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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqalign_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/cobalt/seqalign.cpp Source File

59

vector<

int

>& indices)

const 61  int

num_queries = align.size();

62  int

length = align[0].GetLength();

68

retval->

SetDim

(num_queries);

73

denseg->

SetDim

(num_queries);

79

vector<int> seq_off(num_queries, 0);

80  for

(

int i

= 0;

i

< num_queries;

i

++) {

81  const CSeq_loc

& seqloc = *m_tQueries[indices[

i

]];

88

denseg->

SetIds

().push_back(

id

);

90  else if

(seqloc.

IsInt

()) {

93

denseg->

SetIds

().push_back(

id

);

107  for

(

i

= 1, seg_len = 1;

i

< length;

i

++, seg_len++) {

108  for

(j = 0; j < num_queries; j++) {

120  if

(j < num_queries) {

125  for

(j = 0; j < num_queries; j++) {

130

denseg->

SetStarts

().push_back(seq_off[j]);

131

seq_off[j] += seg_len;

134

denseg->

SetLens

().push_back(seg_len);

142  for

(j = 0; j < num_queries; j++) {

146

denseg->

SetStarts

().push_back(seq_off[j]);

148

denseg->

SetLens

().push_back(seg_len);

151

retval->

SetSegs

().SetDenseg(*denseg);

161  "Results were not computed"

);

165

vector<int> indices(num_queries);

169  for

(

int i

= 0;

i

< num_queries;

i

++) {

179  int

num_selected = indices.size();

180

vector<CSequence> new_align(num_selected);

181

vector<int> new_indices(num_selected);

186  for

(

int i

= 0;

i

< num_selected;

i

++) {

187  if

(indices[

i

] < 0 || indices[

i

] >=

m_Results

.size()) {

189  "Sequence index out of range"

);

192

new_indices[

i

] =

i

;

Simultaneously align multiple protein sequences.

CRef< objects::CSeq_align > x_GetSeqalign(const vector< CSequence > &align, vector< int > &indices) const

Produce a seqalign representing the specified alignment, using a subset of the sequences.

CRef< objects::CSeq_align > GetResults(void) const

Retrieve the current aligned results in Seq-align format.

vector< CSequence > m_Results

Class for representing protein sequences.

static void CompressSequences(vector< CSequence > &seq, vector< int > index_list)

Given a collection of sequences, remove all sequence positions where a subset of the sequences all co...

static const unsigned char kGapChar

The ncbistdaa code for a gap.

Interface for CMultiAligner.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#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.

TLens & SetLens(void)

Assign a value to Lens data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetType(TType value)

Assign a value to Type data member.

TStarts & SetStarts(void)

Assign a value to Starts data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

TIds & SetIds(void)

Assign a value to Ids data member.

const TId & GetId(void) const

Get the Id member data.

const TWhole & GetWhole(void) const

Get the variant data.

TFrom GetFrom(void) const

Get the From member data.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

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