Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/align__cleanup_8cpp_source.html below:

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

aln_container.

(multiple);

count_accepted = 0;

<<

<<

<< e.GetMsg());

(count_accepted != aln_container.

()) {

(count_accepted == 0) {

);

<< count_accepted <<

<< aln_container.

()

<<

);

(*iter)->GetPairwiseAlns()) {

aln->

().SetDenseg(*ds);

pairwise.push_back(aln);

->Assign(*seg.

()[0]);

new_seg->

().push_back(

);

new_seg->

().push_back(

);

((start_0 < 0 && start_1 < 0)

|| (segs==0 && (start_0 < 0 || start_1 < 0))

new_seg->

().push_back(start_0);

new_seg->

().push_back(start_1);

(segs && (new_seg->

()[segs*2-2] < 0 || new_seg->

()[segs*2-1] < 0)) {

new_seg->

().resize(segs);

align->

().SetDenseg(*new_seg);

pairwise.push_back(align);

<<

<<

<< e.

());

: m_SortByScore(

)

, m_PreserveRows(

)

, m_FillUnaligned(

)

, m_SortByScore(

)

, m_PreserveRows(

)

, m_FillUnaligned(

)

(aligns_in.begin(), aligns_in.end(), back_inserter(const_aligns_in));

(const_aligns_in, aligns_out,

, output_seg_type);

= aligns_in.size();

aligns_in.front()->GetSegs().Which() == output_seg_type) {

align->

(*aligns_in.front());

aligns_out.push_back(align);

count_invalid = 0;

aln_container.

(*aln);

<<

<<

<< e.

());

+=

;

(count_invalid ==

) {

count_accepted = 0;

<<

<<

<< e.GetMsg());

(count_accepted != aln_container.

()) {

(count_accepted == 0) {

);

<< count_accepted <<

<< aln_container.

()

<<

);

(ids.

() == 1) {

preserve_rows =

;

(anchored_aln_vec, out_anchored_aln, opts);

vector< CRef<CSeq_align> > ds_aligns;

vector< CRef<CSeq_align> > ds_aligns;

ds_aligns, output_seg_type);

aligns_out.push_back(*it);

(*align_iter)->SetSegs().SetDenseg(*ds);

);

TAlignments align_map;

all_pairwise =

;

all_pairwise =

;

( ; id_iter; ++id_iter) {

align_map[id_set].push_back(al);

(TAlignments, iter, align_map) {

list< CConstRef<CSeq_align> >

;

list<TAlignList> alignments;

neg_strand.push_back(*it);

pos_strand.push_back(*it);

pos_strand.insert(pos_strand.end(),

neg_strand.begin(), neg_strand.end());

( ; it != iter->second.end(); ++it) {

pos_strand.push_back(*it);

(list<TAlignList>, it, alignments) {

mix.

(merge_flags);

);

);

list< CRef<CSeq_align> > aligns;

aligns.push_back(new_align);

((*align)->GetSegs().IsDenseg()) {

(*align)->SetSegs().SetDenseg().Compact();

aligns_out.push_back(*align);

( !

.empty() ) {

static CRef< CScope > m_Scope

void BuildAln(TAnchoredAlnVec &in_alns, CAnchoredAln &out_aln, const CAlnUserOptions &options, TAlnSeqIdIRef pseudo_seqid=TAlnSeqIdIRef())

Build anchored alignment from a set of alignmnets.

void CreateAnchoredAlnVec(_TAlnStats &aln_stats, TAnchoredAlnVec &out_vec, const CAlnUserOptions &options)

Create anchored alignment from each seq-align in the stats.

void CreateSeqAlignFromEachPairwiseAln(const CAnchoredAln::TPairwiseAlnVector pairwises, CAnchoredAln::TDim anchor, vector< CRef< CSeq_align > > &out_seqaligns, CSeq_align::TSegs::E_Choice choice, CScope *scope=NULL)

Create seq-align from each of the pairwise alignments vs the selected anchor row.

