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NCBI C++ ToolKit: include/gui/objutils/density_map.hpp Source File

<

Type>

<

Type>

<

Type>

left > right ? left : right;

<

Type>

left < right ? left : right;

<

CntType>

<

CntType>

(GetPosition() * m_Window + 0.5) + m_Start;

<

CntType>

((GetPosition() + GetRunLength()) * m_Window + 0.5) + m_Start;

<

CntType>

(GetRunLength() * m_Window + 0.5);

<

CntType>

(m_Pos >= 0 && m_Pos < m_Bins.size()) {

CntType this_value = m_Bins[m_Pos];

< m_Bins.size() && m_Bins[

] == this_value;

<

CntType>

m_Pos += m_RunLength;

m_RunLength = x_CalcRunLength();

<

CntType>

container_type::iterator

;

(

objects::CBioseq_Handle& handle,

window = 1,

CntType score = 1,

expand =

);

objects::SAnnotSelector sel);

objects::SAnnotSelector sel);

objects::CSeq_annot& seq_annot);

objects::SAnnotSelector sel,

vector<TSeqPos>& density);

<

CntType>

: m_Range(start, stop)

, m_Bins(x_CalcNbins(), def)

, m_AccumFunc(func ? func : new

<CntType>)

<

CntType>

: m_Range(0, handle.GetSeqVector().

())

, m_Bins(x_CalcNbins(), def)

, m_AccumFunc(func ? func : new

<CntType>)

<

CntType>

: m_Range(

.m_Range)

, m_Window(

.m_Window)

, m_DefVal(

.m_DefVal)

, m_Bins(

.m_Bins)

, m_AccumFunc(

.m_AccumFunc->clone())

<

CntType>

m_Range =

.m_Range;

m_Window =

.m_Window;

m_DefVal =

.m_DefVal;

m_Bins =

.m_Bins;

m_AccumFunc.reset(

.m_AccumFunc->clone());

<

CntType>

m_Bins.resize(x_CalcNbins(), m_DefVal);

<

CntType>

ExtendTo( range.

());

usable_range(m_Range.IntersectionWith(range));

(usable_range.

()) {

m_Max =

(m_Max, score);

m_Min =

(m_Min, score);

begin_bin = x_BinN(usable_range.

());

end_bin = begin_bin;

(m_Window > 1.0) {

end_bin = x_BinN(usable_range.

()) + 1;

end_bin = x_BinN(usable_range.

());

end_bin =

(end_bin, m_Bins.size());

(

= begin_bin;

< end_bin ; ++

) {

CntType& new_val = m_Bins[

];

new_val = (*m_AccumFunc)(new_val, score);

m_Max =

(m_Max, new_val);

m_Min =

(m_Min, new_val);

<

CntType>

CntType score,

expand)

ExtendTo( ranges.

());

(ranges.

()) {

m_Max =

(m_Max, score);

m_Min =

(m_Min, score);

previous_end_bin = 0;

begin_bin = x_BinN(range_it->GetFrom());

end_bin = begin_bin;

(m_Window > 1.0) {

end_bin = x_BinN(range_it->GetTo()) + 1;

end_bin = x_BinN(range_it->GetToOpen());

begin_bin =

(begin_bin, previous_end_bin);

end_bin =

(end_bin, m_Bins.size());

previous_end_bin = end_bin;

(

= begin_bin;

< end_bin ; ++

) {

CntType& new_val = m_Bins[

];

new_val = (*m_AccumFunc)(new_val, score);

m_Max =

(m_Max, new_val);

m_Min =

(m_Min, new_val);

<

CntType>

( objects::CSeq_loc_CI it(loc); it; ++it) {

ranges += it.GetRange();

AddRanges(ranges, 1,

);

<

CntType>

AddLocation(feature.GetLocation());

<

CntType>

objects::CBioseq_Handle& handle,

objects::SAnnotSelector sel)

sel.SetSortOrder(objects::SAnnotSelector::eSortOrder_None);

objects::CFeat_CI feat_iter(handle.GetScope(), *loc, sel);

