of a good piece longer than max_bad_len should not be worse than min_positives More...

int	GetMaxBadLen () const

CProSplignOutputOptions &	SetMinPositives (int)

int	GetMinPositives () const

CProSplignOutputOptions &	SetMinExonId (int)
	minimum exon identity More...

int	GetMinExonId () const

CProSplignOutputOptions &	SetMinExonPos (int)
	minimum exon positives percentage More...

int	GetMinExonPos () const

CProSplignOutputOptions &	SetMinFlankingExonLen (int)
	minimum number of bases in the first and last exon More...

int	GetMinFlankingExonLen () const

CProSplignOutputOptions &	SetMinGoodLen (int)
	good piece should not be shorter than that More...

int	GetMinGoodLen () const

CProSplignOutputOptions &	SetStartBonus (int)
	reward (in # of positives?) for start codon match. More...

int	GetStartBonus () const

CProSplignOutputOptions &	SetStopBonus (int)
	reward for stop codon at the end. Not implemented yet More...

int	GetStopBonus () const

Public Member Functions inherited from CProSplignOptions_Base
	CProSplignOptions_Base ()
	creates scoring parameter object with default values More...

	CProSplignOptions_Base (const CArgs &args)

CProSplignOptions_Base &	SetScoreMatrix (const string &matrix_name)

const string &	GetScoreMatrix () const

CProSplignOptions_Base &	SetAltStarts (bool allow_alt_start)

bool	GetAltStarts () const

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (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 void	SetupArgDescriptions (CArgDescriptions *argdescr)

Static Public Member Functions inherited from CProSplignOptions_Base
static void	SetupArgDescriptions (CArgDescriptions *argdescr)

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
static const bool	default_cut_flanks_with_posit_drop = true

static const int	default_cut_flanks_with_posit_dropoff = 35

static const int	default_cut_flanks_with_posit_window = 90

static const int	default_cut_flanks_with_posit_max_len = 30

static const int	default_cut_flanks_with_posit_gap_ratio = 2

static const bool	default_cut_flank_partial_codons = true

static const bool	default_fill_holes = false

static const int	default_min_hole_len = 200

static const bool	default_cut_ns = false

static const int	default_flank_positives = 55

static const int	default_total_positives = 70

static const int	default_max_bad_len = 45

static const int	default_min_positives = 15

static const int	default_min_exon_id = 30

static const int	default_min_exon_pos = 55

static const int	default_min_flanking_exon_len = 15

static const int	default_min_good_len = 59

static const int	default_start_bonus = 8

static const int	default_stop_bonus = 8
	??? More...

Static Public Attributes inherited from CProSplignOptions_Base
static const char *	default_score_matrix_name = "BLOSUM62"

static const bool	default_allow_alt_starts = false

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...

Additional Inherited Members
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Output filtering parameters.

ProSplign always makes a global alignment, i.e. it aligns the whole protein no matter how bad some parts of this alignment might be. Usually we don't want the bad pieces and remove them. The following parameters define good parts.

Definition at line 155 of file prosplign.hpp.

Member Enumeration Documentation

◆ EMode

enum CProSplignOutputOptions::EMode

Enumerator
eWithHoles	default filtering parameters
ePassThrough	all zeroes - no filtering

Definition at line 158 of file prosplign.hpp.

Constructor & Destructor Documentation

◆ CProSplignOutputOptions() [1/2]

CProSplignOutputOptions::CProSplignOutputOptions ( EMode mode = eWithHoles )

Definition at line 348 of file prosplign.cpp.

