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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/match_8cpp_source.html below:

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

43 bool

is_rrna = type1 ==

"16S"

|| type1 ==

"23S"

|| type1 ==

"5S"

;

44 string

diag_name_rna = is_rrna ?

"rRNA"

:

"tRNA"

;

45 string

diag_name =

(diag_name_rna, type1);

49 int

gleft=0, gright=0;

52 bool

match_ext=

false

;

53 int

input_left, input_right;

62

input_range_stream << (input_left + 1) <<

"..."

<< (input_right + 1) <<

'\0'

;

63 string

input_range = input_range_stream.str();

66 string

type2 = is_rrna ? ext_rna->type : ext_rna->type3;

74

<<

"\t key="

<<ext_rna->key<<

"\n" 75

<<

"\t locus_tag"

<<ext_rna->locus_tag<<

"\n" 76

<<

"\t name"

<<ext_rna->name<<

"\n" 77

<<

"\t description"

<<ext_rna->description<<

"\n" 78

<<

"\t type"

<<ext_rna->type<<

"\n" 79

<<

"\t type3"

<<ext_rna->type3<<

"\n" 80

<<

"\t exons[0].from"

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

"\n" 81

<<

"\t exons[0].to"

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

"\n" 82

<<

"\t exons[0].strand"

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

"\n" 87

cerr <<

" type mismatch, skipping\n"

;

95 int

overlap =

(f1, *ext_rna, left, right, strand_match, abs_left);

99

cerr <<

" overlap 0, skipping\n"

;

107

cerr <<

" strand mismatch, skipping\n"

;

112 if

(!match_ext ||

(left)+

(right)<

(gleft)+

(gright) )

118

gabs_left = abs_left;

125 buffer

<<

"no external tRNA for this aminoacid: " 126

<<type1 <<

"["

<< input_range <<

"]"

<<

;

128 buffer

<<

"no external rRNA for this rRNA type: " 129

<<type1 <<

"["

<< input_range <<

"]"

<<

;

135

misc_feat <<

.str() <<

'\0'

;

138 m_diag

[diag_name].problems.push_back(problem);

141 if

(!match_ext && !absent)

145 buffer

<<

"tRNA does not match strand this aminoacid: " 146

<<type1 <<

"["

<< input_range <<

"]"

<<

;

148 buffer

<<

"rRNA does not match strand this rRNA type: " 149

<<type1 <<

"["

<< input_range <<

"]"

<<

;

155

misc_feat <<

.str() <<

'\0'

;

158 m_diag

[diag_name].problems.push_back(problem);

166 buffer

<<

"closest "

<< diag_name_rna

167

<<

"for ("

<<type1 <<

"["

<< input_range <<

"]" 168

<<

") does not even overlap"

<<

;

172

misc_feat <<

.str() <<

'\0'

;

177 m_diag

[diag_name].problems.push_back(problem);

183 buffer

<<

"closest tRNA for this aminoacid: " 184

<<type1 <<

"["

<< input_range <<

"]" 185

<<

" have mismatched ends:"

<<

;

187 buffer

<<

"closest rRNA for this rRNA type: " 188

<<type1 <<

"["

<< input_range <<

"]" 189

<<

" have mismatched ends:"

<<

;

192 buffer

<<

"left: "

<< gleft <<

", right: "

<< gright <<

" bp shifted relative to the calculated ends"

<<

;

195

misc_feat <<

.str() <<

'\0'

;

198 m_diag

[diag_name].problems.push_back(problem);

227 int

input_left, input_right, calc_left, calc_right;

230

abs_left = input_left;

232

calc_left = ext_rna.

[0].from;

233

calc_right= ext_rna.

[0].to;

236

left = input_left - calc_left;

237

right = input_right - calc_right;

239 int

max_left =

(input_left, calc_left);

240 int

min_right =

(input_right, calc_right);

242 result

= min_right>max_left ? min_right-max_left : 0;

246

<< input_right <<

"," 257

strand_match = input_strand == calc_strand;

259

<<

(input_strand) <<

"," 260

<<

(calc_strand) <<

"," 261

<< strand_match <<

"," 266

strand_match =

true

;

static bool PrintDetails(int current_verbosity=m_current_verbosity)

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

TSimpleSeqs m_extRNAtable2

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

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

namespace ncbi::objects::

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const TLocation & GetLocation(void) const

Get the Location member data.

ENa_strand

strand of nucleic acid

unsigned int

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

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

list< TSimpleSeq > TSimpleSeqs

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