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NCBI C++ ToolKit: src/app/read_blast_result/read_blast_result_lib.cpp Source File

}

(name ==

) {

}

(name ==

) {

(runtime_error,

+ name);

name = (*score)->GetId().GetStr();

(name!=

)

;

.push_back((*score)->GetValue().GetInt());

(vector<long>, gi1, left)

(vector<long>, gi2, right)

fn =

()[

].AsString();

string::size_type ipos=fn.rfind(

);

(ipos!=string::npos) fn.erase(ipos);

ipos=fn.rfind(

);

fncdd = fn +

;

unique_ptr<CNcbiOfstream> out2 (

(fn.c_str()));

unique_ptr<CNcbiOfstream> out2_cdd (

(fncdd.c_str()));

<<

<< range1 <<

<< report->

<<

<<

<<

;

<<

;

<<

;

<<

;

<<

;

<<

;

<<

<< report->

<<

<<

<<

<< report->

<<

<<

<<

<<

<<

<< report->

<<

<<

<<

<< report->

<<

<<

;

<<

<< -report->

<<

<<

;

<<

<<

;

( !(*f)->GetData().IsRna() )

;

<<

<<

;

(aname == loc_map.

())

<<

rna_feats.push_back(aname->second);

(aname == loc_map.

())

& gene=aname->second->GetData().GetGene();

& nu_id = inter->GetId();

(!(*seq_nu)->IsSeq())

;

(!(*seq_nu)->GetSeq().IsNa())

;

& nu_ids = (*seq_nu)->GetSeq().GetId();

((*cnu_id)->Compare(nu_id) ==

)

(*seq_nu)->GetSeq();

<<

<<

;

<<

<< name <<

;

(parent->

())

(parent!=

&& !parent->

())

<<

<< name <<

;

(!parent->

())

;

<<

<< name <<

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

:

;

;

<<

<< let1 <<

<< (

)let1 <<

<<

;

(!(*annot)->GetData().IsAlign())

;

perfect.size();

CBioseq::TAnnot::const_iterator& annot,

qFrom, qTo, sFrom, sTo;

(annot, &qFrom, &qTo, &sFrom, &sTo);

qtails = qLen - qTo + qFrom - 1;

stails = sLen - sTo + sFrom - 1;

(double)qtails/qLen <

&&

(

)stails/sLen <

&&

s_name.find(

) == string::npos;

[ihit].s_name = s_name;

pair<int,int>& second)

(

.first != second.first)

.first < second.first;

.second < second.second;

(

->GetSeq().IsAa())

<<

<<

;

<<

<<

;

from1, to1, from2, to2;

(left_genomic_int, from1, to1, strand1);

(right_genomic_int, from2, to2, strand2);

from1 < from2;

<<

<< seqs.size()

((*seq)->IsSet())

((*seq)->SetSet().SetSeq_set());

(

==

)

(

.find(

) != string::npos)

(*w && !

(*w)) ++w;

(*w &&

(*w)) ++w;

(nums=0 ;seq.

(); ++seq, nums++)

(!inst.

())

;

(nums=0 ;seq; ++seq, nums++)

(!inst.

())

;

( seq != seqs.end() &&

(seq != seqs.end()) ;

( seq != seqs.end() &&

(seq != seqs.end()) ;

CBioseq_set::TSeq_set::const_iterator& seq,

( seq != seqs.end() &&

(seq != seqs.end()) ;

CBioseq_set::TSeq_set::iterator& seq,

( seq != seqs.end() &&

(seq != seqs.end()) ;

max_acc_len=0xF;

ifstream

(

.c_str());

(!

.is_open())

;

list<long> scratch_acc;

[max_acc_len+2];

.getline(

, max_acc_len+1);

string::size_type ipos=string::npos;

((ipos=

.find_first_of(

)) != string::npos)

(

.size()>max_acc_len)

;

(

.find_first_not_of(

) != string::npos)

;

scratch_acc.push_back(atol(

.c_str()));

(!scratch_acc.size())

;

input_acc = scratch_acc;

(

argc,

* argv[])

Class holding information about root of non-modifiable object hierarchy Do not use it directly.

CSeq_entry * GetParentEntry(void) const

Class holding information about root of non-modifiable object hierarchy Do not use it directly.

void GetDate(string *label, bool year_only=false) const

Append a standardized string representation of the date to the label.

FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>

void printGeneralInfo(ostream &out=NcbiCerr)

static bool hasProblems(const CBioseq &seq, diagMap &diag, const EProblem type)

static int m_verbosity_threshold

static bool PrintDetails(int current_verbosity=m_current_verbosity)

static string GetProtName(const CBioseq &seq)

static bool less_pair(const pair< int, int > &first, const pair< int, int > &second)

static bool giMatch(const vector< long > &left, const vector< long > &right)

static int getQueryLen(const CBioseq &seq)

static vector< long > getGIs(CBioseq::TAnnot::const_iterator &annot)