References default_cut_flank_partial_codons, default_cut_flanks_with_posit_drop, default_cut_flanks_with_posit_dropoff, default_cut_flanks_with_posit_gap_ratio, default_cut_flanks_with_posit_max_len, default_cut_flanks_with_posit_window, default_cut_ns, default_fill_holes, default_flank_positives, default_max_bad_len, default_min_exon_id, default_min_exon_pos, default_min_flanking_exon_len, default_min_good_len, default_min_hole_len, default_min_positives, default_start_bonus, default_stop_bonus, default_total_positives, ePassThrough, eWithHoles, SetCutFlankPartialCodons(), SetCutFlanksWithPositDrop(), SetCutFlanksWithPositDropoff(), SetCutFlanksWithPositGapRatio(), SetCutFlanksWithPositMaxLen(), SetCutFlanksWithPositWindow(), SetCutNs(), SetFillHoles(), SetFlankPositives(), SetMaxBadLen(), SetMinExonId(), SetMinExonPos(), SetMinFlankingExonLen(), SetMinGoodLen(), SetMinHoleLen(), SetMinPositives(), SetStartBonus(), SetStopBonus(), and SetTotalPositives().

◆ CProSplignOutputOptions() [2/2]

CProSplignOutputOptions::CProSplignOutputOptions ( const CArgs & args )

Member Function Documentation

◆ GetCutFlankPartialCodons()

bool CProSplignOutputOptions::GetCutFlankPartialCodons ( ) const

Definition at line 613 of file prosplign.cpp.

References cut_flank_partial_codons.

Referenced by FindGoodParts().

◆ GetCutFlanksWithPositDrop()

bool CProSplignOutputOptions::GetCutFlanksWithPositDrop ( ) const

Definition at line 563 of file prosplign.cpp.

References cut_flanks_with_posit_drop.

Referenced by CProSplignTrimmer::CutFromLeft(), and CProSplignTrimmer::CutFromRight().

◆ GetCutFlanksWithPositDropoff()

int CProSplignOutputOptions::GetCutFlanksWithPositDropoff ( ) const

Definition at line 573 of file prosplign.cpp.

References cut_flanks_with_posit_dropoff.

Referenced by CProSplignTrimmer::CutFromLeft(), and CProSplignTrimmer::CutFromRight().

◆ GetCutFlanksWithPositGapRatio()

int CProSplignOutputOptions::GetCutFlanksWithPositGapRatio ( ) const

Definition at line 603 of file prosplign.cpp.

References cut_flanks_with_posit_gap_ratio.

Referenced by CProSplignTrimmer::CutFromLeft(), and CProSplignTrimmer::CutFromRight().

◆ GetCutFlanksWithPositMaxLen()

int CProSplignOutputOptions::GetCutFlanksWithPositMaxLen ( ) const

Definition at line 593 of file prosplign.cpp.

References cut_flanks_with_posit_max_len.

Referenced by CProSplignTrimmer::CutFromLeft(), and CProSplignTrimmer::CutFromRight().

◆ GetCutFlanksWithPositWindow()

int CProSplignOutputOptions::GetCutFlanksWithPositWindow ( ) const

Definition at line 583 of file prosplign.cpp.

References cut_flanks_with_posit_window.

Referenced by CProSplignTrimmer::CutFromLeft(), and CProSplignTrimmer::CutFromRight().

◆ GetCutNs()

bool CProSplignOutputOptions::GetCutNs ( ) const

Definition at line 643 of file prosplign.cpp.

References cut_ns.

Referenced by FindGoodParts().

◆ GetFillHoles()

bool CProSplignOutputOptions::GetFillHoles ( ) const

Definition at line 623 of file prosplign.cpp.

References fill_holes.

Referenced by FindGoodParts().

◆ GetFlankPositives()

int CProSplignOutputOptions::GetFlankPositives ( ) const

Definition at line 673 of file prosplign.cpp.

References flank_positives.

Referenced by CProSplignOutputOptionsExt::CProSplignOutputOptionsExt(), and IsPassThrough().

◆ GetMaxBadLen()

int CProSplignOutputOptions::GetMaxBadLen ( ) const

Definition at line 693 of file prosplign.cpp.

References max_bad_len.

Referenced by CProSplignOutputOptionsExt::Bad().

◆ GetMinExonId()

int CProSplignOutputOptions::GetMinExonId ( ) const

Definition at line 653 of file prosplign.cpp.

References min_exon_id.

Referenced by ExcludeBadExons().

