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NCBI C++ ToolKit: include/algo/align/util/score_lookup.hpp Source File

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1 #ifndef GPIPE_COMMON___SCORE_LOOKUP__HPP 2 #define GPIPE_COMMON___SCORE_LOOKUP__HPP 60  virtual double Get

(

const

objects::CSeq_align& align,

61

objects::CScope* scope)

const

= 0;

92  string

HelpText(

const string

&score_name);

94

IScore::EComplexity Complexity(

const string

&score_name);

96  bool

IsIntegerScore(

const

objects::CSeq_align& align,

97  const string

&score_name);

100  double

GetScore(

const

objects::CSeq_align& align,

101  const string

&score_name);

103  void

UpdateState(

const

objects::CSeq_align& align);

105  static int

GetGeneId(

const

objects::CBioseq_Handle &bsh);

111  const string

&score_name);

static CRef< CScope > m_Scope

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

virtual void UpdateState(const objects::CSeq_align &)

For any IScore subclasses that have an internal state, this function will be called to update it for ...

virtual double Get(const objects::CSeq_align &align, objects::CScope *scope) const =0

virtual EComplexity GetComplexity() const

virtual bool IsInteger() const

virtual void PrintHelp(CNcbiOstream &ostr) const =0

TScoreDictionary m_Scores

CScoreLookup(blast::CBlastOptionsHandle &options)

objects::CScope & GetScope()

void SetScope(objects::CScope &scope)

CScoreLookup uses a scope internally.

map< string, CIRef< IScore > > TScoreDictionary

CScoreLookup(enum blast::EProgram program_type)

set< string > m_ScoresUsed

CRef< objects::CScope > m_Scope

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

#define NCBI_XALGOALIGN_EXPORT

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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