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NCBI C++ ToolKit: include/objtools/alnmgr/score_builder_base.hpp Source File

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1 #ifndef OBJMGR_UTIL___SCORE_BUILDER_BASE__HPP 2 #define OBJMGR_UTIL___SCORE_BUILDER_BASE__HPP 76

eScore_PercentCoverage

122

AddSplignScores(align, align.

SetScore

());

133

EPercentIdentityType

type

= eGapped);

141

EPercentIdentityType

type

= eGapped);

149

EPercentIdentityType

type

= eGapped);

160  int

& identities,

int

& mismatches);

169  int

& identities,

int

& mismatches);

179  int

& identities,

int

& mismatches);

185  int

& positives,

int

& negatives);

196  int

GetGapBaseCount (

const CSeq_align

& align);

197  int

GetGapBaseCount (

const CSeq_align

& align,

199  int

GetGapBaseCount (

const CSeq_align

& align,

206  const TSeqRange

&range,

bool

ungapped=

false

);

209  bool

ungapped=

false

);

211  void

SetSubstMatrix(

const string

&name);

219  void

x_GetMatrixCounts(

CScope

& scope,

221  int

* positives,

int

* negatives);

EErrorMode

Error handling while adding scores that are not implemented or unsupported (cannot be defined) for ce...

@ eError_Report

Print error messages, but do not fail.

@ eError_Silent

Try to ignore errors, continue adding scores.

EPercentIdentityType

Compute percent identity (range 0-100)

void SetErrorMode(EErrorMode mode)

void AddSplignScores(CSeq_align &align)

EErrorMode GetErrorMode(void) const

EScoreType

enum controlling known named scores

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

#define NCBI_XALNMGR_EXPORT

TScore & SetScore(void)

Assign a value to Score data member.

vector< CRef< CScore > > TScore

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

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