CRef< CSeq_align > CreateSeqAlignFromAnchoredAln(const CAnchoredAln &anchored_aln, CSeq_align::TSegs::E_Choice choice, CScope *scope=NULL)

Convert CAnchoredAln to seq-align of the selected type.

CRef< CDense_seg > CreateDensegFromPairwiseAln(const CPairwiseAln &pairwise_aln, CScope *scope=NULL)

set< CRef< CSeq_id >, PPtrLess< CRef< CSeq_id > >> TIdSet

void x_Cleanup_AlignVec(const TConstAligns &aligns_in, TAligns &aligns_out, CSeq_align::TSegs::E_Choice output_seg_type)

void Cleanup(const TAligns &aligns_in, TAligns &aligns_out, EMode mode=eDefault, CSeq_align::TSegs::E_Choice output_seg_type=CSeq_align::TSegs::e_Denseg)

list< CConstRef< CSeq_align > > TConstAligns

list< CRef< CSeq_align > > TAligns

static void CreatePairwiseFromMultiple(const CSeq_align &multiple, TAligns &pairwise)

void x_Cleanup_AnchoredAln(const TConstAligns &aligns_in, TAligns &aligns_out, CSeq_align::TSegs::E_Choice output_seg_type)

const_iterator insert(const CSeq_align &seq_align)

Insert new CSeq_align into the list.

size_type size(void) const

Container mapping seq-aligns to vectors of participating seq-ids.

void push_back(const CSeq_align &aln)

Adding an alignment.

void Add(const CDense_seg &ds, TAddFlags flags=0)

void Merge(TMergeFlags flags=0)

const CSeq_align & GetSeqAlign(void) const

const CDense_seg & GetDenseg(void) const

Helper class which collects seq-align statistics: seq-ids participating in alignments and rows,...

_TAlnIdVec::TIdVec TIdVec

Vector of ids used in all alignments.

const TIdVec & GetIdVec(void) const

Get vector of all ids from all alignments.

Options for different alignment manager operations.

@ eMergeAllSeqs

Merge all sequences (greedy algo).

@ ePreserveRows

Preserve all rows as they were in the input (e.g.

@ eBothDirections

No filtering: use both direct and reverse sequences.

void SetMergeFlags(TMergeFlags flags, bool set)

Set/clear merge flags.

@ fUseAnchorAsAlnSeq

Use the anchor sequence as the alignment sequence.

@ fSkipSortByScore

In greedy algos, skip sorting input alignments by score thus allowing for user-defined sort order.

@ fTruncateOverlaps

Truncate overlapping ranges.

Query-anchored alignment can be 2 or multi-dimentional.

const TPairwiseAlnVector & GetPairwiseAlns(void) const

The vector of pairwise alns.

vector< CRef< CPairwiseAln > > TPairwiseAlnVector

TDim GetAnchorRow(void) const

Which is the anchor row?

CRef< CDense_seg > FillUnaligned() const

Create a new dense-seg with added all unaligned pieces (implicit inserts), if any,...

void Validate(bool full_test=false) const

Template class for iteration on objects of class C (non-medifiable version)

iterator_bool insert(const value_type &val)

list< CRef< CSeq_align > > TAlignList

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define ERR_POST(message)

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

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

const TDenseg & GetDenseg(void) const

Get the variant data.

TLens & SetLens(void)

Assign a value to Lens data member.

bool IsSetStrands(void) const

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

E_Choice

Choice variants.

const TStarts & GetStarts(void) const

Get the Starts member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

const TLens & GetLens(void) const

Get the Lens member data.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetType(TType value)

Assign a value to Type data member.

TDim GetDim(void) const

Get the Dim member data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

TType GetType(void) const

Get the Type member data.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TIds & GetIds(void) const

Get the Ids member data.

TNumseg GetNumseg(void) const

Get the Numseg member data.

TIds & SetIds(void)

Assign a value to Ids data member.

const TStrands & GetStrands(void) const

Get the Strands member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

@ eType_partial

mapping pieces together

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

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

vector< CRef< CAnchoredAln > > TAnchoredAlnVec

Collection of anchored alignments.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4