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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/compartments_8cpp_source.html below:

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

THitComparator sorter (THitComparator::eQueryMin);

stable_sort(hitrefs.begin(), hitrefs.end(), sorter);

stmin = hitrefs.front()->GetQueryMin();

enmax = hitrefs.front()->GetQueryMax();

((*it)->GetQueryMin() <= enmax) {

enmax =

((*it)->GetQueryMax(), enmax);

+= enmax - stmin + 1;

stmin = (*it)->GetQueryMin();

enmax = (*it)->GetQueryMax();

+= enmax - stmin + 1;

is_protein_subject)

subj_start = (*h)->GetSubjStart();

subj_stop = (*h)->GetSubjStop();

qry_start = (*h)->GetQueryStart();

qry_stop = (*h)->GetQueryStop();

(!is_protein_subject) {

(*h)->SetQueryStart(qry_start);

(*h)->SetQueryStop(qry_stop);

undef_score =

;

((*oh)->GetSubjStart() == subj_start &&

subj_stop == (*oh)->GetSubjStop() &&

(*oh)->GetQueryStart() == qry_start &&

qry_stop == (*oh)->GetQueryStop() &&

(undef_score || score < (*oh)->GetScore())) {

score = (*oh)->GetScore();

undef_score =

;

(hits_new.begin(), hits_new.end(), back_inserter(hitrefs));

+= (*i)->GetScore();

+= (*i)->GetRawScore();

->SetId().SetStr(

);

->SetId().SetStr(

);

subj_leftmost = hitrefs.front()->GetSubjMin();

(!(*h)->GetSubjStrand()) {

subj_min = (*h)->GetSubjMin();

subj_max = (*h)->GetSubjMax();

qry_min = (*h)->GetQueryMin();

qry_max = (*h)->GetQueryMax();

pct_identity =(*h) ->GetIdentity();

bit_score = (*h)->GetScore();

score = (*h)->GetRawScore();

subj_leftmost =

(subj_leftmost, subj_min);

subj_rightmost =

(subj_rightmost, subj_max);

qry_id->

(*(*h)->GetQueryId());

std_seg->SetLoc().push_back(qry_loc);

subj_id->

(*(*h)->GetSubjId());

std_seg->SetLoc().push_back(subj_loc);

std_seg->SetScores().push_back(

(

,pct_identity*100));

std_seg->SetScores().push_back(

(

,bit_score));

(score > 0) std_seg->SetScores().push_back(

(

,score));

std_segs.push_back(std_seg);

->SetData().SetAlign().push_back(seq_align);

uo->

().SetStr(

);

->AddUserObject( *uo );

qry_id->

(*hitrefs.front()->GetQueryId());

->SetDesc().Set().push_back( align );

subj_id->

(*hitrefs.front()->GetSubjId());

->SetDesc().Set().push_back(region);

vector<pair<THit::TCoord, THit::TCoord> > *gaps)

unique_ptr<CCompartmentAccessor<THit> > comps_ptr;

(orig_hitrefs.empty())

is_protein_subject;

max_subj_query_ratio = 0;

max_subj_query_ratio =

(max_subj_query_ratio, subj_query_ratio);

is_protein_subject = max_subj_query_ratio < 2;

(!hitref->GetQueryStrand())

(!is_protein_subject) {

hitref->SetQueryMax(hitref->GetQueryMax()*3+2);

hitref->SetQueryMin(hitref->GetQueryMin()*3);

hitref->SetIdentity(0.9999f);

hitref->SetIdentity(hitref->GetScore()/hitref->GetLength());

hitrefs.push_back(hitref);

comps.

(hitrefs.begin(), hitrefs.end(),

, gaps);

}

(comps.