◆ GetMinExonPos()

int CProSplignOutputOptions::GetMinExonPos ( ) const

Definition at line 663 of file prosplign.cpp.

References min_exon_pos.

Referenced by ExcludeBadExons().

◆ GetMinFlankingExonLen()

int CProSplignOutputOptions::GetMinFlankingExonLen ( ) const

Definition at line 715 of file prosplign.cpp.

References min_flanking_exon_len.

Referenced by CProSplignOutputOptionsExt::CProSplignOutputOptionsExt().

◆ GetMinGoodLen()

int CProSplignOutputOptions::GetMinGoodLen ( ) const

Definition at line 725 of file prosplign.cpp.

References min_good_len.

Referenced by FindGoodParts().

◆ GetMinHoleLen()

int CProSplignOutputOptions::GetMinHoleLen ( ) const

Definition at line 633 of file prosplign.cpp.

References min_hole_len.

Referenced by FindGoodParts().

◆ GetMinPositives()

int CProSplignOutputOptions::GetMinPositives ( ) const

Definition at line 704 of file prosplign.cpp.

References min_positives.

◆ GetStartBonus()

int CProSplignOutputOptions::GetStartBonus ( ) const

Definition at line 736 of file prosplign.cpp.

References start_bonus.

Referenced by FindGoodParts().

◆ GetStopBonus()

int CProSplignOutputOptions::GetStopBonus ( ) const

Definition at line 746 of file prosplign.cpp.

References stop_bonus.

◆ GetTotalPositives()

int CProSplignOutputOptions::GetTotalPositives ( ) const

Definition at line 683 of file prosplign.cpp.

References total_positives.

Referenced by CProSplignOutputOptionsExt::CProSplignOutputOptionsExt(), CProSplignOutputOptionsExt::Dropof(), IsPassThrough(), and CProSplignOutputOptionsExt::Perc().

◆ IsPassThrough()

bool CProSplignOutputOptions::IsPassThrough ( ) const

Definition at line 553 of file prosplign.cpp.

References GetFlankPositives(), and GetTotalPositives().

Referenced by FindGoodParts(), and CProSplign::RefineAlignment().

◆ SetCutFlankPartialCodons()

CProSplignOutputOptions & CProSplignOutputOptions::SetCutFlankPartialCodons ( bool val )

cut partial codons and adjecent at the beginning and at the end good pieces called at the end of post processing

Definition at line 608 of file prosplign.cpp.

References cut_flank_partial_codons, and val.

Referenced by CProSplignOutputOptions().

◆ SetCutFlanksWithPositDrop()

CProSplignOutputOptions & CProSplignOutputOptions::SetCutFlanksWithPositDrop ( bool val )

cut flanks if drop of positives is more than a dropoff in comparison to positives in a window next to a flank

Definition at line 558 of file prosplign.cpp.

References cut_flanks_with_posit_drop, and val.

Referenced by CProSplignOutputOptions().

◆ SetCutFlanksWithPositDropoff()

CProSplignOutputOptions & CProSplignOutputOptions::SetCutFlanksWithPositDropoff ( int val )

Definition at line 568 of file prosplign.cpp.

References cut_flanks_with_posit_dropoff, and val.

Referenced by CProSplignOutputOptions().

◆ SetCutFlanksWithPositGapRatio()

CProSplignOutputOptions & CProSplignOutputOptions::SetCutFlanksWithPositGapRatio ( int val )

count gaps as 1+1/gap_ratio, gap_ratio = 1 - standart behaviour.

Definition at line 598 of file prosplign.cpp.

References cut_flanks_with_posit_gap_ratio, and val.

Referenced by CProSplignOutputOptions().

◆ SetCutFlanksWithPositMaxLen()

CProSplignOutputOptions & CProSplignOutputOptions::SetCutFlanksWithPositMaxLen ( int val )

max flank size to cut

Definition at line 588 of file prosplign.cpp.

References cut_flanks_with_posit_max_len, and val.

Referenced by CProSplignOutputOptions().

