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NCBI C++ ToolKit: src/algo/blast/unit_tests/api/seqalign_set_convert.cpp Source File

54 #if defined(VERBOSE_DEBUG) 55

ofstream

out

(fname.c_str());

57  throw

runtime_error(

"Failed to open"

+ fname);

66  if

( !(*s)->CanGetId() ) {

70  _ASSERT

((*s)->GetId().IsStr());

71  const string

score_type = (*s)->GetId().GetStr();

72  if

(score_type ==

"score"

) {

73

retval.

score

= (*s)->GetValue().GetInt();

74

}

else if

(score_type ==

"e_value"

) {

75

retval.

evalue

= (*s)->GetValue().GetReal();

76

}

else if

(score_type ==

"bit_score"

) {

77

retval.

bit_score

= (*s)->GetValue().GetReal();

78

}

else if

(score_type ==

"num_ident"

) {

79

retval.

num_ident

= (*s)->GetValue().GetInt();

86  string

fname(

"densegconvert.asn"

);

90  throw

runtime_error(

"Invalid number of dimensions"

);

96  copy

(denseg.GetStarts().begin(),

97

denseg.GetStarts().end(),

98

back_inserter(retval.

starts

));

100  copy

(denseg.GetLens().begin(),

101

denseg.GetLens().end(),

102

back_inserter(retval.

lengths

));

103  _ASSERT

(retval.

lengths

.size() == (

size_t

)denseg.GetNumseg());

107  _ASSERT

(ids.size() == (

size_t

)denseg.GetDim());

110  if

(query_id->

IsGi

()) {

115  if

(subj_id->

IsGi

()) {

123  string

fname(

"seqalignconvert.asn"

);

127  throw

runtime_error(

"Seq-align is not of partial type"

);

130  throw

runtime_error(

"Invalid number of dimensions"

);

137  switch

(segs.

Which

()) {

146  throw

runtime_error(

"Std-seg support is not implemented"

);

150  throw

runtime_error(

"Unsupported alignment data type"

);

155

std::vector<SeqAlign>& retval)

157  string

fname(

"blastseqalignconvert.asn"

);

162

retval.push_back(neutral_seqalign);

166

std::vector<SeqAlign>& retval)

168  if

( !ss.CanGet() ) {

169  throw

runtime_error(

"Empty Seq-align-set"

);

User-defined methods of the data storage class.

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

main entry point for tests

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define MSerial_AsnText

I/O stream manipulators –.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

const TDenseg & GetDenseg(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

vector< CRef< CScore > > TScore

vector< CRef< CSeq_id > > TIds

bool IsStd(void) const

Check if variant Std is selected.

list< CRef< CSeq_align > > Tdata

bool IsDenseg(void) const

Check if variant Denseg is selected.

@ eType_partial

mapping pieces together

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

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

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

void DensegConvert(const objects::CDense_seg &denseg, SeqAlign &retval)

void s_PrintTextAsnObject(const string fname, const T &obj)

void SetScores(const CSeq_align::TScore &scores, SeqAlign &retval)

void SeqAlignConvert(const objects::CSeq_align &sa, SeqAlign &retval)

void BlastSeqAlignSetConvert(const objects::CSeq_align &sa, std::vector< SeqAlign > &retval)

void SeqAlignSetConvert(const objects::CSeq_align_set &ss, std::vector< SeqAlign > &retval)

Converts a Seq-align-set into a neutral seqalign for use with the CSeqAlignCmp class.

Neutral sequence alignment (for representing an HSP in BLAST)

std::vector< TSeqPos > lengths

Lengths of aligned segments.

double bit_score

HSP bit score.

int num_ident

Number of identical residues.

double evalue

HSP evalue.

CAlignedGis sequence_gis

Gis of the aligned sequences.

std::vector< int > starts

Query/Subject starting offsets.

int query_strand

Strand of the query sequence.

int subject_strand

Strand of the subject sequence.

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