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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/sequpd_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/sequpd.cpp Source File

(synonyms && !synonyms->empty()) {

(

& it : *synonyms) {

(!bsh1 || !bsh2) {

(bsh1.GetBioseqLength() != bsh2.GetBioseqLength()) {

(bsh1.IsNucleotide() && bsh2.IsProtein()) {

(bsh1.IsProtein() && bsh2.IsNucleotide()) {

old_seqvec.

(0, bsh1.GetBioseqLength(), old_seq);

upd_seqvec.

(0, bsh2.GetBioseqLength(), upd_seq);

(

& it : upd_ids) {

has_conflict =

;

(

& upd_id : bseq.

()) {

(

& old_id : seq_ids) {

has_conflict =

;

vector<CRef<CSeq_id>> update_ids;

(

& it : bseq.

()) {

newid->

(it.GetObject());

update_ids.push_back(newid);

lclID_label, gbID_label, accID_label;

(bseq.

().size() == 1) {

((*upd_id)->IsLocal()) {

((*upd_id)->IsGenbank()) {

((*upd_id)->IsOther()) {

accID_label.push_back(

);

(!gbID_label.empty()) {

(!lclID_label.empty()) {

(!accID_label.empty()) {

bseq.

().push_back(newUpdate_Id);

unmatched.push_back(idh);

collide =

;

(matches.

(old_idh) != matches.

()) {

matches.emplace(old_idh, upd_idh);

unmatched.push_back(idh);

(matches.

(old_id_handle) != matches.

())

(

& id1 : oldBseq->

()) {

(

& id2 : upd_bseq.

()) {

(old_dot !=

) {

old_label = old_label.substr(0, old_dot);

(upd_dot !=

) {

upd_label = upd_label.substr(0, upd_dot);

((*it)->IsSetLabel() && (*it)->GetLabel().IsStr()

&& (*it)->IsSetData()

&& (*it)->GetData().IsStr()) {

id_str = (*it)->GetData().GetStr();

vector<CConstRef<CSeq_align> >();

vector<CConstRef<CSeq_align> >();

result_iter,

->Get()) {

assm_iter, result_iter->second->Get()) {

query_iter, assm_iter->second) {

CGPipeAlignmentScorer::s_AddStandardAlignmentScores(

& scope,

& align,

)

vector<CConstRef<CSeq_align> > align_vector;

(

<<

);

(query_seqloc.

() || subject_seqloc.

()) {

->SetLocList().push_back(query_seqloc);

->SetLocList().push_back(subject_seqloc);

*

(

->user_data)->IsCanceled();

useHiWordAligner = (seqLength > 12000);

(useHiWordAligner) {

opts->SetTraditionalBlastnDefaults();

blast::CBlastOptions& options = opts->SetOptions();

options.SetWordSize(100);

options.SetEvalueThreshold(1e-6);

options.SetBestHitOverhang(0.1);

options.SetBestHitScoreEdge(0.1);

blastAligner->SetInterruptCallback(cb, canceled);

opts->SetTraditionalBlastnDefaults();

blast::CBlastOptions& options = opts->SetOptions();

options.SetWordSize(12);

options.SetEvalueThreshold(1e-6);

options.SetBestHitOverhang(0.1);

options.SetBestHitScoreEdge(0.1);

blastAligner->SetInterruptCallback(cb, canceled);

ng_aligner.

(

(0,

));

ng_aligner.

(

(1,

));

ng_aligner.

(

(2,

));

ng_aligner.

(

(3,

));

(accept_atleast_one) {

(align && align->

()) {

vector<CConstRef<CSeq_align> > align_vector;

align_vector.push_back(align);

vector<CConstRef<CSeq_align> > align_vector;

blast::CBlastProteinOptionsHandle prot_opts_handle;

prot_opts_handle.SetEvalueThreshold(1e-6);

prot_opts_handle.SetWordThreshold(100.0);

prot_opts_handle.Validate();

blast::CBl2Seq blaster(

,

, prot_opts_handle);

(!seqaligns.empty()) {

((*it)->IsSet()) {

(

blast::CBlastException& e) {

length_first >= length_sec;

Declares the CBlastProteinOptionsHandle class.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

CSeq_entry * GetParentEntry(void) const

@ eSkipUnsupportedAlignments

void ScoreAlignments(TAlignResultsRef results, CScope &scope)

@ eTreeAlignMerger

Use the new (CTreeAlignMerger) merge algorithm.

void SetQuery(ISequenceSet *Set)

void SetSubject(ISequenceSet *Set)

void AddFilter(IAlignmentFilter *Filter)

void AddAligner(IAlignmentFactory *Aligner)

void AddScorer(IAlignmentScorer *Scorer)

int GetGapCount(const CSeq_align &align)

Compute the number of gaps in the alignment.

void AddScore(CScope &scope, CSeq_align &align, EScoreType score)

deprecated: use CSeq_align::EScoreType directly

Sequence update exception class.

