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NCBI C++ ToolKit: src/algo/align/prosplign/prosplign.cpp Source File

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genomic.Assign(genomic_orig);

vector<pair<int, int> >&

()

vector<pair<int, int> >&

()

(

& lgap,

& rgap)

m_implementation(

::create(scoring,intronless,one_stage,just_second_stage,old))

& prot_start_pos = exons.front()->GetProduct_start().GetProtpos();

& prot_stop_pos = exons.back()->GetProduct_end().GetProtpos();

prot_start_pos.

()==0 && prot_start_pos.

()==1 &&

((*it)->IsSource()) {

(*it)->SetSource().SetOrg().SetOrgname().SetGcode(gcode);

ldesc.push_back(desc);

genomic->

(genomic_orig);

scope, protein, *genomic);

plus_score = plus_data->FindGlobalAlignment_stage1(scope, protein, *genomic);

minus_score =

->FindGlobalAlignment_stage1(scope, protein, *genomic);

(minus_score <= plus_score)

scope, protein, *genomic);

(

->CanGetBounds()) {

((*b)->GetId() !=

&& (*b)->GetId()->Match(*nucid)) {

->SetBounds().erase(

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genomic_bounds->

(genomic_orig);

->SetBounds().push_back(genomic_bounds);

* sid = genomic.GetId();

SeekStartStop(*seq_align);

refined_align->

(seq_align);

refined_align;

(good_parts.empty()) {

(good_parts.size()!=1 || !IsProteinSpanWhole(refined_align->

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())) {

refined_align;

objects::CSeq_align& seq_align,

}

(chunk.

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(

.size() != 3)

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m_matrix.GetTranslationTable().TranslateStartTriplet(

) ==

;

CSeq_loc genomic_seqloc(nucid,stop_codon_start, stop_codon_end,sps.

());

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((*m)->IsStart_codon_found() || (*m)->IsStop_codon_found())

(HasStartOnNuc(sps)) {

modi->SetStart_codon_found(

);

pseq(*m_scope,protid);

(pseq.

() && !chunk->IsMatch()) {

= chunk->GetDiag();

chunk->SetDiag(

-3);

exon.

().push_front(chunk);

(HasStopOnNuc(sps)) {

modi->SetStop_codon_found(

);

list< CNPiece > FindGoodParts(const CProteinAlignText &alignment_text, CProSplignOutputOptionsExt m_options, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)

void RefineAlignment(objects::CScope &scope, objects::CSeq_align &seq_align, const list< CNPiece > &good_parts)

void SetScores(objects::CSeq_align &seq_align, objects::CScope &scope, const string &matrix_name="BLOSUM62")

void FrBackAlign(CBackAlignInfo &bi, CAli &ali)

int FindIGapIntrons(const CProSplignInterrupt &interrupt, vector< pair< int, int > > &igi, const PSEQ &pseq, const CNSeq &nseq, int g, int e, int f, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)

int FindFGapIntronNog(const CProSplignInterrupt &interrupt, vector< pair< int, int > > &igi, const PSEQ &pseq, const CNSeq &nseq, bool &left_gap, bool &right_gap, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)

int FrAlign(const CProSplignInterrupt &interrupt, CBackAlignInfo &bi, const PSEQ &pseq, const CNSeq &nseq, int g, int e, int f, const CProSplignScaledScoring &, const CSubstMatrix &matrix)

void BackAlignNog(CTBackAlignInfo< CBMode > &bi, CAli &ali)

int FrAlignFNog1(const CProSplignInterrupt &interrupt, CBackAlignInfo &bi, const PSEQ &pseq, const CNSeq &nseq, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix, bool left_gap, bool right_gap)

int AlignFNog(const CProSplignInterrupt &interrupt, CTBackAlignInfo< CBMode > &bi, const PSEQ &pseq, const CNSeq &nseq, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)

CRef< CSeq_align > MakeSeq_align(const CPSeq &cpseq, const CNSeq &cnseq) const

virtual CIntronlessNew * clone()

CIntronlessNew(CProSplignScoring scoring)

CIntronlessOld(CProSplignScoring scoring)

virtual CIntronlessOld * clone()

CIntronless(CProSplignScoring scoring)

virtual void stage2(CAli &ali)

void Init(CScope &scope, CSeq_loc &genomic)

COneStage(CProSplignScoring scoring)

CTBackAlignInfo< CBMode > m_bi

virtual COneStage * clone()

virtual void stage2(CAli &ali)

void SetInterruptCallback(TInterruptFnPtr prg_callback, void *data)

Scoring parameters object.