◆ SetCutFlanksWithPositWindow()

CProSplignOutputOptions & CProSplignOutputOptions::SetCutFlanksWithPositWindow ( int val )

window size

Definition at line 578 of file prosplign.cpp.

References cut_flanks_with_posit_window, and val.

Referenced by CProSplignOutputOptions().

◆ SetCutNs()

CProSplignOutputOptions & CProSplignOutputOptions::SetCutNs ( bool val )

cut trailing Ns at the ends of good pieces.

called at the end of post processing

Definition at line 638 of file prosplign.cpp.

References cut_ns, and val.

Referenced by CProSplignOutputOptions(), and CProSplignParams::GetOutputOptions().

◆ SetFillHoles()

CProSplignOutputOptions & CProSplignOutputOptions::SetFillHoles ( bool val )

fill back holes between good pieces.

Flank regions remain unaligned called at the end of post processing

Definition at line 618 of file prosplign.cpp.

References fill_holes, and val.

Referenced by CProSplignOutputOptions(), and CProSplignParams::GetOutputOptions().

◆ SetFlankPositives()

CProSplignOutputOptions & CProSplignOutputOptions::SetFlankPositives ( int val )

any length flank of a good piece should not be worse than this percentage threshold

Definition at line 668 of file prosplign.cpp.

References flank_positives, and val.

Referenced by CProSplignOutputOptions(), and CProSplignParams::GetOutputOptions().

◆ SetMaxBadLen()

CProSplignOutputOptions & CProSplignOutputOptions::SetMaxBadLen ( int val )

any part of a good piece longer than max_bad_len should not be worse than min_positives

Definition at line 688 of file prosplign.cpp.

References max_bad_len, and val.

Referenced by CProSplignOutputOptions().

◆ SetMinExonId()

CProSplignOutputOptions & CProSplignOutputOptions::SetMinExonId ( int val )

minimum exon identity

Definition at line 648 of file prosplign.cpp.

References min_exon_id, and val.

Referenced by CProSplignOutputOptions(), and CProSplignParams::GetOutputOptions().

◆ SetMinExonPos()

CProSplignOutputOptions & CProSplignOutputOptions::SetMinExonPos ( int val )

minimum exon positives percentage

Definition at line 658 of file prosplign.cpp.

References min_exon_pos, and val.

Referenced by CProSplignOutputOptions(), and CProSplignParams::GetOutputOptions().

◆ SetMinFlankingExonLen()

CProSplignOutputOptions & CProSplignOutputOptions::SetMinFlankingExonLen ( int val )

minimum number of bases in the first and last exon

Definition at line 709 of file prosplign.cpp.

References min_flanking_exon_len, and val.

Referenced by CProSplignOutputOptions(), and CProSplignParams::GetOutputOptions().

◆ SetMinGoodLen()

CProSplignOutputOptions & CProSplignOutputOptions::SetMinGoodLen ( int val )

good piece should not be shorter than that

Definition at line 719 of file prosplign.cpp.

References min_good_len, and val.

Referenced by CProSplignOutputOptions(), and CProSplignParams::GetOutputOptions().

◆ SetMinHoleLen()

CProSplignOutputOptions & CProSplignOutputOptions::SetMinHoleLen ( int val )

fill back small holes between good pieces holes with both unaligned protein and nucleotide portions less than min_hole_len will be filled back 0 - don't fill.

Definition at line 628 of file prosplign.cpp.

References min_hole_len, and val.

Referenced by CProSplignOutputOptions(), and CAdvancedAlignCleanup::SetParams().

◆ SetMinPositives()

CProSplignOutputOptions & CProSplignOutputOptions::SetMinPositives ( int val )

Definition at line 698 of file prosplign.cpp.

References min_positives, and val.

Referenced by CProSplignOutputOptions().

◆ SetStartBonus()

CProSplignOutputOptions & CProSplignOutputOptions::SetStartBonus ( int val )

reward (in # of positives?) for start codon match.

Definition at line 730 of file prosplign.cpp.

References start_bonus, and val.

Referenced by CProSplignOutputOptions().

