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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/missing_8cpp_source.html below:

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

49 if

( !(*gen_feature)->GetData().IsFtable() )

continue

;

73 if

( !(*f1)->GetData().IsRna() )

continue

;

77 if

( !(*f1)->GetData().GetRna().CanGetExt() )

79 NcbiCerr

"CReadBlastApp::CheckMissingRibosomalRNA[feats]: FATAL: no ext feature in rRNA"

NcbiEndl

;

83 if

(

type

"5S"

) {has5S =

true

; }

84 if

(

type

"16S"

) {has16S =

true

; }

85 if

(

type

"23S"

) {has23S =

true

; }

89 NcbiCerr

"CReadBlastApp::CheckMissingRibosomalRNA[feats]: ERROR: 5S ribosomal RNA is missing"

NcbiEndl

;

91 NcbiCerr

"CReadBlastApp::CheckMissingRibosomalRNA[feats]: ERROR: 16S ribosomal RNA is missing"

NcbiEndl

;

93 NcbiCerr

"CReadBlastApp::CheckMissingRibosomalRNA[feats]: ERROR: 23S ribosomal RNA is missing"

NcbiEndl

;

100

TSimpleSeqs::iterator& ext_rna,

101

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

103

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

108 if

(first_user_in_range==seqs.end())

110 NcbiCerr

"ugly_simple_overlaps_call: first_user_in_range is already at the end"

NcbiEndl

;

124 if

(first_user_in_range==seqs.end())

126 NcbiCerr

"ugly_simple_overlaps_call: after call: first_user_in_range is already at the end"

NcbiEndl

;

136 for

(TSimpleSeqs::iterator entry = first_ext_in_range; entry!= first_ext_non_in_range; entry++)

138 if

(entry==ext_rna)

continue

;

141 for

(TSimpleSeqs::iterator entry = first_user_in_range; entry!=first_user_non_in_range; entry++)

157

TSimpleSeqs::iterator first_user_in_range = seqs.begin();

158

TSimpleSeqs::iterator first_user_non_in_range = seqs.begin();

159

TSimpleSeqs::iterator first_ext_in_range =

m_extRNAtable2

.begin();

160

TSimpleSeqs::iterator first_ext_non_in_range =

m_extRNAtable2

.begin();

161

TSimpleSeqs::iterator seq = seqs.begin();

165

from = ext_rna->exons[0].from;

166

to = ext_rna->exons[ext_rna->exons.size()-1].to;

168 int

range_scale = to - from;

170 string

type2 = ext_rna->name;

177 string

diag_name = ext_rna->name;

179 int

n_user_neighbors=0;

int

n_ext_neighbors = 0;

string

bufferstr=

""

;

188

"["

<< ext_rna_range <<

"]" 189

"["

<< seq2_range <<

"]" 192

"Overlap = "

<< overlap

198

absent = absent && (!overlap || ext_rna->type != seq2->type);

199 bool

bad_strand = (overlap>0 && ext_rna->type == seq2->type && strand != seq2->exons[0].strand);

200 if

(!bad_strand)

continue

;

201 string

diag_name2 = seq2->name;

203

from2 = seq2->exons[0].from;

204

to2 = seq2->exons[seq2->exons.size()-1].to;

206 if

(!bufferstr.size())

210 if

(first_user_in_range==seqs.end())

212 NcbiCerr

"simple_overlaps: first_user_in_range is already at the end"

NcbiEndl

;

220

ext_rna, first_user_in_range, first_user_non_in_range, seqs, max_distance,

221

first_ext_in_range, first_ext_non_in_range, bufferstr);

226

misc_feat <<

"RNA does not match strand for feature located at "

<< seq_range <<

NcbiEndl

;

229 problemStr

problem = {trnaStrandProblem, bufferstr, misc_feat.str(),

""

, from2, to2, strand};

230 m_diag

[diag_name2].problems.push_back(problem);

233

"eTRNABadStrand"

"\t" 237 problemStr

problem2 = {trnaStrandProblem, bufferstr,

""

, from, to, strand};

238 m_diag

[diag_name].problems.push_back(problem2);

244 if

(!bufferstr.size())

