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NCBI C++ ToolKit: src/algo/seqqa/xcript_tests.cpp Source File

( !

|| !

) {

.AddField(

, (

) feat_iter.

());

(vec[pos - 3] ==

|| vec[pos - 3] ==

)) {

(vec.

() > pos + 3 &&

vec[pos + 3] ==

) {

upstr->

().SetId().Assign(

);

upstr->

().SetFrom(0);

loc.

().AddSeqLoc(*upstr);

standard->

().push_back(code_id);

.AddField(

,

.AddField(

,

.AddField(

,

pos_nearest_best_start = 0;

(

= upstream_length - 3;

>= 0;

-= 3) {

(vec[

] ==

&& vec[

+ 1] ==

&& vec[

+ 2] ==

) {

(strength > best_strength) {

best_strength = strength;

pos_nearest_best_start =

;

.AddField(

, best_strength !=

);

(best_strength !=

) {

.AddField(

,

.AddField(

,

(upstream_length - pos_nearest_best_start - 3));

(

= upstream_length - 3;

>= 0;

-= 3) {

.AddField(

,

.AddField(

,

(upstream_length -

- 3));

.AddField(

,

std::map<string, CRef<CHMMParameters> > s_hmmparams_cache;

(!

->HasKey(

)) {

model_file_name = (*ctx)[

];

(s_hmmparams_cache.find(model_file_name) == s_hmmparams_cache.end()) {

hmm_params = s_hmmparams_cache[model_file_name];

->GetScope(), &gccontent);

.AddField(

, model_file_name);

.AddField(

, gccontent);

.AddField(

,

(score, -1e100));

( !

|| !

) {

=

->GetScope()

.GetBioseqHandle(

&

(obj)).GetInst_Length();

.AddField(

,

);

.AddField(

,

xcript_len =

->GetScope().GetBioseqHandle(

).GetInst_Length();

.SetOutput_data().AddField(

, (

) cds_from);

.SetOutput_data().AddField(

,

(

) (xcript_len - cds_to - 1));

vec.

(upstream_length, upstream_length + 3, seq);

.AddField(

,

.AddField(

, seq);

.AddField(

,

.AddField(

,

start_translating = 0;

start_translating = 1;

start_translating = 2;

premature_stop_found =

;

(

= start_translating;

< vec.

() - 3;

+= 3) {

(!premature_stop_found) {

.AddField(

,

);

.AddField(

,

(

));

premature_stop_found =

;

.AddField(

,

);

.AddField(

,

(

));

.AddField(

,

);

(!premature_stop_found) {

.AddField(

,

);

latest.

(&

);

translation,

);

.SetOutput_data().AddField(

,

(translation.size()));

(prod_vec[

] == translation[

]) {

.SetOutput_data().AddField(

,

(prod_vec.

()));

.AddField(

,

(updated_id->

(prod_id)) {

.AddField(

,

.SetOutput_data().AddField(

,

(prod_vec.

()));

=

->GetScope().GetBioseqHandle(*updated_id);

(updated_prod_vec[

] == translation[

]) {

.AddField(

,

/

(updated_prod_vec.

(),

(

)translation.size()));

.SetOutput_data().AddField(

,

(updated_prod_vec.

()));

.AddField(

, !updated_id->

(prod_id));

.AddField(

, updated_id->

());

( !

|| !

) {

(pos = vec.

() - 1; pos > 0; --pos) {

(vec[pos] !=

) {

->SetOutput_data().AddField(

,

(vec.

() - pos - 1));

w_match = 1;

w_mismatch = -4;

x_dropoff = 15;

best_pos =

;

(

curr_pos = vec.

() - 1;

curr_pos > 0 && curr_score + x_dropoff > best_score;

curr_score += vec[curr_pos] ==

? w_match : w_mismatch;

(curr_score >= best_score) {

best_score = curr_score;

tail_length = (best_pos ==

) ? 0 : vec.

() - best_pos;

->SetOutput_data().AddField(

, tail_length);

end_pos = vec.

() - 1 - tail_length;

begin_pos = end_pos > window ? end_pos - window : 0;

(

ii = 0; ii < 12; ii++) {

->SetOutput_data().AddField(

,

(pos + begin_pos));

->SetOutput_data().AddField(

, (ii <= 1));

.SetOutput_data().AddField(

, (

)overlapping_uorfs.size());

.SetOutput_data().AddField(

, (

)upstream_uorfs.size());

( !

|| !