(comphits));

vector<pair<THit::TCoord, THit::TCoord> > *gaps)

unique_ptr<CCompartmentAccessor<THit> > comps_ptr =

vector<pair<THit::TCoord, THit::TCoord> > *gaps)

(comps_ptr ==

)

cur_begin_extended = cur_begin < max_extent ? 0 : cur_begin - max_extent;

cur_end_extended = cur_end + max_extent;

vector<pair<THit::TCoord, THit::TCoord> >::const_iterator it;

(it = gaps->begin(); it != gaps->end(); ++it) {

( gfrom < cur_begin && cur_begin_extended < gto ) {

( gto < cur_begin ) {

cur_begin_extended = gto + 1;

cur_begin_extended = cur_begin;

( cur_end < gto && gfrom < cur_end_extended ) {

( cur_end < gfrom ) {

cur_end_extended = gfrom - 1;

cur_end_extended = cur_end;

cur_compartment_loc->

().SetFrom(cur_begin_extended);

cur_compartment_loc->

().SetTo(cur_end_extended);

(prev_compartment_loc.

() &&

prev_compartment_loc->

()->

(*cur_compartment_loc->

()) &&

prev_end = prev_end_extended - max_extent;

(prev_end < cur_begin) {

(prev_end_extended >= cur_begin_extended) {

prev_end_extended = (prev_end + cur_begin)/2;

cur_begin_extended = prev_end_extended+1;

(cur_begin_extended <= cur_begin);

prev_compartment_loc->

().SetTo(prev_end_extended);

cur_compartment_loc->

().SetFrom(cur_begin_extended);

prev_compartment_loc->

().SetTo(prev_end);

cur_compartment_loc->

().SetFrom(cur_begin);

prev_compartment_loc=cur_compartment_loc;

.push_back(compartment);

}

(comps.

(comphits));

raw_score = (

) score;

covered_aa, score, raw_score));

,

(

,

,

(

,

,

(

,

,

,

,

,

,

,

m_CompartmentPenalty(default_CompartmentPenalty),

m_MinCompartmentIdty(default_MinCompartmentIdty),

m_MinSingleCompartmentIdty(default_MinSingleCompartmentIdty),

m_MaxExtent(default_MaxExtent),

m_ByCoverage(default_ByCoverage),

m_MaxIntron(default_MaxIntron),

m_MaxOverlap(default_MaxOverlap),

m_Maximizing(default_Maximizing),

m_SubjectMol(default_SubjectMol)

m_CompartmentPenalty(args[

].AsDouble()),

m_MinCompartmentIdty(args[

].AsDouble()),

m_MinSingleCompartmentIdty(args[

]

? args[

].AsDouble()

: default_MinSingleCompartmentIdty),

m_MaxExtent(args[

].AsInteger()),

m_MaxIntron(args[

].AsInteger()),

m_MaxOverlap(args[

].AsInteger())

(args[

]) {

(args[

]) {

(args[

].AsString() ==

) {

}

(args[

].AsString() ==

) {

@ eExtreme_Positional

numerical value

void remove_if(Container &c, Predicate *__pred)

TCoord GetQuerySpan(void) const

TCoord GetSubjSpan(void) const

static const double default_MinCompartmentIdty

static const int default_MaxIntron

static const EMaximizing default_Maximizing

static const double default_MinSingleCompartmentIdty

static const int default_MaxExtent

static void SetupArgDescriptions(CArgDescriptions *argdescr)

static const double default_CompartmentPenalty

static const int default_MaxOverlap

static const char * s_scoreNames[]

static const bool default_ByCoverage

CCompartOptions()

with deafalt params

double m_CompartmentPenalty

double m_MinCompartmentIdty

static const ESubjectMol default_SubjectMol

double m_MinSingleCompartmentIdty

void Run(typename THitRefs::iterator start, typename THitRefs::iterator finish, CScope *scope=NULL, const vector< pair< TCoord, TCoord > > *gaps=NULL)

Execute: identify compartments.

void SetMaxIntron(TCoord mi)

Assign the maximum intron length, in base pairs.

bool GetFirst(THitRefs &compartment)

Initialize iteration over the results.

const TCoord * GetBox(size_t i) const

void SetMaxOverlap(TCoord max_overlap)

Assign the maximum length for compartments to overlap on the subject.

bool GetNext(THitRefs &compartment)

Proceed with iteration over the results.

