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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnvec__multi__ds_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/aln_multiple/alnvec_multi_ds.cpp Source File

(bio_handle.GetScope().GetObjectManager())

.SetValue(s, TlsValCleanup<TScopeRef>, 0);

TaxId =

(fExtOrgLookup);

list<CRef<CSeqdesc> > seqdesclist = bio_handle.

().

();

(

seqdesc : seqdesclist) {

(seqdesc->IsTitle()) {

(!

&& fExtOrgLookup) {

(biosrc.IsSetTaxname()) {

taxonomy = biosrc.GetTaxname();

&org = biosrc.GetOrg();

(taxonomy.empty())

m_CreateConsensus(

),

m_isDataReadSync(

)

(

<<

<<

<< e.

());

m_ConsRowIndex;

vector< CConstRef<CSeq_align> > aligns;

(annot.GetData().IsAlign() ) {

aligns.emplace_back(*it);

(aligns, sync, select_anchor);

vector< CConstRef<CSeq_align> > aligns;

aligns.emplace_back(&*it);

(aligns, sync, select_anchor);

sync,

select_anchor)

(

<< job_id);

progressSoFar->GetText(), progressSoFar->GetNormDone());

(!

->IsConsensus())

= prg->GetText();

(

->GetDenseg().IsSetWidths()) {

}

(exception& e) {

try_reverse_dir)

->GetAlnPosFromSeqPos(for_row, aln_pos,

try_reverse_dir)

(seq_start > seq_stop) {

(seq_start, seq_stop);

from =

(seq_start, it->GetFrom());

(aln_from > aln_to) {

(aln_from, aln_to);

aln_from =

(aln_start, it->GetFrom());

fill_n(base_count, numBases, 0);

(

= 0;

< rows.size(); ++

) {

(col >= rows[

].

())

fill_n(base_count, numBases, 0);

(

= 0;

< rows.size(); ++

) {

(0 <= pos && pos < numBases)

isNucleotide =

->GetBioseqHandle(0).IsNucleotide();

numBases = isNucleotide ? 4 : 26;

num_rows =

->GetNumRows();

num_segs =

->GetNumSegs();

gap_seg_thresh = num_rows - num_rows / 2;

(

j = 0; j < num_segs; ++j) {

seg_len =

->GetLen(j, 0);

(

= 0;

< num_rows; ++

) {

(

->GetStart(

, j, 0) == -1) {

(gap_count > gap_seg_thresh) {

consens[j].resize(seg_len);

(

= 0;

< seg_len; ++

)

consens[j][

] =

->GetGapChar(0);

((num_rows - gap_count) * 7 + 5) / 10;

consens[j].resize(seg_len);

vector<string> segs(num_rows);

->RetrieveSegmentSequences(j, segs);

(

= 0;

< seg_len; ++

) {

(

k = 0; k < numBases; ++k) {

(rev_map.count(rev_map.begin()->first) == 1 &&

rev_map.begin()->first >= base_thresh) {

consens[j][

] = isNucleotide ?

->ToIupac(rev_map.begin()->second) :

(rev_map.begin()->second +

);

c = 0x00;

TRevMap::iterator curr = rev_map.begin();

TRevMap::iterator

= rev_map.begin();

curr != rev_map.end() &&

(freq < base_thresh ||

->first == curr->first);

cur_char = curr->second +

;

:

:

c = (cur_char ==

|| cur_char ==

) ?

:

;

:

:

c = (cur_char ==

|| cur_char ==

) ?

:

;

:

:

c = (cur_char ==

|| cur_char ==

) ?

:

;

consens[j][

] = isNucleotide ?

:

;

consens[j][

] = isNucleotide ?

->ToIupac(c) : c;

unique_ptr<vector<string>> consens(

vector<string>);

consens->resize(

->GetNumSegs());

consensus_id(

);

*bioseq, consensus_id, consens.get());

->GetScope().AddTopLevelSeqEntry(*entry);

& scope = **scope_ptr;

(

);

seq_len = new_seq.size();

seq.resize(seq_len * 3);

(

= 0;

< seq_len; ++

) {

seq[n_i] = seq[n_i + 1] = seq[n_i + 2] = new_seq[

];

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

ambiguous_residue =

;

(align_type == IAlnExplorer::EAlignType::fDNA)

ambiguous_residue =

;

ambiguous_residue =

;

(translate_sequence)

ref_is_consensus = anchor != -1 && anchor == consensus_idx;

* non_ambiguous_set =

;

(consensus_idx >= 0) {

non_ambiguous_set = &ss_NonAmbiguousAA;

non_ambiguous_set = &ss_NonAmbiguousDNA;

(

== consensus_idx)

unique_ptr<IAlnSegmentIterator> p_it

(curr_aln_start < aln_range.