@ eScore_PercentIdentity_GapOpeningOnly

@ eScore_PercentIdentity_Gapped

@ eScore_PercentIdentity_Ungapped

void SetNamedScore(const string &id, int score)

TSeqPos GetAlignLength(bool include_gaps=true) const

Get the length of this alignment.

list< CRef< CSeq_annot > > TAnnot

CSeq_entry * GetParentEntry(void) const

Template class for iteration on objects of class C.

EObjectType GetObjectType() const

Interface for testing cancellation request in a long lasting operation.

const_iterator end() const

const_iterator find(const key_type &key) const

static void FindMatches(objects::CSeq_inst::EMol type, objects::CSeq_entry_Handle &oldSeq, objects::CSeq_entry &updEntry, TSeqIdHMap &matches, TSeqIdHVector &unmatched)

static bool CompareAlignments(const objects::CSeq_align &align_first, const objects::CSeq_align &align_sec)

Returns true if the first alignment is 'better' than the second one Compares the Blast scores and in ...

static vector< CConstRef< objects::CSeq_align > > RunBlast2Seq(const objects::CBioseq_Handle &subject, const objects::CBioseq_Handle &query, bool accept_atleast_one, ICanceled *canceled=nullptr)

static bool HaveIdenticalResidues(const objects::CBioseq_Handle &bsh1, const objects::CBioseq_Handle &bsh2)

vector< objects::CSeq_id_Handle > TSeqIdHVector

static void FixCollidingIDs_Bioseq(objects::CBioseq &bseq, const objects::CBioseq::TId &seq_ids)

static objects::CSeq_id_Handle GetGoodSeqIdHandle(const objects::CBioseq_Handle &bsh)

CRef< objects::CSeq_align > AsSeqAlign(TSeqPos query_start=0, objects::ENa_strand query_strand=objects::eNa_strand_plus, TSeqPos subj_start=0, objects::ENa_strand subj_strand=objects::eNa_strand_plus, int SAFF_flags=eSAFF_None) const

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.

#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.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

E_SIC

Compare return values.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

void Swap(CSeq_id_Handle &idh)

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

@ e_NO

different SeqId types-can't compare

@ e_YES

SeqIds compared, but are different.

@ eContent

Untagged human-readable accession or the like.

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CConstRef< CSeq_id > GetLocalIdOrNull(void) const

bool IsNucleotide(void) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CSeq_id_Handle GetAccessSeq_id_Handle(void) const

Get any CSeq_id_Handle handle that can be used to access this bioseq Use GetSeq_id_Handle() if it's n...

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.

bool IsProtein(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

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,...

CConstRef< CSynonymsSet > GetSynonyms(void) const

Get the bioseq's synonyms.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ 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).

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static bool EqualCase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-sensitive equality of a substring with another string.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

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.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

const TData & GetData(void) const

Get the Data member data.

vector< CRef< CUser_field > > TData

void SetSegs(TSegs &value)

Assign a value to Segs data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

bool IsLocal(void) const

Check if variant Local is selected.

TClass GetClass(void) const

Get the Class member data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSet(void) const

Check if variant Set is selected.

@ eClass_nuc_prot

nuc acid and coded proteins

TId & SetId(void)

Assign a value to Id data member.

void ResetId(void)

Reset Id data member.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsSetMol(void) const

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

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

TMol GetMol(void) const

Get the Mol member data.

EMol

molecule class in living organism

bool IsSetId(void) const

equivalent identifiers Check if a value has been assigned to Id data member.

@ e_User

user defined object

const string version

version string

Uint1 Boolean

bool replacment for C

@ fScore_GapCount

add a 'gap_count' score

@ fScore_Identities

add BLAST-style 'num_ident' score

@ fScore_Default

default flags: everything

@ fScore_Mismatches

add a 'mismatch' core with a count of mismatches

@ fScore_PercentCoverage

add a score for percent coverage of query (sequence 0)

@ fScore_PercentIdentity

add scores for ungapped and gapped percent identity

const SNCBIPackedScoreMatrix NCBISM_Blosum62

static const char * kUpdateSuffix

static void s_FixCollidingIDs_Annot(CBioseq &bseq, CSeq_entry::TAnnot &annot, const vector< CRef< CSeq_id >> &upd_ids)

static CBioseq_Handle s_GetMatchingSequence(CSeq_inst::EMol type, CSeq_entry_Handle &oldSeq, const CBioseq &upd_bseq, bool &collide, const sequpd::TSeqIdHMap &matches)

static CConstRef< CSeq_id > s_GetOriginalId(const CBioseq_Handle &bsh)

static bool s_MatchSeqIds(CScope &scope, const CSeq_id &old_id, const CSeq_id &upd_id, bool &collide)

static vector< CConstRef< CSeq_align > > s_RunBlast2NASeq(const CBioseq_Handle &sh, const CBioseq_Handle &qh, bool accept_atleast_one, ICanceled *canceled)

static vector< CConstRef< CSeq_align > > s_RunBlast2NWSeq(const CBioseq_Handle &sh, const CBioseq_Handle &qh)

static vector< CConstRef< CSeq_align > > s_RunBlast2AASeq(const CBioseq_Handle &sh, const CBioseq_Handle &qh)

Progress monitoring structure.

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