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

vector< CRef< CSeq_id > >

;

vector< TSeqPos >

;

vector< CRef< CScore > >

;

IsSetDim(

)

;

CanGetDim(

)

;

ResetDim(

);

SetDefaultDim(

);

GetDim(

)

;

& SetDim(

);

IsSetNumseg(

)

;

CanGetNumseg(

)

;

ResetNumseg(

);

GetNumseg(

)

;

IsSetIds(

)

;

CanGetIds(

)

;

ResetIds(

);

& SetIds(

);

IsSetStarts(

)

;

CanGetStarts(

)

;

ResetStarts(

);

& GetStarts(

)

;

IsSetPresent(

)

;

CanGetPresent(

)

;

ResetPresent(

);

& GetPresent(

)

;

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")

for (multiway) global or partial alignments

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

vector< CRef< CSeq_id > > TIds

TNumseg & SetNumseg(void)

Assign a value to Numseg data member.

vector< TSeqPos > TStarts

vector< CRef< CSeq_id > > m_Ids

vector< ENa_strand > TStrands

DECLARE_INTERNAL_TYPE_INFO()

TPresent & SetPresent(void)

Assign a value to Present data member.

vector< CRef< CScore > > m_Scores

const TStarts & GetStarts(void) const

Get the Starts member data.

bool IsSetNumseg(void) const

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

TStarts & SetStarts(void)

Assign a value to Starts data member.

vector< CRef< CScore > > TScores

TScores & SetScores(void)

Assign a value to Scores data member.

CPacked_seg_Base & operator=(const CPacked_seg_Base &)

bool IsSetScores(void) const

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

TNumseg GetNumseg(void) const

Get the Numseg member data.

bool CanGetDim(void) const

Check if it is safe to call GetDim method.

Tparent::CMemberIndex< E_memberIndex, 9 > TmemberIndex

void ResetDim(void)

Reset Dim data member.

bool IsSetLens(void) const

length of each segment Check if a value has been assigned to Lens data member.

vector< ENa_strand > m_Strands

bool IsSetStrands(void) const

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

const TScores & GetScores(void) const

Get the Scores member data.

TIds & SetIds(void)

Assign a value to Ids data member.

bool CanGetScores(void) const

Check if it is safe to call GetScores method.

const TLens & GetLens(void) const

Get the Lens member data.

const TIds & GetIds(void) const

Get the Ids member data.

const TPresent & GetPresent(void) const

Get the Present member data.

bool CanGetStarts(void) const

Check if it is safe to call GetStarts method.

TDim & SetDim(void)

Assign a value to Dim data member.

bool IsSetDim(void) const

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

const TStrands & GetStrands(void) const

Get the Strands member data.

void SetDefaultDim(void)

Assign default value to Dim data member.

bool CanGetIds(void) const

Check if it is safe to call GetIds method.

bool CanGetStrands(void) const

Check if it is safe to call GetStrands method.

bool IsSetIds(void) const

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

vector< TSeqPos > m_Starts

CPacked_seg_Base(const CPacked_seg_Base &)

void ResetNumseg(void)

Reset Numseg data member.

bool IsSetPresent(void) const

Boolean if each sequence present or absent in each segment Check if a value has been assigned to Pres...

TDim GetDim(void) const

Get the Dim member data.

bool IsSetStarts(void) const

start OFFSETS in ids order for whole alignment Check if a value has been assigned to Starts data memb...

TStrands & SetStrands(void)

Assign a value to Strands data member.

bool CanGetPresent(void) const

Check if it is safe to call GetPresent method.

bool CanGetNumseg(void) const

Check if it is safe to call GetNumseg method.

bool CanGetLens(void) const

Check if it is safe to call GetLens method.

TLens & SetLens(void)

Assign a value to Lens 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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