◆ SetStopBonus()

CProSplignOutputOptions & CProSplignOutputOptions::SetStopBonus ( int val )

reward for stop codon at the end. Not implemented yet

Definition at line 740 of file prosplign.cpp.

References stop_bonus, and val.

Referenced by CProSplignOutputOptions().

◆ SetTotalPositives()

CProSplignOutputOptions & CProSplignOutputOptions::SetTotalPositives ( int val )

good piece total percentage threshold

Definition at line 678 of file prosplign.cpp.

References total_positives, and val.

Referenced by CProSplignOutputOptions(), and CProSplignParams::GetOutputOptions().

◆ SetupArgDescriptions()

void CProSplignOutputOptions::SetupArgDescriptions ( CArgDescriptions * argdescr )

static

Member Data Documentation

◆ cut_flank_partial_codons

bool CProSplignOutputOptions::cut_flank_partial_codons

private

Definition at line 278 of file prosplign.hpp.

Referenced by GetCutFlankPartialCodons(), and SetCutFlankPartialCodons().

◆ cut_flanks_with_posit_drop

bool CProSplignOutputOptions::cut_flanks_with_posit_drop

private

???

Definition at line 272 of file prosplign.hpp.

Referenced by GetCutFlanksWithPositDrop(), and SetCutFlanksWithPositDrop().

◆ cut_flanks_with_posit_dropoff

int CProSplignOutputOptions::cut_flanks_with_posit_dropoff

private

Definition at line 273 of file prosplign.hpp.

Referenced by GetCutFlanksWithPositDropoff(), and SetCutFlanksWithPositDropoff().

◆ cut_flanks_with_posit_gap_ratio

int CProSplignOutputOptions::cut_flanks_with_posit_gap_ratio

private

Definition at line 276 of file prosplign.hpp.

Referenced by GetCutFlanksWithPositGapRatio(), and SetCutFlanksWithPositGapRatio().

◆ cut_flanks_with_posit_max_len

int CProSplignOutputOptions::cut_flanks_with_posit_max_len

private

Definition at line 275 of file prosplign.hpp.

Referenced by GetCutFlanksWithPositMaxLen(), and SetCutFlanksWithPositMaxLen().

◆ cut_flanks_with_posit_window

int CProSplignOutputOptions::cut_flanks_with_posit_window

private

Definition at line 274 of file prosplign.hpp.

Referenced by GetCutFlanksWithPositWindow(), and SetCutFlanksWithPositWindow().

◆ cut_ns

bool CProSplignOutputOptions::cut_ns

private

Definition at line 281 of file prosplign.hpp.

Referenced by GetCutNs(), and SetCutNs().

◆ default_cut_flank_partial_codons

const bool CProSplignOutputOptions::default_cut_flank_partial_codons = true

static

Definition at line 251 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), and SetupArgDescriptions().

◆ default_cut_flanks_with_posit_drop

const bool CProSplignOutputOptions::default_cut_flanks_with_posit_drop = true

static

Definition at line 245 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), and SetupArgDescriptions().

◆ default_cut_flanks_with_posit_dropoff

const int CProSplignOutputOptions::default_cut_flanks_with_posit_dropoff = 35

static

Definition at line 246 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), and SetupArgDescriptions().

◆ default_cut_flanks_with_posit_gap_ratio

const int CProSplignOutputOptions::default_cut_flanks_with_posit_gap_ratio = 2

static

Definition at line 249 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), and SetupArgDescriptions().

◆ default_cut_flanks_with_posit_max_len

const int CProSplignOutputOptions::default_cut_flanks_with_posit_max_len = 30

static

Definition at line 248 of file prosplign.hpp.

Referenced by CProSplignOutputOptions().

◆ default_cut_flanks_with_posit_window

const int CProSplignOutputOptions::default_cut_flanks_with_posit_window = 90

static

Definition at line 247 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), and SetupArgDescriptions().

◆ default_cut_ns

const bool CProSplignOutputOptions::default_cut_ns = false

static

Definition at line 254 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), and CProSplignParams::Init().

