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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/fasta__exception_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/readers/fasta_exception.cpp Source File

50 out

"No Bad Residues"

;

54 out

"Bad Residues = "

;

55 if

( m_BadResiduePositions.m_SeqId ) {

56 out

<< m_BadResiduePositions.m_SeqId->GetSeqIdString(

true

);

58 out

"Seq-id ::= NULL"

;

60 out

", positions: "

;

61

m_BadResiduePositions.ConvertBadIndexesToString(

out

);

67 const int

lineNum = new_line_iter->first;

68 const

vector<TSeqPos> & src_seqpos_vec = new_line_iter->second;

70 if

( src_seqpos_vec.empty() ) {

74

vector<TSeqPos> & dest_seqpos_vec =

75

m_BadIndexMap[lineNum];

76 copy

( src_seqpos_vec.begin(), src_seqpos_vec.end(),

77

back_inserter(dest_seqpos_vec) );

83 unsigned int

maxRanges )

const 85 const char

*line_prefix =

""

;

86 unsigned int

iRangesFound = 0;

88 const int

lineNum = index_map_iter->first;

89 const

vector<TSeqPos> & badIndexesOnLine = index_map_iter->second;

92 _ASSERT

(adjacent_find(badIndexesOnLine.begin(), badIndexesOnLine.end(),

93

std::greater<int>()) == badIndexesOnLine.end() );

95 typedef

pair<TSeqPos, TSeqPos>

TRange

;

100 ITERATE

( vector<TSeqPos>, idx_iter, badIndexesOnLine ) {

104 if

( rangesFound.empty() ) {

105

rangesFound.push_back(

TRange

(idx, idx));

110 const TSeqPos

last_idx = rangesFound.back().second;

111 if

( idx == (last_idx+1) ) {

113

++rangesFound.back().second;

117 if

( iRangesFound >= maxRanges ) {

122

rangesFound.push_back(

TRange

(idx, idx));

127 out

<< line_prefix <<

"On line "

<< lineNum <<

": "

;

130 const char

*pos_prefix =

""

;

131 for

(

unsigned int

rng_idx = 0;

132

( rng_idx < rangesFound.size() );

136 const TRange

&range = rangesFound[rng_idx];

137 out

<< (range.first + 1);

138 if

( range.first != range.second ) {

139 out

"-"

<< (range.second + 1);

144 if

(iRangesFound > maxRanges) {

145 out

", and more"

;

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

The NCBI C++ standard methods for dealing with std::string.

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

main entry point for tests

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

constexpr bool empty(list< Ts... >) noexcept

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

vector< CRef< CSeq_interval > > TRangeVec

void AddBadIndexMap(const TBadIndexMap &additionalBadIndexMap)

void ConvertBadIndexesToString(CNcbiOstream &out, unsigned int maxRanges=1000) const

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