CProSplignOptions_Base & SetScoreMatrix(const string &matrix_name)

static void SetupArgDescriptions(CArgDescriptions *argdescr)

CProSplignOptions_Base & SetAltStarts(bool allow_alt_start)

CProSplignOptions_Base()

creates scoring parameter object with default values

const string & GetScoreMatrix() const

static const bool default_allow_alt_starts

static const char * default_score_matrix_name

bool GetAltStarts() const

Output filtering parameters.

static const int default_cut_flanks_with_posit_window

CProSplignOutputOptions & SetCutFlanksWithPositDropoff(int)

CProSplignOutputOptions & SetMinExonPos(int)

minimum exon positives percentage

bool cut_flanks_with_posit_drop

???

bool GetCutFlankPartialCodons() const

int GetTotalPositives() const

int cut_flanks_with_posit_max_len

CProSplignOutputOptions & SetMinGoodLen(int)

good piece should not be shorter than that

CProSplignOutputOptions & SetMinPositives(int)

CProSplignOutputOptions & SetMinFlankingExonLen(int)

minimum number of bases in the first and last exon

int GetCutFlanksWithPositGapRatio() const

CProSplignOutputOptions & SetCutFlanksWithPositMaxLen(int)

max flank size to cut

static const int default_total_positives

static const int default_cut_flanks_with_posit_dropoff

CProSplignOutputOptions(EMode mode=eWithHoles)

int GetCutFlanksWithPositWindow() const

int GetCutFlanksWithPositMaxLen() const

int cut_flanks_with_posit_window

CProSplignOutputOptions & SetMinHoleLen(int)

fill back small holes between good pieces holes with both unaligned protein and nucleotide portions l...

static const bool default_fill_holes

static const int default_flank_positives

CProSplignOutputOptions & SetCutFlanksWithPositWindow(int)

window size

CProSplignOutputOptions & SetCutNs(bool)

cut trailing Ns at the ends of good pieces.

bool GetFillHoles() const

int cut_flanks_with_posit_gap_ratio

bool GetCutFlanksWithPositDrop() const

CProSplignOutputOptions & SetCutFlankPartialCodons(bool)

cut partial codons and adjecent at the beginning and at the end good pieces called at the end of post...

static const bool default_cut_flanks_with_posit_drop

static const int default_cut_flanks_with_posit_max_len

static const int default_min_hole_len

CProSplignOutputOptions & SetCutFlanksWithPositDrop(bool)

cut flanks if drop of positives is more than a dropoff in comparison to positives in a window next to...

static const int default_min_good_len

bool cut_flank_partial_codons

CProSplignOutputOptions & SetTotalPositives(int)

good piece total percentage threshold

CProSplignOutputOptions & SetCutFlanksWithPositGapRatio(int)

count gaps as 1+1/gap_ratio, gap_ratio = 1 - standart behaviour.

int GetMinHoleLen() const

int GetMinFlankingExonLen() const

int GetMinGoodLen() const

static void SetupArgDescriptions(CArgDescriptions *argdescr)

int GetFlankPositives() const

int GetCutFlanksWithPositDropoff() const

int min_flanking_exon_len

static const int default_cut_flanks_with_posit_gap_ratio

CProSplignOutputOptions & SetMinExonId(int)

minimum exon identity

int GetMinExonPos() const

static const int default_min_flanking_exon_len

CProSplignOutputOptions & SetMaxBadLen(int)

any part of a good piece longer than max_bad_len should not be worse than min_positives

int GetStartBonus() const

bool IsPassThrough() const

CProSplignOutputOptions & SetStopBonus(int)

reward for stop codon at the end. Not implemented yet

static const int default_max_bad_len

static const int default_start_bonus

CProSplignOutputOptions & SetStartBonus(int)

reward (in # of positives?) for start codon match.

