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

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45 if

(seq->type !=

"CDS"

)

continue

;

49 len

+= e2->to - e2->from + 1;

57 bool

edge_from =

false

;

58 bool

edge_to =

false

;

59 bool

fuzzy_edge =

false

;

66 if

(e2->from < 3) { edge=

true

; edge_from=

true

;

if

(e2->fuzzy_from) fuzzy_edge =

true

; }

67 if

(e2->to > len_nu - 4 ) { edge=

true

; edge_to=

true

;

if

(e2->fuzzy_to) fuzzy_edge =

true

; }

69 if

(edge_from && edge_to && seq->exons.size()>1 ) { edge=

false

; }

72

misc <<

"Annotation is too short "

<< seq->name <<

'\0'

;

74

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

75

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

80 string

diag_name = seq->name;

81

bufferstr <<

"Short protein "

<< diag_name <<

" "

<< range <<

'\0'

;

85 m_diag

[diag_name].problems.push_back(problem);

88

"eShortProtein"

"\t" 89

<< bufferstr.str() <<

"\t" 96 NcbiCerr

"WARNING: short annotation on the edge does not have corresponding fuzzy ends "

<< diag_name <<

" "

<< range <<

NcbiEndl

;

100 NcbiCerr

"INFO: short annotation on the edge with corresponding fuzzy end "

<< diag_name <<

" "

<< range <<

NcbiEndl

;

static bool PrintDetails(int current_verbosity=m_current_verbosity)

TSimpleSeqs m_simple_seqs

const CBioseq & get_nucleotide_seq(const CBioseq &seq)

static int m_shortProteinThreshold

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

#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.

ENa_strand

strand of nucleic acid

list< CRef< CSeq_entry > > TSeq_set

const TInst & GetInst(void) const

Get the Inst member data.

TLength GetLength(void) const

Get the Length member data.

vector< TSimplePair > TSimplePairs

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

list< TSimpleSeq > TSimpleSeqs

string printed_range(const TSeqPos from2, const TSeqPos to2)

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