) {

vector<CRef<CSeq_loc> > orfs;

max_orf_length_forward = 0;

max_orf_length_either = 0;

largest_forward_orf_end = 0;

max_orf_length_either =

(max_orf_length_either, orf_length);

(orf_length > max_orf_length_forward) {

max_orf_length_forward = orf_length;

largest_forward_orf_end = (*orf)->GetInt().GetTo();

max_orf_length_forward =

(max_orf_length_forward, orf_length);

->SetOutput_data().AddField(

,

(max_orf_length_forward));

->SetOutput_data().AddField(

,

(largest_forward_orf_end));

->SetOutput_data().AddField(

,

(max_orf_length_either));

vector<string> allowable_starts;

allowable_starts.push_back(

);

max_orf_length_forward = 0;

max_orf_length_either = 0;

max_orf_length_either =

(max_orf_length_either, orf_length);

(orf_length > max_orf_length_forward) {

max_orf_length_forward = orf_length;

largest_forward_orf_end = (*orf)->GetInt().GetTo();

max_orf_length_forward =

(max_orf_length_forward, orf_length);

->SetOutput_data().AddField(

,

(max_orf_length_forward));

->SetOutput_data().AddField(

,

(largest_forward_orf_end));

->SetOutput_data().AddField(

,

(max_orf_length_either));

, not_start_not_sec_count;

not_start_not_sec_count = 0;

++not_start_not_sec_count;

not_start_not_sec_count = 0;

.AddField(

,

);

.AddField(

,

not_start_not_sec_count);

vector<int> starts(

+ 1, upstream_length);

(

= upstream_length - 3;

>= 0;

-= 3) {

(codon ==

) {

starts[strength] =

;

(codon ==

|| codon ==

|| codon ==

) {

upstream_utr_atg_count(0);

(

= upstream_length - 3;

>= 0;

-= 1) {

(codon ==

) {

upstream_utr_atg_count++;

.AddField(

,

(upstream_length - starts[

]));

.AddField(

,

(upstream_length - starts[

]));

.AddField(

,

(upstream_length - starts[

]));

.AddField(

,

upstream_utr_atg_count);

vector<TSeqPos> out_indices;

.AddField(

,

( !

|| !

) {

->SetOutput_data()

.AddField(

,

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

size_t GetSize(void) const

static double GetScore(CConstRef< CHMMParameters > hmm_params, const objects::CSeq_loc &cds, objects::CScope &scope, int *const gccontent, double *const startscore=0)

static const CTrans_table & GetTransTable(int id)

HMM model parameters just create it and pass to a Gnomon engine.

static void FindStrongKozakUOrfs(const objects::CSeqVector &seq, TSeqPos cds_start, TLocVec &overlap_results, TLocVec &non_overlap_results, unsigned int min_length_bp=3, unsigned int non_overlap_min_length_bp=105, int genetic_code=1, size_t max_seq_gap=k_default_max_seq_gap)

Specifically find ORFS with a strong Kozak signal that are upstream of cds_start.

vector< CRef< objects::CSeq_loc > > TLocVec

static void FindOrfs(const string &seq, TLocVec &results, unsigned int min_length_bp=3, int genetic_code=1, const vector< string > &allowable_starts=vector< string >(), bool longest_orfs=true, size_t max_seq_gap=k_default_max_seq_gap)

Find ORFs in both orientations.

CSeqTestContext defines any contextual information that a derived class might need.

CRef< objects::CSeq_test_result > x_SkeletalTestResult(const string &test_name)

Create a Seq-test-result with some fields filled in, including a name for this test,...

CRef< objects::CSeq_test_result_set > x_TestAllCdregions(const CSerialObject &obj, const CSeqTestContext *ctx, const string &test_name, TCdregionTester cdregion_tester)

Given a Seq-id and a context, analyze all coding regions by calling a supplied function.

