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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnmix_8hpp_source.html below:

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

fForceTranslation = 0x02,

& GetInputDensegs (

)

;

& GetInputSeqAligns(

)

;

fTruncateOverlaps = 0x0001,

fNegativeStrand = 0x0002,

fRemoveLeadTrailGaps = 0x0010,

fSortSeqsByScore = 0x0020,

fSortInputByScore = 0x0040,

fQuerySeqMergeOnly = 0x0080,

fFillUnalignedRegions = 0x0100,

fAllowTranslocation = 0x0200

& GetSeqAlign (

)

;

x_Init (

);

x_Reset (

);

&

(*m_Scope);

int(* TCalcScoreMethod)(const string &s1, const string &s2, bool s1_is_prot, bool s2_is_prot, int gene_code1, int gene_code2)

Typedefs.

const TConstAlns & GetInputSeqAligns(void) const

CRef< CAlnMixSequences > m_AlnMixSequences

CRef< CAlnMixMerger > m_AlnMixMerger

TCalcScoreMethod x_CalculateScore

CAlnMixMatches::TCalcScoreMethod TCalcScoreMethod

vector< CConstRef< CSeq_align > > TConstAlns

CRef< CAlnMixMatches > m_AlnMixMatches

map< void *, CConstRef< CDense_seg > > TConstDSsMap

vector< CConstRef< CDense_seg > > TConstDSs

TConstDSsMap m_InputDSsMap

map< void *, CConstRef< CSeq_align > > TConstAlnsMap

CAlnMix(const CAlnMix &value)

const TConstDSs & GetInputDensegs(void) const

CScope & GetScope(void) const

CAlnMix & operator=(const CAlnMix &value)

TConstAlnsMap m_InputAlnsMap

Tasks that report progress derive from this class.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_XALNMGR_EXPORT

const GenericPointer< typename T::ValueType > T2 value

Create a Dense-seg from a Std-seg Used by AlnMgr to handle nucl2prot alignments.

virtual void ChooseSeqId(CSeq_id &id1, const CSeq_id &id2)=0

void Merge(wxMenu &menu_1, const wxMenu &menu_2)

merges all items form menu_2 into menu_1, preserving the structure if possible

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