CProSplignOutputOptions & SetFlankPositives(int)

any length flank of a good piece should not be worse than this percentage threshold

@ ePassThrough

all zeroes - no filtering

@ eWithHoles

default filtering parameters

int cut_flanks_with_posit_dropoff

CProSplignOutputOptions & SetFillHoles(bool)

fill back holes between good pieces.

static const int default_stop_bonus

???

static const bool default_cut_ns

static const int default_min_positives

static const bool default_cut_flank_partial_codons

static const int default_min_exon_pos

static const int default_min_exon_id

int GetMinPositives() const

CProSplignScoring & SetFrameshiftOpeningCost(int)

int inverted_intron_extension

CProSplignScoring & SetInvertedIntronExtensionCost(int)

Inverted Intron Extension Cost intron_extension cost for 1 base = 1/(inverted_intron_extension*3)

int GetGapOpeningCost() const

int GetMinIntronLen() const

int GetFrameshiftOpeningCost() const

static const int default_min_intron_len

int GetInvertedIntronExtensionCost() const

CProSplignScoring()

creates scoring parameter object with default values

CProSplignScoring & SetGapOpeningCost(int)

in addition to ScoreMatrix prosplign uses following costs (negate to get a score)

int GetGCIntronCost() const

static const int default_intron_GT

static const int default_gap_extension

static const int default_intron_GC

static const int default_intron_non_consensus

static const int default_frameshift_opening

CProSplignScoring & SetATIntronCost(int)

AT/AC intron opening cost.

int GetATIntronCost() const

static const int default_gap_opening

static const int default_inverted_intron_extension

CProSplignScoring & SetNonConsensusIntronCost(int)

Non Consensus Intron Cost should not exceed a sum of lowest two intron opening costs,...

int GetGapExtensionCost() const

CProSplignScoring & SetGapExtensionCost(int)

Gap Extension Cost for one aminoacid (three bases)

CProSplignScoring & SetGCIntronCost(int)

GC/AG intron opening cost.

CProSplignScoring & SetMinIntronLen(int)

CProSplignScoring & SetGTIntronCost(int)

GT/AG intron opening cost.

static void SetupArgDescriptions(CArgDescriptions *argdescr)

int GetGTIntronCost() const

int GetNonConsensusIntronCost() const

static const int default_intron_AT

CImplementation(CProSplignScoring scoring)

CProSplignInterrupt m_Interrupt

virtual void SetFlanks(bool, bool)

bool HasStartOnNuc(const CSpliced_seg &sps)

shared_ptr< CNSeq > m_cnseq

void SeekStartStop(CSeq_align &seq_align)

const CProSplignScaledScoring & GetScaleScoring() const

void SetTranslationTable(int gcode)

const CSeq_id * m_protein

CProSplignScaledScoring m_scoring

static CImplementation * create(CProSplignScoring scoring, bool intronless, bool one_stage, bool just_second_stage, bool old)

const CSubstMatrix & GetSubstMatrix() const

CRef< CSeq_loc > m_genomic

virtual void stage2(CAli &ali)=0

shared_ptr< CPSeq > m_protseq

int FindGlobalAlignment_stage1(CScope &scope, const CSeq_id &protein, const CSeq_loc &genomic)

void SetInterruptCallback(CProSplign::TInterruptFnPtr prg_callback, void *data)

bool HasStopOnNuc(const CSpliced_seg &sps)

virtual const vector< pair< int, int > > & GetExons() const

CRef< CSeq_align > FindGlobalAlignment_stage2()

virtual void GetFlanks(bool &, bool &) const

virtual ~CImplementation()

void SetScope(CScope &scope)

virtual CImplementation * clone()=0

virtual vector< pair< int, int > > & SetExons()

CRef< CSeq_align > FindGlobalAlignment(CScope &scope, const CSeq_id &protein, const CSeq_loc &genomic_orig)

spliced protein to genomic alignment

bool(* TInterruptFnPtr)(void *callback_data)

User interrupt logic for GBENCH.

void AssignGeneticCode(objects::CScope &scope, const objects::CSeq_id &gid, int gcode)

CProSplign(CProSplignScoring scoring=CProSplignScoring(), bool intronless=false)

By default ProSplign looks for introns.

void SetInterruptCallback(TInterruptFnPtr prg_callback, void *data)

void SetScores(objects::CScope &scope, objects::CSeq_align &seq_align, CProSplignOutputOptions output_options=CProSplignOutputOptions())

Sets scores expected from execution of ProSplign.

void Interrupt(void)

for MT usage set a signal for core algirithm to interrupt calculations after this method is called fr...

CRef< objects::CSeq_align > FindGlobalAlignment(objects::CScope &scope, const objects::CSeq_id &protein, const objects::CSeq_loc &genomic)

Globally aligns protein to a region on genomic sequence.

void GetFlanks(bool &lgap, bool &rgap) const

unique_ptr< CImplementation > m_implementation

void SetFlanks(bool lgap, bool rgap)

vector< pair< int, int > > & SetExons()

const vector< pair< int, int > > & GetExons() const

void SetTranslationTable(int gcode)

CRef< objects::CSeq_align > RefineAlignment(objects::CScope &scope, const objects::CSeq_align &seq_align, CProSplignOutputOptions output_options=CProSplignOutputOptions())

Refines Spliced-seg alignment by removing bad pieces according to output_options.

