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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gap__analysis_8cpp_source.html below:

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

eGapType_UnknownBases:

;

;

max_resolve_count)

( ; bioseq_ci; ++bioseq_ci ) {

(*bioseq_ci, add_flags, fFlags, max_resolve_count);

max_resolve_count)

end_of_last_segment = 0;

all_segments_and_in_order =

;

( ; seqmap_ci; ++seqmap_ci ) {

( seqmap_ci.

() != end_of_last_segment ) {

all_segments_and_in_order =

;

<<

(seg_type) );

( end_of_last_segment != bioseq_len ) {

all_segments_and_in_order =

;

( ! all_segments_and_in_order ) {

<<

(iGapStartPos < iGapEndPosExclusive);

((iGapEndPosExclusive - iGapStartPos) == iGapLength);

( iGapStartPos == 0 ||

iGapEndPosExclusive == iBioseqLength )

s <<

<<

<< one_gap_len_summary.

<<

<< one_gap_len_summary.

<<

<< one_gap_len_summary.

s <<

<< endl;

s << **summ_it << endl;

iGapLength = gap_map_iter->first;

m_mapGapLengthToNumAppearances.

(iGapLength);

( find_iter != m_mapGapLengthToNumAppearances.

() );

num_gaps = find_iter->second;

stable_sort(pAnswer->begin(), pAnswer->end(), sorter );

find_it->second;

find_it->second;

: sort_gap_length(sort_gap_length_arg), sort_dir(sort_dir_arg)

(sort_gap_length) {

(sort_gap_length) );

find_iter->second->GetData();

pair<TGapTypeToHistogramBinner::iterator, bool> TInsertResult;

make_pair(eGapType, new_value));

(insert_result.second);

insert_result.first->second->GetData();

(begin_pos + seqmap_ci.

() - 1)));

size_of_curr_gap = 0;

( ; seq_vec_ci; ++seq_vec_ci ) {

start_pos_of_curr_gap = (begin_pos + seq_vec_ci.

());

}

( size_of_curr_gap > 0 ) {

start_pos_of_curr_gap, (begin_pos + seq_vec_ci.

()),

size_of_curr_gap = 0;

( size_of_curr_gap > 0 ) {

start_pos_of_curr_gap, (begin_pos + seq_vec_ci.

()),

This class does comparison of SOneGapLengthSummary, and it is adjustable which field to sort on and w...

bool operator()(const CConstRef< SOneGapLengthSummary > &lhs, const CConstRef< SOneGapLengthSummary > &rhs) const

less-than

SOneGapLengthSummarySorter(ESortGapLength sort_gap_length_arg, ESortDir sort_dir_arg)

Give this gaps, or handles containing gaps and then you can get statistics on those gaps.

const TMapGapLengthToSeqIds & GetGapLengthSeqIds(EGapType eGapType) const

Returns a map of gap_length to the set of all seq-ids that contain at least one gap of that length.

@ fFlag_IncludeEndGaps

include gaps that are at the very start or very end of their sequence.

void AddSeqEntryGaps(const CSeq_entry_Handle &entry_h, CSeq_inst::EMol filter=CSeq_inst::eMol_not_set, CBioseq_CI::EBioseqLevelFlag level=CBioseq_CI::eLevel_All, TAddFlag add_flags=fAddFlag_All, TFlag fFlags=0, size_t max_resolve_count=kMax_Int)

Calls AddGap for each gap anywhere under the given CSeq_entry.

void AddGap(EGapType eGapType, TSeqIdConstRef pSeqId, TGapLength iGapLength, TSeqPos iBioseqLength, TSeqPos iGapStartPos, TSeqPos iGapEndPosExclusive, TFlag fFlags=0)

AddSeqEntryGaps is more convenient, but if you want finer-grained control you can use this function t...

vector< CConstRef< SOneGapLengthSummary > > TVectorGapLengthSummary

This holds the information for every encountered gap length.

@ fAddFlag_IncludeSeqGaps

include seq-gaps

@ fAddFlag_IncludeUnknownBases

include runs of N for nucs or X for prots.

ESortGapLength

Use this to control what results are sorted on.