(feat_iter.GetSize() == 0) {

(; feat_iter; ++feat_iter) {

objects::CMappedFeat feat = *feat_iter;

AddLocation(feat.GetLocation());

<

CntType>

objects::CBioseq_Handle& handle,

objects::SAnnotSelector sel)

objects::CAlign_CI align_iter(handle, range, sel);

(

ai = 0; align_iter; ++align_iter, ++ai) {

objects::CSeq_align& align = *align_iter;

(! align.CanGetDim()) {

(

<< ai);

dim = align.GetDim();

(

<< ai);

(align.GetSegs().IsStd()) {

(ai <<

);

= align.CreateDensegFromStdseg();

aln_map =

objects::CAlnMap( ds_align->GetSegs().GetDenseg());

}

(align.GetSegs().IsDenseg()) {

aln_map =

objects::CAlnMap(align.GetSegs().GetDenseg());

(ai <<

);

all_ids =

;

all_ids += aln_map->GetSeqId(di).AsFastaString() +

;

range_final(aln_map->GetSeqStart(0), aln_map->GetSeqStop(0));

AddRange(range_final, 1,

);

<

CntType>

objects::CBioseq_Handle& handle,

objects::CSeq_annot& seq_annot)

objects::SAnnotSelector sel;

objects::CSeq_annot_Handle sah

= handle.GetScope().GetSeq_annotHandle(seq_annot);

sel.SetLimitSeqAnnot(sah)

.SetSortOrder(objects::SAnnotSelector::eSortOrder_None);

objects::CAlign_CI align_iter(handle, range, sel);

objects::CAlnMix mix(handle.GetScope());

(

ai = 0; align_iter; ++align_iter, ++ai) {

objects::CSeq_align& align = *align_iter;

(! align.CanGetDim() || align.GetDim() != 2) {

(align.GetSegs().IsStd()) {

align.CreateDensegFromStdseg();

objects::CAlnMap(ds_align->GetSegs().GetDenseg());

all_ids =

;

di < aln_map->GetNumRows(); ++di) {

all_ids += aln_map->GetSeqId(di).AsFastaString() +

;

}

(

objects::CSeqalignException&

) {

}

(align.GetSegs().IsDenseg()) {

aln_map =

objects::CAlnMap(mix.GetDenseg());

(aln_map->GetNumSegs() < 2)

(ai <<

);

objects::CAlnMap::TNumrow

= 0;

(

= 0;

!= aln_map->GetNumRows(); ++

) {

( handle.IsSynonym(aln_map->GetSeqId(

)) ) {

aln_map->SetAnchor(

);

(

== aln_map->GetNumRows()) {

<

CntType>

objects::SAnnotSelector sel,

vector<TSeqPos>& density)

(stop == start && stop == 0) {

objects::CSeqVector vec = handle.GetSeqVector();

objects::CFeat_CI feat_iter(handle.GetScope(),

*handle.GetRangeSeq_loc(start, stop),

(feat_iter.GetSize() == 0) {

bins = (stop - start) / window;

(bins * window < stop - start) {

density.resize(bins, 0);

deque<objects::CMappedFeat> feats;

bin_start = start + bin_count * window;

bin_stop = bin_start + window;

objects::CMappedFeat feat = *feat_iter;

range = feat.GetLocation().GetTotalRange();

(range.

() < bin_stop) {

feats.push_back(feat);

range = feat.GetLocation().GetTotalRange();

(feats.size()) {

objects::CMappedFeat& feat = feats.front();

range = feat.GetLocation().GetTotalRange();

(range.

() < bin_start) {

*bin_iter = feats.size();

max_val =

(*bin_iter, max_val);

Run iterator. iterate through runs of equal values in the bins.

class CDensityMap generates a low-resolution view of a set of features.

position_type GetTo() const

TThisType & IntersectWith(const TRange &r)

Include a standard set of the NCBI C++ Toolkit most basic headers.