◆ default_fill_holes

const bool CProSplignOutputOptions::default_fill_holes = false

static

Definition at line 252 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), CProSplignParams::Init(), and SetupArgDescriptions().

◆ default_flank_positives

const int CProSplignOutputOptions::default_flank_positives = 55

static

Definition at line 256 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), CProSplignParams::Init(), and SetupArgDescriptions().

◆ default_max_bad_len

const int CProSplignOutputOptions::default_max_bad_len = 45

static

Definition at line 259 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), and SetupArgDescriptions().

◆ default_min_exon_id

const int CProSplignOutputOptions::default_min_exon_id = 30

static

Definition at line 262 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), CProSplignParams::Init(), and SetupArgDescriptions().

◆ default_min_exon_pos

const int CProSplignOutputOptions::default_min_exon_pos = 55

static

Definition at line 263 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), CProSplignParams::Init(), and SetupArgDescriptions().

◆ default_min_flanking_exon_len

const int CProSplignOutputOptions::default_min_flanking_exon_len = 15

static

Definition at line 265 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), CProSplignParams::Init(), and SetupArgDescriptions().

◆ default_min_good_len

const int CProSplignOutputOptions::default_min_good_len = 59

static

Definition at line 266 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), CProSplignParams::Init(), and SetupArgDescriptions().

◆ default_min_hole_len

const int CProSplignOutputOptions::default_min_hole_len = 200

static

Definition at line 253 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), CAdvancedAlignCleanup::SetParams(), and SetupArgDescriptions().

◆ default_min_positives

const int CProSplignOutputOptions::default_min_positives = 15

static

Definition at line 260 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), and SetupArgDescriptions().

◆ default_start_bonus

const int CProSplignOutputOptions::default_start_bonus = 8

static

Definition at line 268 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), and SetupArgDescriptions().

◆ default_stop_bonus

const int CProSplignOutputOptions::default_stop_bonus = 8

static

???

Definition at line 269 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), and SetupArgDescriptions().

◆ default_total_positives

const int CProSplignOutputOptions::default_total_positives = 70

static

Definition at line 257 of file prosplign.hpp.

Referenced by CProSplignOutputOptions(), CProSplignParams::Init(), and SetupArgDescriptions().

◆ fill_holes

bool CProSplignOutputOptions::fill_holes

private

Definition at line 279 of file prosplign.hpp.

Referenced by GetFillHoles(), and SetFillHoles().

◆ flank_positives

int CProSplignOutputOptions::flank_positives

private

Definition at line 282 of file prosplign.hpp.

Referenced by GetFlankPositives(), and SetFlankPositives().

◆ max_bad_len

int CProSplignOutputOptions::max_bad_len

private

Definition at line 284 of file prosplign.hpp.

Referenced by GetMaxBadLen(), and SetMaxBadLen().

◆ min_exon_id

int CProSplignOutputOptions::min_exon_id

private

Definition at line 286 of file prosplign.hpp.

Referenced by GetMinExonId(), and SetMinExonId().

◆ min_exon_pos

int CProSplignOutputOptions::min_exon_pos

private

Definition at line 287 of file prosplign.hpp.

Referenced by GetMinExonPos(), and SetMinExonPos().

◆ min_flanking_exon_len

int CProSplignOutputOptions::min_flanking_exon_len

private

Definition at line 288 of file prosplign.hpp.

Referenced by GetMinFlankingExonLen(), and SetMinFlankingExonLen().

◆ min_good_len

int CProSplignOutputOptions::min_good_len

private

Definition at line 289 of file prosplign.hpp.

Referenced by GetMinGoodLen(), and SetMinGoodLen().

◆ min_hole_len

int CProSplignOutputOptions::min_hole_len

private

Definition at line 280 of file prosplign.hpp.

Referenced by GetMinHoleLen(), and SetMinHoleLen().

◆ min_positives

int CProSplignOutputOptions::min_positives

private

Definition at line 285 of file prosplign.hpp.

Referenced by GetMinPositives(), and SetMinPositives().

