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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/data4xmlformat_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/format/data4xmlformat.cpp Source File

39 #ifndef SKIP_DOXYGEN_PROCESSING 48 const

blast::CSearchResultSet&

results

49 const

blast::CBlastOptions& opts,

50 const string

dbname

bool

db_is_aa,

51 int

qgencode,

int

dbgencode,

53 int

dbfilt_algorithm

)

54

: m_Queries(queries), m_Options(opts),

56

m_QueryGeneticCode(qgencode),

57

m_DbGeneticCode(dbgencode),

58

m_NoHitsFound(

false

64

vector<CBlastFormatUtil::SDbInfo> dbinformation;

66

CBlastFormatUtil::GetBlastDbInfo(dbinformation,

m_DbName

, db_is_aa,

67

dbfilt_algorithm, is_remote);

70 x_Init

(queries,

results

, opts, dbinformation, qgencode, dbgencode, is_remote, dbfilt_algorithm);

76 const

blast::CSearchResultSet&

results

77 const

blast::CBlastOptions& opts,

78 const

vector<CAlignFormatUtil::SDbInfo> & dbInfo,

83

: m_Queries(queries), m_Options(opts),

85

m_QueryGeneticCode(qgencode),

86

m_DbGeneticCode(dbgencode),

87

m_NoHitsFound(

false

94 ITERATE

(vector<CBlastFormatUtil::SDbInfo>,

, dbInfo) {

95 if

(

!= dbInfo.begin())

99 x_Init

(queries,

results

, opts, dbInfo, qgencode, dbgencode, is_remote, dbfilt_algorithm);

105 const

blast::CSearchResultSet&

results

106 const

blast::CBlastOptions& opts,

107 const

vector<CAlignFormatUtil::SDbInfo> & dbInfo,

111 int

dbfilt_algorithm)

116 if

(!dbInfo.empty()) {

117 ITERATE

(vector<CBlastFormatUtil::SDbInfo>,

, dbInfo) {

137

CBlastFormatUtil::kNoHitsFound);

144 for

(

size_t i

= 0;

results

.size() - 1;

++) {

158 string

errors =

results

[

].GetErrorStrings();

160 if

( !errors.empty() ) {

163

errors +=

results

[

].GetWarningStrings();

165 if

( !

results

[

].HasAlignments() ) {

166

errors += (errors.empty() ?

kEmptyStr

" "

);

167

errors += CBlastFormatUtil::kNoHitsFound;

190 if

(matrix_name ==

NULL

)

195 if

(

strcmp

(matrix_name,

"BLOSUM45"

) == 0)

197 else if

(

strcmp

(matrix_name,

"BLOSUM50"

) == 0)

199 else if

(

strcmp

(matrix_name,

"BLOSUM62"

) == 0)

201 else if

(

strcmp

(matrix_name,

"BLOSUM80"

) == 0)

203 else if

(

strcmp

(matrix_name,

"BLOSUM90"

) == 0)

205 else if

(

strcmp

(matrix_name,

"PAM30"

) == 0)

207 else if

(

strcmp

(matrix_name,

"PAM70"

) == 0)

209 else if

(

strcmp

(matrix_name,

"PAM250"

) == 0)

211 else if

(

strcmp

(matrix_name,

"IDENTITY"

) == 0)

216 if

(prog_name !=

"blastn"

&& prog_name !=

"megablast"

) {

217 NCBI_THROW

(blast::CBlastException, eInvalidArgument,

218 "unsupported score matrix"

);

256x256 matrix used for calculating positives etc.

CRef< blast::CBlastQueryVector > m_Queries

Query sequences.

vector< CRef< blast::CBlastAncillaryData > > m_AncillaryData

ancillary results data

int m_NumSequences

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

bool m_NoHitsFound

True if results did not find any hits.

int * m_Matrix[kMatrixCols]

Score matrix used to determine neighboring protein residues.

TSeqLocInfoVector m_Masks

masks for the queries

unsigned int GetNumQueries(void) const

@inheritDoc

const blast::CBlastOptions & m_Options

BLAST algorithm options.

Int8 m_NumBases

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

void x_FillScoreMatrix(const char *matrix_name=BLAST_DEFAULT_MATRIX)

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

string m_DbName

name of blast database

int GetLengthAdjustment(int) const

@inheritDoc

CCmdLineBlastXMLReportData(CRef< blast::CBlastQueryVector > queries, const blast::CSearchResultSet &results, const blast::CBlastOptions &opts, const string &dbname, bool db_is_aa, int qgencode=BLAST_GENETIC_CODE, int dbgencode=BLAST_GENETIC_CODE, bool is_remote=false, int dbfilt_algorithm=-1)

Constructor.

double GetEntropy(int query_index) const

@inheritDoc

vector< string > m_Errors

Error messages (one element per query)

void x_Init(CRef< blast::CBlastQueryVector > queries, const blast::CSearchResultSet &results, const blast::CBlastOptions &opts, const vector< align_format::CAlignFormatUtil::SDbInfo > &dbInfo, int qgencode, int dbgencode, bool is_remote, int dbfilt_algorith)

vector< CConstRef< CSeq_align_set > > m_Alignments

the alignments

double GetLambda(int query_index) const

@inheritDoc

~CCmdLineBlastXMLReportData()

Destructor.

double GetKappa(int query_index) const

@inheritDoc

static const unsigned int kMatrixCols

Number of columns used in score matrices.

CBlastFormattingMatrix * GetMatrix(void) const

@inheritDoc

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

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

char * dbname(DBPROCESS *dbproc)

Get name of current database.

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

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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