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

{

q_left_left, q_left_middle, q_left_right,

, q_right_left, q_right_middle, q_right_right;

(

);

(

);

in_pool_prot,

against_prot);

TSimpleSeqs::iterator& ext_rna,

TSimpleSeqs::iterator& first_user_in_range, TSimpleSeqs::iterator& first_user_non_in_range,

TSimpleSeqs::iterator& first_ext_in_range, TSimpleSeqs::iterator& first_ext_non_in_range,

<

t>

( CBioseq::TAnnot::iterator& annot,

& tranStrMap);

*

(

*w);

CBioseq_set::TSeq_set::const_iterator& seq,

CBioseq_set::TSeq_set::iterator& seq,

(CBioseq_set::TSeq_set::const_iterator& seq,

(CBioseq_set::TSeq_set::iterator& seq,

(CBioseq::TAnnot::const_iterator& annot);

(CBioseq::TAnnot::const_iterator& annot);

vector<long>

(CBioseq::TAnnot::const_iterator& annot);

( CBioseq::TAnnot::const_iterator& annot);

CBioseq::TAnnot::const_iterator& annot,

* qFrom,

* qTo,

* sFrom,

* sTo

(

vector<long>& left,

vector<long>& right);

CBioseq::TAnnot::const_iterator& annot,

pair<int,int>& second);

TSimpleSeqs::iterator& ext_rna,

TSimpleSeqs::iterator& first_user_in_range, TSimpleSeqs::iterator& first_user_non_in_range,

from,

to,

);

from,

to,

,

max_distance);

max_distance);

(TSimpleSeqs::iterator& seq,

TSimpleSeqs::iterator& ext_rna,

(TSimpleSeqs::iterator& seq,

TSimpleSeqs::iterator& ext_rna,

& left,

& right,

& strand_match,

& abs_left );

(

TSimpleSeqs::iterator& seq1,

TSimpleSeqs::iterator& seq2,

& overlap);

<

t1,

t2>

(

t1& l1,

t2& l2,

& overlap);

& common_subject

CBioseq::TAnnot::const_iterator& left_annot,

CBioseq::TAnnot::const_iterator& right_annot,

<

erval_type>

(

interval_type& loc);

(list<problemStr>& dest,

list<problemStr>& src);

(

TSimpleSeqs::iterator& ext_rna);

(

TSimpleSeqs::iterator& ext_rna,

TSimpleSeqs::iterator& end);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

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

@RNA_ref.hpp User-defined methods of the data storage class.

void printGeneralInfo(ostream &out=NcbiCerr)

int CollectFrameshiftedSeqs(map< string, string > &problem_names)

int CollectRNAFeatures(TProblem_locs &problem_locs)

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)

map< string, string > m_tagmap

void addLocation(string &prot_id, CBioseq &seq, CRef< CSeq_loc > &loc, const string &locus_tag)

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)

static int sequence_proximity(const int target_from, const int target_to, const int from, const int to, const int key)

CConstBeginInfo ConstBegin(void)

static stack< int > m_saved_verbosity

void erase_problems(const string &qname, diagMap &diag, const EProblem type)

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

static bool has_blast_hits(const CBioseq &seq)

int RemoveInterim2(CBioseq::TAnnot &annots)

static void IncreaseVerbosity(void)

static char * next_w(char *w)

list< long > m_previous_genome

static int get_neighboring_sequences(const TSimpleSeqs::iterator &ext_rna, TSimpleSeqs::iterator &first_user_in_range, TSimpleSeqs::iterator &first_user_non_in_range, TSimpleSeqs &seqs, const int max_distance)

bool overlaps_na(const CBioseq::TAnnot &annots)

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

void reportProblemMessage(const string &message, ostream &out=NcbiCout)

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

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

void processFeature(CSeq_annot::C_Data::TFtable::iterator &feat, TranStrMap3 &tranStrMap)

TSimpleSeqs m_simple_seqs

int find_overlap(TSimpleSeqs::iterator &seq, const TSimpleSeqs::iterator &ext_rna, TSimpleSeqs &seqs, int &overlap)

static bool hasGenomicInterval(const CBioseq &seq)

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

void reportProblemType(const EProblem type, ostream &out=NcbiCout)

static string ProblemType(const EProblem type)

static void addSimpleTab(CNcbiStrstream &buffer, const string tag, const TSimpleSeqs::iterator &ext_rna, const int max_distance)

static const CSeq_interval & getGenomicInterval(const CBioseq &seq)

int ProcessCDD(map< string, blastStr > &blastMap)

void processAnnot(CBioseq::TAnnot::iterator &annot, t &tranStrMap)

int ReadRRNA2(const string &file)

static double m_trnascan_scoreThreshold

int simple_overlaps(void)

void addLoctoSimpleSeq(TSimpleSeq &seq, const CSeq_loc &loc)

static bool hasGenomicLocation(const CBioseq &seq)

static int m_current_verbosity

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

void reportProblemSequenceName(const string &name, ostream &out=NcbiCout)

static int skip_toprot(CTypeIterator< CBioseq > &seq)

int RemoveProblems(map< string, string > &problem_seqs, LocMap &loc_map)

bool complete_overlap(const CSeq_loc &l1, const CSeq_loc &l2)

virtual void Init(void)

