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NCBI C++ ToolKit: include/objects/seqalign/Dense_seg_.hpp Source File

vector< CRef< CSeq_id > >

;

IsSetDim(

)

;

CanGetDim(

)

;

ResetDim(

);

SetDefaultDim(

);

GetDim(

)

;

& SetDim(

);

IsSetNumseg(

)

;

CanGetNumseg(

)

;

ResetNumseg(

);

GetNumseg(

)

;

IsSetIds(

)

;

CanGetIds(

)

;

ResetIds(

);

& SetIds(

);

IsSetStarts(

)

;

CanGetStarts(

)

;

ResetStarts(

);

& GetStarts(

)

;

IsSetLens(

)

;

CanGetLens(

)

;

ResetLens(

);

& GetLens(

)

;

& SetLens(

);

IsSetStrands(

)

;

CanGetStrands(

)

;

ResetStrands(

);

& GetStrands(

)

;

IsSetScores(

)

;

CanGetScores(

)

;

ResetScores(

);

& GetScores(

)

;

Reset(

);

void SetScores(objects::CSeq_align &seq_align, objects::CScope &scope, const string &matrix_name="BLOSUM62")

Dense-seg: the densist packing for sequence alignments only.

Base class for all serializable objects.

static char UnassignedByte(void)

void ThrowUnassigned(TMemberIndex index) const

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_SEQALIGN_EXPORT

bool CanGetDim(void) const

Check if it is safe to call GetDim method.

bool IsSetLens(void) const

lengths in ids order within segs Check if a value has been assigned to Lens data member.

bool CanGetScores(void) const

Check if it is safe to call GetScores method.

bool IsSetDim(void) const

dimensionality Check if a value has been assigned to Dim data member.

TLens & SetLens(void)

Assign a value to Lens data member.

bool IsSetNumseg(void) const

number of segments here Check if a value has been assigned to Numseg data member.

bool IsSetStrands(void) const

Check if a value has been assigned to Strands data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

CDense_seg_Base & operator=(const CDense_seg_Base &)

bool IsSetScores(void) const

score for each seg Check if a value has been assigned to Scores data member.

vector< ENa_strand > TStrands

TDim & SetDim(void)

Assign a value to Dim data member.

const TLens & GetLens(void) const

Get the Lens member data.

TScores & SetScores(void)

Assign a value to Scores data member.

bool CanGetNumseg(void) const

Check if it is safe to call GetNumseg method.

vector< TSignedSeqPos > TStarts

bool CanGetIds(void) const

Check if it is safe to call GetIds method.

vector< CRef< CScore > > m_Scores

vector< CRef< CSeq_id > > TIds

vector< CRef< CSeq_id > > m_Ids

TDim GetDim(void) const

Get the Dim member data.

TNumseg & SetNumseg(void)

Assign a value to Numseg data member.

TStarts & SetStarts(void)

Assign a value to Starts data member.

void ResetNumseg(void)

Reset Numseg data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

bool IsSetStarts(void) const

start OFFSETS in ids order within segs Check if a value has been assigned to Starts data member.

Tparent::CMemberIndex< E_memberIndex, 8 > TmemberIndex

const TIds & GetIds(void) const

Get the Ids member data.

bool CanGetStrands(void) const

Check if it is safe to call GetStrands method.

CDense_seg_Base(const CDense_seg_Base &)

vector< CRef< CScore > > TScores

bool CanGetStarts(void) const

Check if it is safe to call GetStarts method.

TNumseg GetNumseg(void) const

Get the Numseg member data.

vector< TSignedSeqPos > m_Starts

TIds & SetIds(void)

Assign a value to Ids data member.

DECLARE_INTERNAL_TYPE_INFO()

const TScores & GetScores(void) const

Get the Scores member data.

void ResetDim(void)

Reset Dim data member.

vector< ENa_strand > m_Strands

const TStrands & GetStrands(void) const

Get the Strands member data.

bool CanGetLens(void) const

Check if it is safe to call GetLens method.

void SetDefaultDim(void)

Assign default value to Dim data member.

bool IsSetIds(void) const

sequences in order Check if a value has been assigned to Ids data member.

const GenericPointer< typename T::ValueType > T2 value

static bool GetIds(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

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