()) {

pos = aln_range.

() - curr_aln_start;

off = curr_aln_start - aln_range.

();

curr_pos = off;

(translate_sequence)

(pos < seg_len && curr_pos < ref_len) {

base = aln_seq[pos];

}

(anchor >=0 && curr_pos < ref_len) {

(non_ambiguous_set && non_ambiguous_set->count(ref_str[curr_pos]) == 0)

(base != ref_str[curr_pos] && base != ambiguous_residue) {

(ref_str[curr_pos] != ambiguous_residue || ref_is_consensus) {

static CRef< CScope > m_Scope

static void s_GetTaxonomyInfoFromService(int tax_id, string &taxonomy)

USING_SCOPE(ncbi::objects)

static void s_TranslateAndExpand(string &seq, int gen_code)

static objects::CScope & s_GetPristineScope(const objects::CBioseq_Handle &bio_handle)

static void s_GetTaxonomyInfoFromBiosrc(const objects::CBioSource &biosrc, std::string &taxonomy)

void CollectNucleotideFrequences(const vector< string > &rows, int col, int base_count[], int numBases)

ON_EVENT(CAppJobNotification, CAppJobNotification::eStateChanged, &CAlnVecMultiDataSource::OnAppJobNotification) ON_EVENT(CAppJobNotification

void CollectProteinFrequences(const vector< string > &rows, int col, int base_count[], int numBases)

void TlsValCleanup(T *oldVal, void *)

#define ADD_BASE_TO_GRAPH(b)

static CStaticTls< TScopeRef > s_ScopeTls

CAlnVecMultiDataSource - implementation of IAlnMultiDataSource for CAlnVec-based alignments.

virtual const IAlignRowHandle * GetRowHandle(TNumrow row) const

virtual void x_OnJobProgress(CAppJobNotification &notn)

virtual bool IsPositiveStrand(TNumrow row) const

virtual TSeqPos GetSeqStop(TNumrow row) const

virtual void GetAlnFromSeq(TNumrow row, const TRangeColl &seq_coll, TRangeColl &aln_coll) const

virtual TNumrow GetNumRows(void) const

number of rows in alignment

virtual void CreateConsensus()

virtual TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, TSearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const

virtual void GetSeqFromAln(TNumrow row, const TRangeColl &aln_coll, TRangeColl &seq_coll) const

virtual void Init(const objects::CSeq_annot &annot, bool sync=false, bool select_anchor=false)

virtual bool SetAnchor(TNumrow anchor)

virtual TSeqPos GetSeqStart(TNumrow row) const

virtual void SetGapChar(TResidue gap_char)

vector< CAlnVecRowHandle * > THandleVector

virtual void x_DeleteJob()

virtual TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, TSearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const

virtual TSeqPos GetBaseWidth(TNumrow row) const

virtual bool IsNegativeStrand(TNumrow row) const

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) const

CAlnVecMultiDataSource(objects::CScope &scope)

virtual string & GetAlnSeqString(TNumrow row, string &buffer, const IAlnExplorer::TSignedRange &aln_range) const

virtual TSeqPos GetAlnStart(void) const

virtual bool IsSetAnchor(void) const

Anchoring methods.

virtual IAlnExplorer::EAlignType GetAlignType() const

virtual void x_CreateHandles()

void OnAppJobNotification(CEvent *evt)

virtual TSeqPos GetAlnStop(void) const

virtual bool UnsetAnchor(void)

CRef< objects::CScope > m_Scope

virtual const objects::CSeq_id & GetSeqId(TNumrow row) const

CRef< objects::CAlnVec > m_AlnVec

virtual bool x_IsJobRunning()

virtual void x_ClearHandles()

~CAlnVecMultiDataSource()

virtual bool CanGetId(TNumrow row) const

virtual void x_Assign(objects::CAlnVec &aln_vec)

virtual bool CanCreateConsensus()

virtual const objects::CBioseq_Handle & GetBioseqHandle(TNumrow row) const

CRef< CBuildAlnVecJob > m_Job

virtual bool IsEmpty() const

virtual TNumrow GetAnchor(void) const

static void s_CleanScope()

virtual bool CanChangeAnchor(void) const

virtual int GetGenCode(IAlnExplorer::TNumrow row) const

CAlnVecRowHandle is inherited from IAlignRowHandle and represents a row of CAlnVec-based alignment.

static void TranslateNAToAA(const string &na, string &aa, int gen_code=kDefaultGenCode)

CAppJobNotification Notification send by CAppJobEventTranslator.