static TCoord s_GetDefaultMaxOverlap(void)

Retrieve the default compartment overlap behaviour (no overlap).

static TCoord s_GetDefaultMaxIntron(void)

Retrieve the default maximum length of an intron.

vector< THitRef > THitRefs

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

TCompartments FormatAsAsn(CCompartmentAccessor< THit > *comps_ptr, CCompartOptions compart_options, const vector< pair< THit::TCoord, THit::TCoord > > *gaps)

unique_ptr< CCompartmentAccessor< THit > > CreateCompartmentAccessor(const THitRefs &orig_hitrefs, CCompartOptions compart_options, const vector< pair< THit::TCoord, THit::TCoord > > *gaps)

Selects compartments.

CRef< CScore > IntScore(const string &id, int value)

CRef< CSeq_annot > MakeCompartment(THitRefs &hitrefs)

USING_SCOPE(ncbi::objects)

void RemoveOverlaps(THitRefs &hitrefs)

TCompartments SelectCompartmentsHits(const THitRefs &orig_hitrefs, CCompartOptions compart_options, const vector< pair< THit::TCoord, THit::TCoord > > *gaps)

Composition of first two functions.

CRef< CScore > RealScore(const string &id, double value)

double TotalScore(THitRefs &hitrefs)

void RestoreOriginalHits(THitRefs &hitrefs, const THitRefs &orig_hitrefs, bool is_protein_subject)

int TotalRawScore(THitRefs &hitrefs)

int CountQueryCoverage(THitRefs &hitrefs)

TCompartmentStructs MakeCompartments(const TCompartments &compartments, CCompartOptions compart_options)

CSplign::THitRefs THitRefs

vector< SCompartment > TCompartmentStructs

list< CRef< CSeq_annot > > TCompartments

static void s_RunGreedy(typename THitRefs::iterator hri_beg, typename THitRefs::iterator hri_end, THitRefs *phits_new, TCoord min_hit_len=100, double min_hit_idty=.9, TCoord margin=1, TCoord retain_overlap=0, EUnique_type unique_type=e_Strict)

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.

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

Set additional user defined constraint on argument value.

void SetDependency(const string &arg1, EDependency dep, const string &arg2)

Define a dependency.

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.

@ eExcludes

One argument excludes another.

@ eBoolean

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

@ eDouble

Convertible into a floating point number (double)

@ 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)

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

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

ENa_strand GetStrand(void) const

Get the location's strand.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

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

TSeqPos GetStop(ESeqLocExtremes ext) const

bool NotEmpty(void) const THROWS_NONE

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

#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.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

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

Convert int to string.

bool IsStr(void) const

Check if variant Str is selected.

const TData & GetData(void) const

Get the Data member data.

const TStr & GetStr(void) const

Get the variant data.

TInt GetInt(void) const

Get the variant data.

TReal GetReal(void) const

Get the variant data.

void SetType(TType &value)

Assign a value to Type data member.

const TType & GetType(void) const

Get the Type member data.

list< CRef< CStd_seg > > TStd

void SetSegs(TSegs &value)

Assign a value to Segs data member.

void SetType(TType value)

Assign a value to Type data member.

@ eType_partial

mapping pieces together

const Tdata & Get(void) const

Get the member data.

TIds & SetIds(void)

Assign a value to Ids data member.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

void SetAlign_type(TAlign_type value)

Assign a value to Align_type data member.

const TUser & GetUser(void) const

Get the variant data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsRegion(void) const

Check if variant Region is selected.

TRegion & SetRegion(void)

Select the variant.

TAlign & SetAlign(void)

Select the variant.

const TRegion & GetRegion(void) const

Get the variant data.

bool IsUser(void) const

Check if variant User is selected.

list< CRef< CAnnotdesc > > Tdata

@ eAlign_type_ref

set of alignments to the same sequence

unsigned int

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

constexpr auto sort(_Init &&init)

Magic spell ;-) needed for some weird compilers... very empiric.

const GenericPointer< typename T::ValueType > T2 value

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

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