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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCProSplignOutputOptions.html below:

NCBI C++ ToolKit: CProSplignOutputOptions Class Reference

Search Toolkit Book for CProSplignOutputOptions

Output filtering parameters. More...

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

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 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 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...
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

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.

◆ EMode Enumerator eWithHoles

default filtering parameters

ePassThrough

all zeroes - no filtering

Definition at line 158 of file prosplign.hpp.

◆ 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 )

Definition at line 410 of file prosplign.cpp.

References SetCutFlankPartialCodons(), SetCutFlanksWithPositDrop(), SetCutFlanksWithPositDropoff(), SetCutFlanksWithPositGapRatio(), SetCutFlanksWithPositMaxLen(), SetCutFlanksWithPositWindow(), SetCutNs(), SetFillHoles(), SetFlankPositives(), SetMaxBadLen(), SetMinExonId(), SetMinExonPos(), SetMinFlankingExonLen(), SetMinGoodLen(), SetMinHoleLen(), SetMinPositives(), SetStartBonus(), SetStopBonus(), and SetTotalPositives().

◆ GetCutFlankPartialCodons() bool CProSplignOutputOptions::GetCutFlankPartialCodons ( ) const ◆ 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 ◆ GetFillHoles() bool CProSplignOutputOptions::GetFillHoles ( ) const ◆ GetFlankPositives() int CProSplignOutputOptions::GetFlankPositives ( ) const ◆ GetMaxBadLen() int CProSplignOutputOptions::GetMaxBadLen ( ) const ◆ GetMinExonId() int CProSplignOutputOptions::GetMinExonId ( ) const ◆ GetMinExonPos() int CProSplignOutputOptions::GetMinExonPos ( ) const ◆ GetMinFlankingExonLen() int CProSplignOutputOptions::GetMinFlankingExonLen ( ) const ◆ GetMinGoodLen() int CProSplignOutputOptions::GetMinGoodLen ( ) const ◆ GetMinHoleLen() int CProSplignOutputOptions::GetMinHoleLen ( ) const ◆ GetMinPositives() int CProSplignOutputOptions::GetMinPositives ( ) const ◆ GetStartBonus() int CProSplignOutputOptions::GetStartBonus ( ) const ◆ GetStopBonus() int CProSplignOutputOptions::GetStopBonus ( ) const ◆ GetTotalPositives() int CProSplignOutputOptions::GetTotalPositives ( ) const ◆ IsPassThrough() bool CProSplignOutputOptions::IsPassThrough ( ) const ◆ SetCutFlankPartialCodons() ◆ SetCutFlanksWithPositDrop() ◆ SetCutFlanksWithPositDropoff() ◆ SetCutFlanksWithPositGapRatio() ◆ SetCutFlanksWithPositMaxLen() ◆ SetCutFlanksWithPositWindow() ◆ SetCutNs() ◆ SetFillHoles() ◆ SetFlankPositives() ◆ SetMaxBadLen() ◆ SetMinExonId() ◆ SetMinExonPos() ◆ SetMinFlankingExonLen() ◆ SetMinGoodLen() ◆ SetMinHoleLen() ◆ SetMinPositives() ◆ SetStartBonus() ◆ SetStopBonus() ◆ SetTotalPositives() ◆ SetupArgDescriptions() void CProSplignOutputOptions::SetupArgDescriptions ( CArgDescriptions * argdescr ) static

Definition at line 194 of file prosplign.cpp.

References CArgDescriptions::AddDefaultKey(), CArgDescriptions::AddFlag(), 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_window, 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, CArgDescriptions::eBoolean, CArgDescriptions::eInteger, NStr::IntToString(), CArgDescriptions::SetConstraint(), and CProSplignOptions_Base::SetupArgDescriptions().

Referenced by CProSplignApp::Init(), and CAdvancedAlignCleanup::SetupArgDescriptions().

◆ cut_flank_partial_codons bool CProSplignOutputOptions::cut_flank_partial_codons private ◆ cut_flanks_with_posit_drop bool CProSplignOutputOptions::cut_flanks_with_posit_drop private ◆ cut_flanks_with_posit_dropoff int CProSplignOutputOptions::cut_flanks_with_posit_dropoff private ◆ cut_flanks_with_posit_gap_ratio int CProSplignOutputOptions::cut_flanks_with_posit_gap_ratio private ◆ cut_flanks_with_posit_max_len int CProSplignOutputOptions::cut_flanks_with_posit_max_len private ◆ cut_flanks_with_posit_window int CProSplignOutputOptions::cut_flanks_with_posit_window private ◆ cut_ns bool CProSplignOutputOptions::cut_ns private ◆ default_cut_flank_partial_codons const bool CProSplignOutputOptions::default_cut_flank_partial_codons = true static ◆ default_cut_flanks_with_posit_drop const bool CProSplignOutputOptions::default_cut_flanks_with_posit_drop = true static ◆ default_cut_flanks_with_posit_dropoff const int CProSplignOutputOptions::default_cut_flanks_with_posit_dropoff = 35 static ◆ default_cut_flanks_with_posit_gap_ratio const int CProSplignOutputOptions::default_cut_flanks_with_posit_gap_ratio = 2 static ◆ default_cut_flanks_with_posit_max_len const int CProSplignOutputOptions::default_cut_flanks_with_posit_max_len = 30 static ◆ default_cut_flanks_with_posit_window const int CProSplignOutputOptions::default_cut_flanks_with_posit_window = 90 static ◆ default_cut_ns ◆ default_fill_holes ◆ default_flank_positives const int CProSplignOutputOptions::default_flank_positives = 55 static ◆ default_max_bad_len const int CProSplignOutputOptions::default_max_bad_len = 45 static ◆ 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 ◆ default_start_bonus const int CProSplignOutputOptions::default_start_bonus = 8 static ◆ default_stop_bonus const int CProSplignOutputOptions::default_stop_bonus = 8 static ◆ default_total_positives const int CProSplignOutputOptions::default_total_positives = 70 static ◆ fill_holes bool CProSplignOutputOptions::fill_holes private ◆ flank_positives int CProSplignOutputOptions::flank_positives private ◆ max_bad_len int CProSplignOutputOptions::max_bad_len private ◆ min_exon_id int CProSplignOutputOptions::min_exon_id private ◆ min_exon_pos int CProSplignOutputOptions::min_exon_pos private ◆ min_flanking_exon_len int CProSplignOutputOptions::min_flanking_exon_len private ◆ min_good_len int CProSplignOutputOptions::min_good_len private ◆ min_hole_len int CProSplignOutputOptions::min_hole_len private ◆ min_positives int CProSplignOutputOptions::min_positives private ◆ start_bonus int CProSplignOutputOptions::start_bonus private ◆ stop_bonus int CProSplignOutputOptions::stop_bonus private ◆ total_positives int CProSplignOutputOptions::total_positives private

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

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

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