Initialize the application.

int CollectSimpleSeqs(TSimpleSeqs &seqs)

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

static int m_cds_overlapThreshold

int CopyInfoFromGenesToProteins(void)

===========================================================================

int ReadBlast(const char *file, map< string, blastStr > &blastMap)

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)

virtual int Run(void)

Run the application.

int StoreBlast(map< string, blastStr > &blastMap)

static char * skip_space(char *w)

static void DecreaseVerbosity(void)

int AnalyzeSeqsViaBioseqs(bool in_pool_prot, bool against_prot)

int overlaps(const TSimpleSeqs::iterator &seq1, const TSimpleSeqs::iterator &seq2, int &overlap)

TSimpleSeqs m_extRNAtable2

int ReadTagMap(const char *file)

int ReadParents(CNcbiIstream &in, const list< long > &nacc)

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)

bool overlaps_prot_na(CBioseq &seq, const CBioseq::TAnnot &annots)

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

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

bool CheckMissingRibosomalRNA(const CBioseq::TAnnot &annots)

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

void ugly_simple_overlaps_call(int &n_user_neighbors, int &n_ext_neighbors, TSimpleSeqs::iterator &ext_rna, TSimpleSeqs::iterator &first_user_in_range, TSimpleSeqs::iterator &first_user_non_in_range, TSimpleSeqs &seqs, int max_distance, TSimpleSeqs::iterator &first_ext_in_range, TSimpleSeqs::iterator &first_ext_non_in_range, string &bufferstr)

void reportProblems(const bool report_and_forget, diagMap &diag, ostream &out, const CBioseq::TAnnot &annots, const EProblem type)

bool fit_blast(const CBioseq &left, const CBioseq &right, string &common_subject)

static double m_small_tails_threshold

static double m_partThreshold

int AnalyzeSeqsViaBioseqs1(CBioseq &left)

static string getLocusTag(const CBioseq &seq)

bool match_na(const CSeq_feat &f1, const string &type1)

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 NormalizeSeqentry(CSeq_entry &entry)

void dump_fasta_for_pretty_blast(diagMap &diag)

void append_misc_feature(CBioseq_set::TSeq_set &seqs, const string &name, EProblem problem_type)

int ReadTRNA2(const string &file)

static void PushVerbosity(void)

namespace ncbi::objects::

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

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

main entry point for tests

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

unsigned int TSeqPos

Type for sequence locations and lengths.

ESerialDataFormat

Data file format.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

ENa_strand

strand of nucleic acid

list< CRef< CSeq_entry > > TSeq_set

list< CRef< CSeq_feat > > TFtable

list< CRef< CSeq_annot > > TAnnot

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

const struct ncbi::grid::netcache::search::fields::KEY key

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

const GenericPointer< typename T::ValueType > T2 value

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

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

@ eMyFeatureType_normal_tRNA

@ eMyFeatureType_atypical_tRNA

@ eMyFeatureType_pseudo_tRNA

@ eMyFeatureType_hypo_CDS

@ eMyFeatureType_normal_CDS

ESerialDataFormat s_GetFormat(const string &name)

vector< TExtRNA > TExtRNAtable

int addProblems(list< problemStr > &dest, const list< problemStr > &src)

vector< TSimplePair > TSimplePairs

string get_trna_string(const CSeq_feat &feat)

string GetStringDescr(const CBioseq &bioseq)

string Get3type(const CRNA_ref &rna)

EMyFeatureType get_my_feat_type(const CSeq_feat &feat, const LocMap &loc_map)

map< string, TProblem_loc > TProblem_locs

string GetLocationString(const interval_type &loc)

string get_title(const CBioseq &seq)

map< CSeq_id::EAccessionInfo, TGenfo > TranStr3

string let1_2_let3(char let1)

EMyFeatureType get_my_seq_type(const CBioseq &seq)

map< string, TranStr3 > TranStrMap3

string diagName(const string &type, const string &value)

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

map< string, CRef< CSeq_feat > > LocMap

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

string printed_ranges(const CSeq_loc &seq_interval)

map< string, diagStr > diagMap

map< long, long > parent_map

string GetRNAname(const CSeq_feat &feat)

list< TSimpleSeq > TSimpleSeqs

string GetRRNAtype(const CRNA_ref &rna)

string printed_range(const TSeqPos from2, const TSeqPos to2)

list< problemStr > problems

CRef< const CSeq_loc > loc2

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