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

CSeq_test_result_set –.

static TSeqPos GetAmbigs(const CSeq_data &in_seq, CSeq_data *out_seq, vector< TSeqPos > *out_indices, CSeq_data::E_Choice to_code=CSeq_data::e_Ncbi2na, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

Base class for all serializable objects.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

bool CanTest(const CSerialObject &obj, const CSeqTestContext *ctx) const

Test to see whether the given object *can* be used in this test.

bool IsOrfStart(int state) const

static int SetCodonState(unsigned char ch1, unsigned char ch2, unsigned char ch3)

bool IsOrfStop(int state) const

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

const string AsFastaString(void) const

const CSeq_loc & GetEmbeddingSeq_loc(void) const

Get the nearest seq-loc containing the current range.

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

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

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

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

TSeqPos LocationOffset(const CSeq_loc &outer, const CSeq_loc &inner, EOffsetType how=eOffset_FromStart, CScope *scope=0)

returns (TSeqPos)-1 if the locations don't overlap

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

@ eOffset_FromStart

For positive-orientation strands, start = left and end = right; for reverse-orientation strands,...

CConstRef< CSeq_id > FindLatestSequence(const CSeq_id &id, CScope &scope)

Given a seq-id check its replace history and try to find the latest revision.

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

bool IsSetExcept(void) const

bool GetExcept(void) const

bool GetPseudo(void) const

const CSeqFeatData & GetData(void) const

TInst_Mol GetInst_Mol(void) const

bool IsSetPseudo(void) const

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

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

bool CanGetInst_Mol(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

bool IsSetPartial(void) const

const CSeq_loc & GetLocation(void) const

bool GetPartial(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

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

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

void SetIupacCoding(void)

Set coding to either Iupacaa or Iupacna depending on molecule type.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

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.

@ eReverseSearch

Search in a backward direction.

@ eCase

Case sensitive compare.

#define DEFINE_STATIC_FAST_MUTEX(id)

Define static fast mutex and initialize it.

Tdata & Set(void)

Assign a value to data member.

TNcbi8aa GetNcbi8aa(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TLoc & GetLoc(void) const

Get the Loc member data.

Tdata & Set(void)

Assign a value to data member.

const TLocation & GetLocation(void) const

Get the Location member data.

list< CRef< CCode_break > > TCode_break

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

const TCode & GetCode(void) const

Get the Code member data.

const TCdregion & GetCdregion(void) const

Get the variant data.

const TAa & GetAa(void) const

Get the Aa member data.

const TProduct & GetProduct(void) const

Get the Product member data.

TNcbieaa GetNcbieaa(void) const

Get the variant data.

bool CanGetCode(void) const

Check if it is safe to call GetCode method.

bool CanGetProduct(void) const

Check if it is safe to call GetProduct method.

TNcbistdaa GetNcbistdaa(void) const

Get the variant data.

const TCode_break & GetCode_break(void) const

Get the Code_break member data.

bool IsSetCode_break(void) const

individual exceptions Check if a value has been assigned to Code_break data member.

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

@ e_Ncbi8aa

NCBI8aa code.

@ e_not_set

No variant selected.

@ e_Ncbieaa

ASCII value of NCBIeaa code.

TIupacna & SetIupacna(void)

Select the variant.

Defines: CTimeFormat - storage class for time format.

static CConstRef< CSeq_id > s_FindLatest(const CSeq_id &id, CScope &scope)

static void s_CdsStopCodon(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

static void s_CdsFlags(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

static void s_InframeUpstreamStart(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

static void s_CdsLength(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

static void s_CdsCountAmbiguities(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

static CSeqVector s_GetCdregionPlusUpstream(CFeat_CI feat_iter, const CSeqTestContext *ctx, TSeqPos &upstream_length)

string s_KozakStrengthToString(EKozakStrength strength)

static void s_CompareProtProdToTrans(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

static void s_OrfExtension(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

static void s_InframeUpstreamStop(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

CConstRef< CGenetic_code > s_GetCode(const CCdregion &cdr)

static void s_Code_break(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

EKozakStrength s_GetKozakStrength(const CSeqVector &vec, TSeqPos pos)

static bool s_IsSelenocysteine(const CCode_break &code_break)

static void s_CdsStartCodon(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

static void s_Utrs(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

static void s_PrematureStopCodon(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

static void s_CodingPropensity(const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result)

static TSeqPos s_CountAmbiguities(const CSeqVector &vec)

TSeqPos CodeBreakPosInCds(const CCode_break &code_break, const CSeq_feat &feat, CScope &scope)

void TestStrongKozakUorfs(const CBioseq_Handle bsh, CSeq_test_result &result)

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