CRef< objects::CAlnVec > m_AlnVec

CUpdate - notification send by CUIDataSource to the listener.

virtual void NotifyListener(CUpdate &update)

CEvent - generic event implementation TODO TODO - Attachments.

void GetLabel(string *label) const

TThisType & CombineWith(const TRange &r)

string GetTaxname(int tax_id)

static CTaxonCache & GetInstance()

string GetCommon(int tax_id)

string GetLabel(int tax_id)

string GetBlastName(int tax_id)

IAlignRowHandle provides an abstract way to access alignment row data.

virtual bool CanGetBioseqHandle() const =0

virtual const string & GetOrgLabel(bool fExtOrgLookup=false) const

virtual int GetGenCode() const =0

virtual const objects::CBioseq_Handle & GetBioseqHandle() const =0

virtual void GetTaxonomy(string &taxonomy, bool fExtOrgLookup=false) const

virtual int GetTaxId(bool fExtOrgLookup=false) const

virtual IAlnSegmentIterator * CreateSegmentIterator(const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) const =0

virtual const string & GetText() const =0

ESearchDirection

Position search options.

@ eRight

Towards higher aln coord (always to the right)

@ eLeft

Towards lower aln coord (always to the left)

virtual IAlnExplorer::EAlignType GetAlignType() const =0

virtual int GetConsensusRow() const =0

returns index of the Consensus row or -1 if it doesn't exist

void CollectAlignStats(const TSignedSeqRange &range, TStatGraphs &graphs, bool translate_sequence=false) const

IAlnExplorer::TResidue TResidue

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) const =0

IAlnExplorer::TNumrow TNumrow

virtual TNumrow GetNumRows(void) const =0

number of rows in alignment

virtual bool IsSetAnchor(void) const =0

Anchoring methods.

virtual TNumrow GetAnchor(void) const =0

virtual string & GetAlnSeqString(TNumrow row, string &buffer, const IAlnExplorer::TSignedRange &aln_range) const =0

Alignment segment iterator interface.

@ eAllSegments

Iterate all segments.

Alignment segment interface.

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

@ fAligned

Aligned segment.

@ fIndel

Either anchor or the selected row is not present in the segment.

@ fGap

Both anchor row and the selected row are not included in the segment (some other row is present and t...

virtual TSegTypeFlags GetType(void) const =0

Get current segment type.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

virtual int GetGenCode(IAlnExplorer::TNumrow row) const =0

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define ERR_POST(message)

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

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

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.

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

static bool IsVDBAccession(const string &acc)

Check if string starts with ("SRA", "SRR", "DRR", "ERR")

CConstIRef< IAppJobError > GetError() const

returns non-null pointer only if job Failed

void RunSync(IAppJob &job, TJobID &jobId, CEventHandler &listener)

Runs jon synchronously sending job notifications synchronously Returns when job is finished.

static CAppJobDispatcher & GetInstance()

CRef< CObject > GetResult() const

returns non-null pointer only if Completed or Running and has temporary results available

bool DeleteJob(TJobID job_id)

when a Job is deleted the listener is not notified

TJobID StartJob(IAppJob &job, const string &engine_name, IEngineParams *params=NULL)

Starts a Job on the specified engine in "passive mode" - no notifications or progress reports will be...

CConstIRef< IAppJobProgress > GetProgress() const

returns non-null pointer only if notification type is eProgress

#define END_EVENT_MAP()

Ends definition of Command Map.

#define BEGIN_EVENT_MAP(thisClass, baseClass)

Begins definition of Command Map for CEventHandler-derived class.

TJobState GetState() const

const CBioSource * GetBioSource(const CBioseq &bioseq)

Retrieve the BioSource object for a given bioseq handle.

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

void ResetDataAndHistory(void)

Clear all information in the scope except added data loaders.

CConstRef< CSeq_id > GetSeqId(void) const

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

const TDescr & GetDescr(void) const

bool CanGetDescr(void) const

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

position_type GetLength(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.

const TOrg & GetOrg(void) const

Get the Org member data.

TFrom GetFrom(void) const

Get the From member data.

bool CanGetCommon(void) const

Check if it is safe to call GetCommon method.

const TCommon & GetCommon(void) const

Get the Common member data.

TSeq & SetSeq(void)

Select the variant.

bool CanGet(void) const

Check if it is safe to call Get method.

const TInst & GetInst(void) const

Get the Inst member data.

list< CRef< CSeq_align > > TAlign

const Tdata & Get(void) const

Get the member data.

TMol GetMol(void) const

Get the Mol member data.

static void text(MDB_val *v)

constexpr bool empty(list< Ts... >) noexcept

double value_type

The numeric datatype used by the parser.

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

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

#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