CProt_pos_Base::TFrame GetFrame() const

Text representation of ProSplign alignment.

CSpliced_seg_modifier –.

Substitution Matrix for Scoring Amino-Acid Alignments.

void SetTranslationTable(const CTranslationTable *trans_table)

void Init(int oilen, int ojlen)

CTwoStageNew(CProSplignScoring scoring, bool just_second_stage)

virtual CTwoStageNew * clone()

virtual void stage2(CAli &ali)

CTwoStageOld(CProSplignScoring scoring, bool just_second_stage)

virtual void stage2(CAli &ali)

virtual CTwoStageOld * clone()

vector< pair< int, int > > m_igi

virtual const vector< pair< int, int > > & GetExons() const

virtual void GetFlanks(bool &lgap, bool &rgap) const

CTwoStage(CProSplignScoring scoring, bool just_second_stage)

virtual vector< pair< int, int > > & SetExons()

virtual void SetFlanks(bool lgap, bool rgap)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void AddFlag(const string &name, const string &comment, CBoolEnum< EFlagValue > set_value=eFlagHasValueIfSet, TFlags flags=0)

Add description for flag argument.

void SetConstraint(const string &name, const CArgAllow *constraint, EConstraintNegate negate=eConstraint)

Set additional user defined constraint on argument value.

bool Exist(const string &name) const

Check if there is already an argument description with specified name.

void AddDefaultKey(const string &name, const string &synopsis, const string &comment, EType type, const string &default_value, TFlags flags=0, const string &env_var=kEmptyStr, const char *display_value=nullptr)

Add description for optional key with default value.

@ eBoolean

{'true', 't', 'false', 'f'}, case-insensitive

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

#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)

Set object to copy of another one.

C * SerialClone(const C &src)

Create on heap a clone of the source object.

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

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

ENa_strand GetStrand(void) const

Get the location's strand.

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

Override Assign() to incorporate cache invalidation.

TRange GetTotalRange(void) const

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

const COrg_ref & GetOrg_ref(const CBioseq_Handle &handle)

Return the org-ref associated with a given sequence.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void SetDescr(TDescr &v) const

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer)

Fill the buffer string with the sequence data for the interval [start, stop).

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

void SetOrg(TOrg &value)

Assign a value to Org data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TProtpos & GetProtpos(void) const

Get the variant data.

TModifiers & SetModifiers(void)

Assign a value to Modifiers data member.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

TMatch GetMatch(void) const

Get the variant data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

bool IsMismatch(void) const

Check if variant Mismatch is selected.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TExons & SetExons(void)

Assign a value to Exons data member.

TProduct_length GetProduct_length(void) const

Get the Product_length member data.

TDiag GetDiag(void) const

Get the variant data.

bool IsSetModifiers(void) const

alignment descriptors / modifiers this provides us a set for extension Check if a value has been assi...

TMismatch GetMismatch(void) const

Get the variant data.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

TAmin GetAmin(void) const

Get the Amin member data.

void SetType(TType value)

Assign a value to Type data member.

const TParts & GetParts(void) const

Get the Parts member data.

const TProduct_start & GetProduct_start(void) const

Get the Product_start member data.

const TProduct_end & GetProduct_end(void) const

Get the Product_end member data.

const TSpliced & GetSpliced(void) const

Get the variant data.

list< CRef< CSeq_loc > > TBounds

bool IsGenomic_ins(void) const

Check if variant Genomic_ins is selected.

bool IsMatch(void) const

Check if variant Match is selected.

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

TParts & SetParts(void)

Assign a value to Parts data member.

bool IsDiag(void) const

Check if variant Diag is selected.

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

bool IsProduct_ins(void) const

Check if variant Product_ins is selected.

const TModifiers & GetModifiers(void) const

Get the Modifiers member data.

void ResetModifiers(void)

Reset Modifiers data member.

const TSegs & GetSegs(void) const

Get the Segs member data.

@ eType_disc

discontinuous alignment

bool IsWhole(void) const

Check if variant Whole is selected.

@ eNa_strand_both_rev

in reverse orientation

@ eNa_strand_both

in forward orientation

TSource & SetSource(void)

Select the variant.

unsigned int

A callback function used to compare two keys in a database.

USING_SCOPE(ncbi::objects)

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