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

virtual ~binary_functor()

void ExtendTo(TSeqPos stop)

extend our density map to cover the sequence position stop.

virtual Type operator()(const Type &left, const Type &right) const

void SetMin(const CntType &min)

CntType AddAlignments(const objects::CBioseq_Handle &handle, const objects::CSeq_annot &seq_annot)

All alignments in a given annotation on this bioseq within the range of this.

const accum_functor * GetAccum() const

CntType m_Min

Smallest count in a bin.

CntType m_DefVal

Default value.

vector< size_t > TDataPoints

CntType m_Max

maximum Count accumulated in the bins so far.

const_iterator end() const

TSeqPos GetSeqPosition() const

Type operator()(const Type &left, const Type &right) const

position_type m_RunLength

virtual binary_functor< Type > * clone() const

container_type::const_iterator const_iterator

CntType operator[](typename container_type::size_type n) const

TSeqRange m_Range

closed range on a sequence this covers.

const_iterator begin() const

void SetMax(const CntType &max)

container_type::iterator iterator

runlen_iterator RunLenBegin() const

size_t x_BinN(TSeqPos p)

convert from sequence coords to a bin number.

static TSeqPos GetDensityMap(const objects::CBioseq_Handle &handle, TSeqPos start, TSeqPos stop, TSeqPos window, objects::SAnnotSelector sel, vector< TSeqPos > &density)

OLD static method.

bool operator==(const CDenMapRunIterator< CntType > &rhs) const

TSeqPos GetSeqRunEndPosition() const

CntType AddAlignments(const objects::CBioseq_Handle &handle, objects::SAnnotSelector sel)

All alignments on this bioseq selected by sel in the range of this.

virtual void AddRanges(CRangeCollection< TSeqPos > ranges, CntType score=1, bool expand=false)

position_type GetRunLength() const

CDenMapRunIterator(position_type here, const container_type &bins, TSeqPos start, double window)

double m_Window

coordinates per bin.

const container_type & m_Bins

size_t x_CalcNbins()

given the range and window size, how many bins should there be?

CDensityMap< CntType > & operator=(const CDensityMap< CntType > &map)

CDenMapRunIterator< CntType > runlen_iterator

CDensityMap(TSeqPos start=0, TSeqPos stop=0, double window=1, accum_functor *func=NULL, CntType def=(CntType) 0)

vector< CntType > container_type

virtual binary_functor< Type > * clone() const =0

virtual void AddRange(TSeqRange range, CntType score=1, bool expand=false)

runlen_iterator RunLenIterator(typename container_type::size_type n) const

CntType GetDefVal() const

CDensityMap(const CDensityMap< CntType > &map)

CntType & operator[](typename container_type::size_type n)

CntType AddLocation(const objects::CSeq_loc &loc)

virtual Type operator()(const Type &left, const Type &right) const

CntType AddFeature(const objects::CSeq_feat &feature)

vector< CntType > container_type

position_type x_CalcRunLength() const

CDensityMap(const objects::CBioseq_Handle &handle, double window=1, accum_functor *func=NULL, CntType def=(CntType) 0)

CntType AddFeatures(const objects::CBioseq_Handle &handle, objects::SAnnotSelector sel)

All features on this bioseq selected by sel in the range of this.

container_type m_Bins

Where we actually keep the accumulated counts/scores/whatever.

TSeqPos GetSeqRunLength() const

TSeqRange GetRange() const

virtual binary_functor< Type > * clone() const

DECLARE_OPERATOR_BOOL(Valid())

unique_ptr< accum_functor > m_AccumFunc

position_type GetPosition() const

binary_functor< CntType > accum_functor

virtual Type operator()(const Type &left, const Type &right) const =0

virtual binary_functor< Type > * clone() const

container_type::size_type position_type

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

position_type GetToOpen(void) const

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const struct ncbi::grid::netcache::search::fields::SIZE size

#define row(bind, expected)

TEMPLATE binary functor base struct.

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