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NCBI C++ ToolKit: src/algo/sequence/util.cpp Source File

bioseq->

().push_back(

);

loc.GetLabel( &title_str );

bioseq->

().Set().push_back( title );

(handle.

()) {

process_whole =

;

process_whole =

;

}

(loc.IsInt()) {

process_whole =

;

inst.

().SetIupacaa().Set().swap(seq_string);

inst.

().SetIupacna().Set().swap(seq_string);

total = sequence.

() - word_size;

(

= word_size;

< sequence.

(); ++

) {

TCounts::iterator it =

(TCounts, it, counts) {

entropy += it->second *

(it->second);

denom = pow(4, word_size);

denom =

(denom, total);

entropy = -entropy /

(denom);

max<double>(0.0, entropy);

total = double(sequence.

() - word_size + 1);

(

= word_size;

<= sequence.

(); ++

) {

TCounts::iterator it =

(TCounts, it, counts) {

entropy += it->second *

(it->second);

denom = pow(20, word_size);

denom =

(denom, total);

entropy = -entropy /

(denom);

max<double>(0.0, entropy);

: m_WordSize(word_size)

, m_NumWords(sequence_size - word_size)

, m_Denom(

(

((double)m_NumWords,

pow(4.0, (

)word_size))))

(word_size > sequence_size) {

);

);

max<double>(0.0, entropy);

);

(

pos = 0; pos < sequence.

()-window; ++pos) {

--counts[removed_word];

(entropy_value < 0) {

entropy_value = -fraction *

(fraction) /

;

entropy_value;

max<double>(0.0, entropy);

double ComputeNormalizedEntropy(const CTempString &sequence, size_t word_size)

Compute the normalized Shannon entropy for a sequence of IUPACna bases.

double ComputeNormalizedProteinEntropy(const CTempString &sequence, size_t word_size)

Sequence Entropy Calculation.

CRef< objects::CBioseq > SeqLocToBioseq(const objects::CSeq_loc &loc, objects::CScope &scope)

CDelta_seq & AddLiteral(TSeqPos len)

add a literal segment at the end this variant adds a gap literal

vector< CTempString > m_Words

double ComputeEntropy(const CTempString &sequence)

vector< double > m_EntropyValues

double x_Entropy(size_t count)

CEntropyCalculator(size_t sequence_size, size_t word_size)

vector< double > ComputeSlidingWindowEntropy(const CTempString &sequence)

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

static TSeqPos Pack(CSeq_data *in_seq, TSeqPos uLength=ncbi::numeric_limits< TSeqPos >::max())

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

container_type::iterator iterator

iterator_bool insert(const value_type &val)

container_type::value_type value_type

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_ASSERT(expr, mess)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

string GetLabel(const CSeq_id &id)

TRange GetRange(void) const

Get the range.

ENa_strand GetStrand(void) const

TSeqPos GetBioseqLength(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

bool IsProtein(void) const

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

size_type size(void) const

Return the length of the represented array.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

ENa_strand

strand of nucleic acid

TId & SetId(void)

Assign a value to Id data member.

TTitle & SetTitle(void)

Select the variant.

void SetExt(TExt &value)

Assign a value to Ext data member.

void SetInst(TInst &value)

Assign a value to Inst data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

void SetRepr(TRepr value)

Assign a value to Repr data member.

void SetLength(TLength value)

Assign a value to Length data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

void SetMol(TMol value)

Assign a value to Mol data member.

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_raw

continuous sequence

@ eMol_na

just a nucleic acid

unsigned int

A callback function used to compare two keys in a database.

constexpr auto sort(_Init &&init)

double value_type

The numeric datatype used by the parser.

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