CConstBeginInfo ConstBegin(void)

static stack< int > m_saved_verbosity

static bool has_blast_hits(const CBioseq &seq)

static void IncreaseVerbosity(void)

static char * next_w(char *w)

static int collectPerfectHits(vector< perfectHitStr > &perfect, const CBioseq &seq)

static void printOverlapReport(distanceReportStr *report, ostream &out=NcbiCout)

static string getAnnotName(CBioseq::TAnnot::const_iterator &annot)

static double m_trnascan_scoreThreshold

static bool hasGenomicLocation(const CBioseq &seq)

static int m_current_verbosity

bool ReadPreviousAcc(const string &file, list< long > &input_acc)

static int skip_toprot(CTypeIterator< CBioseq > &seq)

static void dumpAlignment(const string &alignment, const string &file)

static int m_cds_overlapThreshold

static double m_entireThreshold

static int m_rna_overlapThreshold

void GetRNAfeats(const LocMap &loc_map, CSeq_annot::C_Data::TFtable &rna_feats, const CSeq_annot::C_Data::TFtable &feats)

int SetParents(CSeq_entry *parent, CBioseq_set::TSeq_set &where)

static void check_alignment(CBioseq::TAnnot::const_iterator &annot, const CBioseq &seq, vector< perfectHitStr > &results)

static ECoreDataType getCoreDataType(istream &in)

static bool is_prot_entry(const CBioseq &seq)

const CBioseq & get_nucleotide_seq(const CBioseq &seq)

static char * skip_space(char *w)

static void DecreaseVerbosity(void)

static bool less_simple_seq(const TSimpleSeq &first, const TSimpleSeq &second)

static void getBounds(CBioseq::TAnnot::const_iterator &annot, int *qFrom, int *qTo, int *sFrom, int *sTo)

static void printPerfectHit(const perfectHitStr &hit, ostream &out=NcbiCout)

static int m_shortProteinThreshold

static void PopVerbosity(void)

ECoreDataType m_coreDataType

static const CSeq_loc & getGenomicLocation(const CBioseq &seq)

static void printReport(distanceReportStr *report, ostream &out=NcbiCout)

static int getLenScore(CBioseq::TAnnot::const_iterator &annot)

static bool less_seq(const CRef< CSeq_entry > &first, const CRef< CSeq_entry > &second)

static void getFromTo(const CSeq_loc &loc, TSeqPos &from, TSeqPos &to, ENa_strand &strand)

static double m_small_tails_threshold

static double m_partThreshold

static double m_eThreshold

static bool skip_to_valid_seq_cand(CBioseq_set::TSeq_set::const_iterator &seq, const CBioseq_set::TSeq_set &seqs)

void dump_fasta_for_pretty_blast(diagMap &diag)

static void PushVerbosity(void)

CSeq_entry * GetParentEntry(void) const

namespace ncbi::objects::

static bool IsAa(EMol mol)

Template class for iteration on objects of class C (non-medifiable version)

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

std::ofstream out("events_result.xml")

main entry point for tests

#define test(a, b, c, d, e)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

#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.

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

#define THROW1_TRACE(exception_class, exception_arg)

Throw trace.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

@ e_YES

SeqIds compared, but are different.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

virtual void Write(const CSeq_entry_Handle &handle, const CSeq_loc *location=0)

Unspecified locations designate complete sequences; non-empty custom titles override the usual title ...

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

vector< CRef< CScore > > TScore

ENa_strand

strand of nucleic acid

const TSeq & GetSeq(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

bool CanGetSeq_set(void) const

Check if it is safe to call GetSeq_set method.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

list< CRef< CSeq_entry > > TSeq_set

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

const TInst & GetInst(void) const

Get the Inst member data.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

list< CRef< CSeq_id > > TId

list< CRef< CSeq_feat > > TFtable

list< CRef< CSeq_annot > > TAnnot

const TTool & GetTool(void) const

Get the Tool member data.

const TReldate & GetReldate(void) const

Get the Reldate member data.

const TComment & GetComment(void) const

Get the Comment member data.

bool CanGetTool(void) const

Check if it is safe to call GetTool method.

bool CanGetReldate(void) const

Check if it is safe to call GetReldate method.

bool CanGetComment(void) const

Check if it is safe to call GetComment method.

const TEntrys & GetEntrys(void) const

Get the variant data.

const TUser_tag & GetUser_tag(void) const

Get the User_tag member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TSub & GetSub(void) const

Get the Sub member data.

bool IsEntrys(void) const

Check if variant Entrys is selected.

bool CanGetUser_tag(void) const

Check if it is safe to call GetUser_tag method.

unsigned int

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

string GetLocationString(const CSeq_feat &f)

std::istream & in(std::istream &in_, double &x_)

string GetStringDescr(const CBioseq &bioseq)

string printed_ranges(const CSeq_loc &seq_interval)

string printed_range(const TSeqPos from2, const TSeqPos to2)

ESerialDataFormat s_GetFormat(const string &name)

string let1_2_let3(char let1)

int main(int argc, const char *argv[])

string GetLocusTag(const CSeq_feat &f, const LocMap &loc_map)

CBioseq_set::TSeq_set * get_parent_seqset(const CBioseq &seq)

CRef< const CSeq_loc > loc1

CRef< const CSeq_loc > loc2

CRef< CTestThread > thr[k_NumThreadsMax]

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