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CProSplignOutputOptions Class Reference

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< Uint8TCounter
 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
 
CProSplignOutputOptionsSetCutFlanksWithPositDrop (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
 
CProSplignOutputOptionsSetCutFlanksWithPositDropoff (int)
 
int GetCutFlanksWithPositDropoff () const
 
CProSplignOutputOptionsSetCutFlanksWithPositWindow (int)
 window size More...
 
int GetCutFlanksWithPositWindow () const
 
CProSplignOutputOptionsSetCutFlanksWithPositMaxLen (int)
 max flank size to cut More...
 
int GetCutFlanksWithPositMaxLen () const
 
CProSplignOutputOptionsSetCutFlanksWithPositGapRatio (int)
 count gaps as 1+1/gap_ratio, gap_ratio = 1 - standart behaviour. More...
 
int GetCutFlanksWithPositGapRatio () const
 
CProSplignOutputOptionsSetCutFlankPartialCodons (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
 
CProSplignOutputOptionsSetFillHoles (bool)
 fill back holes between good pieces. More...
 
bool GetFillHoles () const
 
CProSplignOutputOptionsSetMinHoleLen (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
 
CProSplignOutputOptionsSetCutNs (bool)
 cut trailing Ns at the ends of good pieces. More...
 
bool GetCutNs () const
 
CProSplignOutputOptionsSetFlankPositives (int)
 any length flank of a good piece should not be worse than this percentage threshold More...
 
int GetFlankPositives () const
 
CProSplignOutputOptionsSetTotalPositives (int)
 good piece total percentage threshold More...
 
int GetTotalPositives () const
 
CProSplignOutputOptionsSetMaxBadLen (int)
 any part of a good piece longer than max_bad_len should not be worse than min_positives More...
 
int GetMaxBadLen () const
 
CProSplignOutputOptionsSetMinPositives (int)
 
int GetMinPositives () const
 
CProSplignOutputOptionsSetMinExonId (int)
 minimum exon identity More...
 
int GetMinExonId () const
 
CProSplignOutputOptionsSetMinExonPos (int)
 minimum exon positives percentage More...
 
int GetMinExonPos () const
 
CProSplignOutputOptionsSetMinFlankingExonLen (int)
 minimum number of bases in the first and last exon More...
 
int GetMinFlankingExonLen () const
 
CProSplignOutputOptionsSetMinGoodLen (int)
 good piece should not be shorter than that More...
 
int GetMinGoodLen () const
 
CProSplignOutputOptionsSetStartBonus (int)
 reward (in # of positives?) for start codon match. More...
 
int GetStartBonus () const
 
CProSplignOutputOptionsSetStopBonus (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_BaseSetScoreMatrix (const string &matrix_name)
 
const stringGetScoreMatrix () const
 
CProSplignOptions_BaseSetAltStarts (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...
 
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 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...
 

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
 

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

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)

◆ 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

◆ GetCutFlanksWithPositDropoff()

int CProSplignOutputOptions::GetCutFlanksWithPositDropoff ( ) const

◆ GetCutFlanksWithPositGapRatio()

int CProSplignOutputOptions::GetCutFlanksWithPositGapRatio ( ) const

◆ GetCutFlanksWithPositMaxLen()

int CProSplignOutputOptions::GetCutFlanksWithPositMaxLen ( ) const

◆ GetCutFlanksWithPositWindow()

int CProSplignOutputOptions::GetCutFlanksWithPositWindow ( ) const

◆ 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

◆ 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

◆ 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

◆ 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

◆ default_flank_positives

const int CProSplignOutputOptions::default_flank_positives = 55
static

◆ 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

◆ default_min_exon_pos

const int CProSplignOutputOptions::default_min_exon_pos = 55
static

◆ default_min_flanking_exon_len

const int CProSplignOutputOptions::default_min_flanking_exon_len = 15
static

◆ default_min_good_len

const int CProSplignOutputOptions::default_min_good_len = 59
static

◆ default_min_hole_len

const int CProSplignOutputOptions::default_min_hole_len = 200
static

◆ 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

◆ 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:
Modified on Mon Feb 26 04:05:46 2024 by modify_doxy.py rev. 669887