247

ext_rna, first_user_in_range, first_user_non_in_range, seqs, max_distance,

248

first_ext_in_range, first_ext_non_in_range, bufferstr);

251

misc_feat <<

"no RNA in the input this type: "

<<type2 <<

"["

<< ext_rna_range <<

"]"

NcbiEndl

;

254 m_diag

[diag_name].problems.push_back(problem);

257

"eTRNAAbsent"

"\t" 261 m_diag

[diag_name].problems.push_back(problem2);

265 if

(first_user_in_range==seqs.end()) first_user_in_range=seq;

276 const

TSimpleSeqs::iterator& ext_rna,

277

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

282 int

from = ext_rna->exons[0].from;

283 int

to = ext_rna->exons[ext_rna->exons.size()-1].to;

285 bool

first_in_range_set =

false

;

289 if

(first_user_in_range==seqs.end())

291 NcbiCerr

"get_neighboring_sequences: first_user_in_range is already at the end"

NcbiEndl

;

295 NcbiCerr

"get_neighboring_sequences: first_user_in_range = " 300

TSimpleSeqs::iterator seq = first_user_in_range;

301 for

(; seq !=seqs.end(); seq++)

304 int

from2 = seq->exons[0].from;

305 int

to2 = seq->exons[seq->exons.size()-1].to;

306 if

(to2-from2> 50000)

308 NcbiCerr

"get_neighboring_sequences: WARNING: span of annotation " 309

<< seq->locus_tag <<

"" 310

"["

<< seq->name<<

"]," 311

"["

<< seq->description<<

"]" 312

" is > 50000, probably a break in a circular molecule cutting across the annotation. This annotation will be ignored."

NcbiEndl

;

318 NcbiCerr

"get_neighboring_sequences: first_in_range_set = "

<< first_in_range_set <<

NcbiEndl

;

321 if

(proximity<0)

continue

;

324 if

(!first_in_range_set) { first_user_in_range = seq; first_in_range_set=

true

; }

332 if

(

PrintDetails

())

NcbiCerr

"get_neighboring_sequences: after cycle first_in_range_set = " 334

first_user_non_in_range = seq;

335 if

(!first_in_range_set) {first_user_in_range = first_user_non_in_range = seqs.end();}

336 if

(first_user_non_in_range==seqs.end())

340 if

(first_user_in_range==seqs.end())

349 const int

from,

const int

to,

const int key

)

352 int

range_scale = target_to - target_from;

359 int

neighbor_factor = 10;

361 int

max_range = 5000;

362 int

max_distance = range_scale * neighbor_factor;

363 if

(max_distance < min_range) max_distance = min_range;

364 if

(max_distance > max_range) max_distance = max_range;

369 const int

from,

const int

to,

const int key

const int

max_distance)

371 if

(to < target_from - max_distance )

return

-1;

372 if

(from > target_to + max_distance )

return

+1;

377 const int

max_distance)

383

<< max_distance <<

"\t" 384

<< ext_rna->type <<

"\t" 385

<< ext_rna->name <<

"("

<< ext_rna->locus_tag <<

")"

"\t" 386

<< ext_rna->exons[0].from <<

"\t" 387

<< ext_rna->description <<

"\t"

static int m_verbosity_threshold

static bool PrintDetails(int current_verbosity=m_current_verbosity)

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

static void IncreaseVerbosity(void)

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)

TSimpleSeqs m_simple_seqs

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

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

int simple_overlaps(void)

static void DecreaseVerbosity(void)

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

TSimpleSeqs m_extRNAtable2

bool CheckMissingRibosomalRNA(const CBioseq::TAnnot &annots)

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)

#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.

EType

type of RNA feature

ENa_strand

strand of nucleic acid

list< CRef< CSeq_feat > > TFtable

list< CRef< CSeq_annot > > TAnnot

unsigned int

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

static int get_max_distance(const int range_scale)

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

vector< TSimplePair > TSimplePairs

list< TSimpleSeq > TSimpleSeqs

string GetRRNAtype(const CRNA_ref &rna)

string printed_range(const TSeqPos from2, const TSeqPos to2)

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