@ eSortGapLength_NumGaps

Sort gap lengths by number of times they appear anywhere.

@ eSortGapLength_Length

Sort by gap length.

@ eSortGapLength_NumSeqs

Sort gap lengths by number of sequences that contain one or more gaps of the given length.

AutoPtr< TVectorGapLengthSummary > GetGapLengthSummary(EGapType eGapType, ESortGapLength eSortGapLength=eSortGapLength_Length, ESortDir eSortDir=eSortDir_Ascending) const

This gives summary information about every gap-length encountered so far.

Uint8 TGapLength

Use typedef in case we change the underlying.

void AddBioseqGaps(const CBioseq_Handle &bioseq_h, TAddFlag add_flags=fAddFlag_All, TFlag fFlags=0, size_t max_resolve_count=kMax_Int)

Similar to AddSeqEntryGaps, but for one Bioseq.

const TMapGapLengthToNumAppearances & GetGapLengthToNumAppearances(EGapType eGapType) const

Returns a map of gap_length to the number of times such a gap appears.

TGapTypeToHistogramBinner m_gapTypeToHistogramBinner

void clear(void)

Start analysis over again.

CHistogramBinning & x_GetOrCreateHistogramBinner(EGapType eGapType)

Use this instead of operator[] because the default constructor of TRefHistogramBinning is an empty re...

AutoPtr< CHistogramBinning::TListOfBins > GetGapHistogram(EGapType eGapType, Uint8 num_bins=0, CHistogramBinning::EHistAlgo eHistAlgo=CHistogramBinning::eHistAlgo_Default)

This returns a histogram of gap length vs.

TGapTypeAndLengthToNumAppearances m_gapTypeAndLengthToNumAppearances

void x_AddGapsFromBases(const CSeqMap_CI &seqmap_ci, TSeqIdConstRef bioseq_seq_id, TSeqPos iBioseqLength, TFlag fFlags)

Add gaps based on unknown bases which are letters.

TGapTypeAndLengthToSeqIds m_gapTypeAndLengthToSeqIds

For each gap-type and gap length, this holds all the seq-ids which have one or more gaps of that leng...

ESortDir

This controls the direction of sort order for functions that also take ESortGapLength.

Given a set of integer data, this will bin the data for use in histograms.

void SetNumBins(Uint8 num_bins)

This should not normally be needed, since number of bins is usually picked in the constructor.

TListOfBins * CalcHistogram(EHistAlgo eHistAlgo=eHistAlgo_Default) const

Call this after data is loaded via AddNumber, etc.

void AddNumber(TValue the_number, Uint8 num_appearances=1)

Give this histogram another number to bin.

EHistAlgo

Pick which binning algorithm to use when generating the histogram.

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

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

ostream & operator<<(ostream &s, const CGapAnalysis::SOneGapLengthSummary &one_gap_len_summary)

Analyzes gaps and produces various statistics.

static const char kGapChar('-')

The representation of a gap in ASCII format.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_USER_THROW_FMT(message)

Throw a "user exception" with message processed as output to ostream.

void Warning(CExceptionArgs_Base &args)

C * SerialClone(const C &src)

Create on heap a clone of the source object.

const string AsFastaString(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.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

SSeqMapSelector & SetResolveCount(size_t res_cnt)

Set max depth of resolving seq-map.

EBioseqLevelFlag

Class of bioseqs to iterate.

TSeqPos GetPos(void) const

CScope * GetScope(void) const

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

CSeqMap::ESegmentType GetType(void) const

TSeqPos GetPosition(void) const

return position of current segment in sequence

TSeqPos GetLength(void) const

return length of current segment

const_iterator begin(void) const

TResidue GetGapChar(ECaseConversion case_cvt=eCaseConversion_none) const

Return gap symbol corresponding to the selected coding.

@ eSeqData

real sequence data

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

EMol

molecule class in living organism

This holds information about a given gap_length.

Uint8 num_gaps

number of times gaps of this length appear anywhere

Uint8 num_seqs

number of sequences which contain one or more gaps of the given length

Selector used in CSeqMap methods returning iterators.

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