Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCProSplignOutputOptionsExt.html below:
NCBI C++ ToolKit: CProSplignOutputOptionsExt Class Reference
CProSplignOutputOptionsExt (const CProSplignOutputOptions &options) bool Dropof (int efflen, int posit, list< prosplign::CNPiece >::iterator it) void Join (list< prosplign::CNPiece >::iterator it, list< prosplign::CNPiece >::iterator last) bool Perc (list< prosplign::CNPiece >::iterator it, int efflen, int posit, list< prosplign::CNPiece >::iterator last) bool Bad (list< prosplign::CNPiece >::iterator it) bool ForwCheck (list< prosplign::CNPiece >::iterator it1, list< prosplign::CNPiece >::iterator it2) bool BackCheck (list< prosplign::CNPiece >::iterator it1, list< prosplign::CNPiece >::iterator it2) 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
Extended output filtering parameters deprecated, used in older programs.
Definition at line 60 of file Info.hpp.
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