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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/data4xml2format_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/format/data4xml2format.cpp Source File

38 #ifndef SKIP_DOXYGEN_PROCESSING 50 const

vector<align_format::CAlignFormatUtil::SDbInfo> & dbsInfo) :

52

m_DbName(

kEmptyStr

), m_NumSequences(0), m_NumBases(0),

57 results

.GetMaskedQueryRegions(m_QueryMasks);

68

m_DbName(

kEmptyStr

), m_NumSequences(0), m_NumBases(0),

72

x_InitSubjects(subjectsInfo);

73 results

.GetMaskedQueryRegions(m_QueryMasks);

82 const

vector<CAlignFormatUtil::SDbInfo> & dbsInfo) :

84

m_DbName(

kEmptyStr

), m_NumSequences(0), m_NumBases(0),

87

x_InitCommon(resultSet[0], opts);

89

resultSet[0].GetMaskedQueryRegions(m_QueryMasks);

90 for

(

unsigned int i

= 0;

< resultSet.

size

();

++) {

91

x_InitResults(resultSet[

]);

102

m_DbName(

kEmptyStr

), m_NumSequences(0), m_NumBases(0),

103

m_TaxDBFound(

), m_isBl2seq(

), m_isIterative(

), m_Matrix(

)

105

x_InitCommon(resultSet[0], opts);

106

x_InitSubjects(subjectsInfo);

107

resultSet[0].GetMaskedQueryRegions(m_QueryMasks);

108 for

(

unsigned int i

= 0;

< resultSet.

size

();

++) {

109

x_InitResults(resultSet[

]);

118 string

errors =

results

.GetErrorStrings();

120 if

( !errors.empty() ) {

123

errors +=

results

.GetWarningStrings();

125 if

( !

results

.HasAlignments() ) {

126

errors += (errors.empty() ?

kEmptyStr

" "

);

127

errors += CBlastFormatUtil::kNoHitsFound;

138 if

(opts.

Empty

()) {

149 if

(!resolved.empty()) {

158 const

vector<CAlignFormatUtil::SDbInfo> & dbsInfo)

160 if

(dbsInfo.empty()){

163 ITERATE

(vector<CBlastFormatUtil::SDbInfo>,

, dbsInfo) {

164 if

(

!= dbsInfo.begin()) {

176 if

(subjectsInfo->Size() == 0) {

180 for

(

unsigned int i

=0;

< subjectsInfo->Size();

++) {

181

list<CRef<objects::CSeq_id> > ids = subjectsInfo->GetId(

);

196 if

(matrix_name ==

NULL

)

203 if

(

strcmp

(matrix_name,

"BLOSUM45"

) == 0)

205 else if

(

strcmp

(matrix_name,

"BLOSUM50"

) == 0)

207 else if

(

strcmp

(matrix_name,

"BLOSUM62"

) == 0)

209 else if

(

strcmp

(matrix_name,

"BLOSUM80"

) == 0)

211 else if

(

strcmp

(matrix_name,

"BLOSUM90"

) == 0)

213 else if

(

strcmp

(matrix_name,

"PAM30"

) == 0)

215 else if

(

strcmp

(matrix_name,

"PAM70"

) == 0)

217 else if

(

strcmp

(matrix_name,

"PAM250"

) == 0)

219 else if

(

strcmp

(matrix_name,

"IDENTITY"

) == 0)

224 if

(prog_name !=

"blastn"

&& prog_name !=

"megablast"

) {

225 NCBI_THROW

(blast::CBlastException, eInvalidArgument,

226 "unsupported score matrix"

);

236 tmp

[

] = matrix[

];

238

matrix[

][j] = m.

[

][j];

252 return "deltablast"

;

347 return m_Options

->GetQueryGeneticCode();

static CRef< CScope > m_Scope

Boolean Blast_QueryIsTranslated(EBlastProgramType p)

Returns true if the query is translated.

Boolean Blast_SubjectIsTranslated(EBlastProgramType p)

Returns true if the subject is translated.

@ eDeltaBlast

Delta Blast.

static string GetSeqIdString(const objects::CBioseq &cbs, bool believe_local_id=true)

Returns a full '|'-delimited Seq-id string for a Bioseq.

