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NCBI C++ ToolKit: src/gui/packages/pkg_alignment/prosplign_params.cpp Source File

ddc.

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void SetFrame(const string &frame)

void Log(const string &name, const char *value, CDebugDumpFormatter::EValueType type=CDebugDumpFormatter::eValue, const string &comment=kEmptyStr)

CRegistryWriteView GetWriteView(const string &section)

get a read-write view at a particular level.

static CGuiRegistry & GetInstance()

access the application-wide singleton

CRegistryReadView GetReadView(const string &section) const

get a read-only view at a particular level.

Output filtering parameters.

CProSplignOutputOptions & SetMinExonPos(int)

minimum exon positives percentage

CProSplignOutputOptions & SetMinGoodLen(int)

good piece should not be shorter than that

CProSplignOutputOptions & SetMinFlankingExonLen(int)

minimum number of bases in the first and last exon

static const int default_total_positives

static const bool default_fill_holes

static const int default_flank_positives

CProSplignOutputOptions & SetCutNs(bool)

cut trailing Ns at the ends of good pieces.

static const int default_min_good_len

CProSplignOutputOptions & SetTotalPositives(int)

good piece total percentage threshold

CProSplignOutputOptions & SetMinExonId(int)

minimum exon identity

static const int default_min_flanking_exon_len

CProSplignOutputOptions & SetFlankPositives(int)

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

@ ePassThrough

all zeroes - no filtering

CProSplignOutputOptions & SetFillHoles(bool)

fill back holes between good pieces.

static const bool default_cut_ns

static const int default_min_exon_pos

static const int default_min_exon_id

int m_MinFlankingExonLength

CRef< CProSplignScoring > GetScoringParams() const

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

CRef< CProSplignOutputOptions > GetOutputOptions() const

virtual void LoadSettings()

virtual void SaveSettings() const

virtual void SetRegistryPath(const string &reg_path)

CProSplignScoring & SetFrameshiftOpeningCost(int)

CProSplignScoring & SetGapOpeningCost(int)

in addition to ScoreMatrix prosplign uses following costs (negate to get a score)

static const int default_gap_extension

static const int default_frameshift_opening

static const int default_gap_opening

CProSplignScoring & SetGapExtensionCost(int)

Gap Extension Cost for one aminoacid (three bases)

class CRegistryReadView provides a nested hierarchical view at a particular key.

int GetInt(const string &key, int default_val=0) const

access a named key at this level, with no recursion

bool GetBool(const string &key, bool default_val=false) const

void Set(const string &key, int val)

access a named key at this level, with no recursion

static unsigned char depth[2 *(256+1+29)+1]

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static const char * kGapOpenCostTag

static const char * kGapExtendCostTag

static const char * kFrameshiftCostTag

static const char * kRemoveFlanksTag

static const char * kNuclStrandTag

static const char * kMinGoodLenTag

static const char * kMinExonPosTag

static const char * kRefineAlignTag

static const char * kWithIntronsTag

static const char * kMinFlankExonLenTag

static const char * kGeneticCodeTag

static const char * kMinExonIdTag

static const char * kFlankPosTag

static const char * kTotalPosTag

static const char * kRemoveNsTag

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