◆ start_bonus

int CProSplignOutputOptions::start_bonus

private

Definition at line 290 of file prosplign.hpp.

Referenced by GetStartBonus(), and SetStartBonus().

◆ stop_bonus

int CProSplignOutputOptions::stop_bonus

private

Definition at line 291 of file prosplign.hpp.

Referenced by GetStopBonus(), and SetStopBonus().

◆ total_positives

int CProSplignOutputOptions::total_positives

private

Definition at line 283 of file prosplign.hpp.

Referenced by GetTotalPositives(), and SetTotalPositives().

The documentation for this class was generated from the following files:

include/algo/align/prosplign/prosplign.hpp
src/algo/align/prosplign/prosplign.cpp

Private Attributes
bool	cut_flanks_with_posit_drop
	??? More...

int	cut_flanks_with_posit_dropoff

int	cut_flanks_with_posit_window

int	cut_flanks_with_posit_max_len

int	cut_flanks_with_posit_gap_ratio

bool	cut_flank_partial_codons

bool	fill_holes

int	min_hole_len

bool	cut_ns

int	flank_positives

int	total_positives

int	max_bad_len

int	min_positives

int	min_exon_id

int	min_exon_pos

int	min_flanking_exon_len

int	min_good_len

int	start_bonus

int	stop_bonus

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ EMode

Constructor & Destructor Documentation

◆ CProSplignOutputOptions() [1/2]

◆ CProSplignOutputOptions() [2/2]

Member Function Documentation

◆ GetCutFlankPartialCodons()

◆ GetCutFlanksWithPositDrop()

◆ GetCutFlanksWithPositDropoff()

◆ GetCutFlanksWithPositGapRatio()

◆ GetCutFlanksWithPositMaxLen()

◆ GetCutFlanksWithPositWindow()

◆ GetCutNs()

◆ GetFillHoles()

◆ GetFlankPositives()

◆ GetMaxBadLen()

◆ GetMinExonId()

◆ GetMinExonPos()

◆ GetMinFlankingExonLen()

◆ GetMinGoodLen()

◆ GetMinHoleLen()

◆ GetMinPositives()

◆ GetStartBonus()

◆ GetStopBonus()

◆ GetTotalPositives()

◆ IsPassThrough()

◆ SetCutFlankPartialCodons()

◆ SetCutFlanksWithPositDrop()

◆ SetCutFlanksWithPositDropoff()

◆ SetCutFlanksWithPositGapRatio()

◆ SetCutFlanksWithPositMaxLen()

◆ SetCutFlanksWithPositWindow()

◆ SetCutNs()

◆ SetFillHoles()

◆ SetFlankPositives()

◆ SetMaxBadLen()

◆ SetMinExonId()

◆ SetMinExonPos()

◆ SetMinFlankingExonLen()

◆ SetMinGoodLen()

◆ SetMinHoleLen()

◆ SetMinPositives()

◆ SetStartBonus()

◆ SetStopBonus()

◆ SetTotalPositives()

◆ SetupArgDescriptions()

Member Data Documentation

◆ cut_flank_partial_codons

◆ cut_flanks_with_posit_drop

◆ cut_flanks_with_posit_dropoff

◆ cut_flanks_with_posit_gap_ratio

◆ cut_flanks_with_posit_max_len

◆ cut_flanks_with_posit_window

◆ cut_ns

◆ default_cut_flank_partial_codons

◆ default_cut_flanks_with_posit_drop

◆ default_cut_flanks_with_posit_dropoff

◆ default_cut_flanks_with_posit_gap_ratio

◆ default_cut_flanks_with_posit_max_len

◆ default_cut_flanks_with_posit_window

◆ default_cut_ns

◆ default_fill_holes

◆ default_flank_positives

◆ default_max_bad_len

◆ default_min_exon_id

◆ default_min_exon_pos

◆ default_min_flanking_exon_len

◆ default_min_good_len

◆ default_min_hole_len

◆ default_min_positives

◆ default_start_bonus

◆ default_stop_bonus

◆ default_total_positives