256x256 matrix used for calculating positives etc.

void x_InitSubjects(CConstRef< blast::IBlastSeqInfoSrc > subjectsInfo)

Int8 m_NumSequences

Number of sequences in all BLAST databases involved in this search.

static const unsigned int kMatrixCols

Number of columns used in score matrices.

CBlastFormattingMatrix * GetMatrix(void) const

Returns a 256x256 ASCII-alphabet matrix, needed for formatting.

void x_FillScoreMatrix(const char *matrix_name=BLAST_DEFAULT_MATRIX)

Initialize the score matrix to be used for formatting (if applicable)

double GetKappa(int num) const

Returns Karlin-Altschul K parameter for a given query.

int GetDbGeneticCode() const

slave genetic code

vector< CConstRef< CSeq_align_set > > m_Alignments

the alignments

double GetEntropy(int num) const

Returns Karlin-Altschul H parameter for a given query.

int GetQueryGeneticCode() const

master genetic code

int GetLengthAdjustment(int num) const

Returns length adjustment for a given query.

CConstRef< blast::CBlastOptions > m_Options

BLAST algorithm options.

CBlastFormattingMatrix * m_Matrix

Score matrix used to determine neighboring protein residues.

Int8 GetEffectiveSearchSpace(int num) const

Returns effective search space for a given query.

CCmdLineBlastXML2ReportData(CConstRef< blast::CBlastSearchQuery > query, const blast::CSearchResults &results, CConstRef< blast::CBlastOptions > opts, CRef< objects::CScope > scope, const vector< align_format::CAlignFormatUtil::SDbInfo > &dbsInfo)

Constructor db search.

Int8 m_NumBases

Number of bases in all BLAST databases involved in this search.

CRef< objects::CScope > m_Scope

CConstRef< CSeq_align_set > GetAlignmentSet(int num) const

Returns a vector continaing set of alignments found for a given query.

string m_DbName

name of blast database

void x_InitDB(const vector< align_format::CAlignFormatUtil::SDbInfo > &dbsInfo)

vector< string > m_Errors

Error messages.

~CCmdLineBlastXML2ReportData()

Destructor.

list< string > m_SubjectIds

string GetBlastProgramName(void) const

@inheritDoc

void x_InitResults(const blast::CSearchResults &results)

vector< CRef< blast::CBlastAncillaryData > > m_AncillaryData

ancillary results data

double GetLambda(int num) const

Returns Karlin-Altschul Lambda parameter for a given query.

void x_InitCommon(const blast::CSearchResults &results, CConstRef< blast::CBlastOptions > opts)

Search Results for All Queries.

Search Results for One Query.

Implementation of interface class to produce data required for generating BLAST XML2 output.

bool IsIterativeSearch() const

size_type size() const

Identical to GetNumResults, provided to facilitate STL-style iteration.

string Blast_ProgramNameFromType(EBlastProgramType program)

Returns a string program name, given a blast::EBlastProgramType enumeration.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty â not pointing to any object which means having a null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty â not pointing to any object, which means having a null value.

int64_t Int8

8-byte (64-bit) signed integer

int strcmp(const char *str1, const char *str2)

const SNCBIPackedScoreMatrix NCBISM_Pam30

const SNCBIPackedScoreMatrix NCBISM_Blosum62

const SNCBIPackedScoreMatrix NCBISM_Pam250

const SNCBIPackedScoreMatrix NCBISM_Blosum50

const SNCBIPackedScoreMatrix NCBISM_Blosum80

void NCBISM_Unpack(const SNCBIPackedScoreMatrix *psm, SNCBIFullScoreMatrix *fsm)

Expand a packed score matrix into an unpacked one, which callers can proceed to index directly by sta...

const SNCBIPackedScoreMatrix NCBISM_Pam70

const SNCBIPackedScoreMatrix NCBISM_Blosum45

The standard matrices.

const SNCBIPackedScoreMatrix NCBISM_Identity

const SNCBIPackedScoreMatrix NCBISM_Blosum90

string SeqDB_ResolveDbPath(const string &filename)

Resolve a file path using SeqDB's path algorithms.

Structure to hold the Karlin-Altschul parameters.

double K

K value used in statistics.

double Lambda

Lambda value used in statistics.

double H

H value used in statistics.

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