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

program_uc = program;

(program_uc) +

+ blast::CBlastVersion().Print();

blast::CReference::EPublication pub,

reference(

);

(pub == blast::CReference::eCompAdjustedMatrices) {

reference +=

;

}

(pub == blast::CReference::eCompBasedStats) {

reference +=

;

reference +=

;

}

(pub == blast::CReference::eIndexedMegablast) {

reference +=

;

reference +=

;

httpProt =

;

(!config_reg.

()) {

(config_reg.

(

,

)) {

httpProt = config_reg.

(

,

);

<<

<< blast::CReference::GetPubmedUrl(pub)

<<

<< reference <<

x_WrapOutputLine(

.str() + blast::CReference::GetString(pub),

<< reference <<

;

x_WrapOutputLine(

.str() + blast::CReference::GetHTMLFreeString(pub),

definition_line,

dbString = (html) ?

:

;

<< dbString << definition_line << endl;

(!(html && with_links)) x_WrapOutputLine(

.str(),line_len,

);

(

objects::CPssmWithParameters& pssm_with_params,

vector<double> info_content, gapless_col_weights, sigma;

blast::CScorematPssmConverter::GetInformationContent(pssm_with_params,

blast::CScorematPssmConverter::GetGaplessColumnWeights(pssm_with_params,

gapless_col_weights);

blast::CScorematPssmConverter::GetSigma(pssm_with_params, sigma);

pssm_calculation_done = info_content.empty() ?

:

;

(pssm_calculation_done) {

<<

;

<<

;

<<

;

<<

;

kQueryLength = pssm_with_params.GetPssm().GetQueryLength();

(

)pssm_with_params.GetPssm().GetNumColumns());

unique_ptr< TNcbiMatrixInt > pssm

(blast::CScorematPssmConverter::GetScores(pssm_with_params));

unique_ptr< TNcbiMatrixDouble > weighted_res_freqs

(blast::CScorematPssmConverter::

GetWeightedResidueFrequencies(pssm_with_params));

vector<int> interval_sizes, num_matching_seqs;

blast::CScorematPssmConverter::GetIntervalSizes(pssm_with_params,

blast::CScorematPssmConverter::GetNumMatchingSeqs(pssm_with_params,

(*it > max_score) {

(-*it > max_score) {

(max_score > 0) {

width = num_digits + 2;

(pssm_calculation_done) {

pssm_with_params.GetPssm().GetQuerySequenceData(

);

vector<char>& query_seq =

.Get();

<<

<< setw(5) << (

+1) <<

<<

(pssm_calculation_done) {

<<

<< setprecision(2) << info_content[

] <<

;

((num_matching_seqs[

] > 1) && (query_seq[

] != kXResidue)) {

<< setprecision(2) << gapless_col_weights[

];

ancillary_data->GetUngappedKarlinBlk();

ancillary_data->GetGappedKarlinBlk();

ancillary_data->GetPsiUngappedKarlinBlk();

ancillary_data->GetPsiGappedKarlinBlk();

<<

<< setprecision(4);

<<

;

<<

<< ungapped_kbp->

<<

<< ungapped_kbp->

<<

;

<<

<< gapped_kbp->

<<

<< gapped_kbp->

<<

;

(psi_ungapped_kbp) {

<<

<< psi_ungapped_kbp->

<<

<< psi_ungapped_kbp->

<<

;

(psi_gapped_kbp) {

<< psi_gapped_kbp->

<<

<< psi_gapped_kbp->

<<

;

& db_name,

& db_title,

kHistSeqalign(

);

hist_align_obj->

().SetStr(kHistSeqalign);

hist_align_obj->

(kHistSeqalign,

);

kBlastType(

);

blast_type->

().SetStr(kBlastType);

kVDBNames(

);

blast_db_info->

().SetStr(kVDBNames);

blast_db_info->

( db_name,

);

kBlastDBTitle(

);

blast_db_info->

().SetStr(kBlastDBTitle);

blast_db_info->

(

,

);

blast_db_info->

( db_name,

);

blast_db_info->

( db_title, is_nucl );

retval->

().SetAlign();

retval->

().SetAlign().push_back(*itr);

kAsciiSize = 256;

(kAsciiSize, kAsciiSize, INT_MIN);

kNumValues =

(ncols, nrows);

vector<char> ncbistdaa_values(kNumValues);

(

index = 0; index < kNumValues; ++index)

ncbistdaa_values[index] = (

) index;

vector<char> iupacaa_values(kNumValues);

(

index = 0; index < kNumValues; ++index)

iupacaa_values[index] = iupacaa_seq.

().

()[index];

(

= 0;

< nrows; ++

) {

(

col = 0; col < ncols; ++col) {

(iupacaa_values[

] >= 0 && iupacaa_values[col] >= 0) {

(*this)((

)iupacaa_values[

], (

)iupacaa_values[col]) =

ncbi::TMaskedQueryRegions& mask_info,

align_format::CDisplaySeqalign::SeqLocCharOption mask_char,

vector<CRange<int> > segs_v;

(

index = 0; index < kNumSegs; ++index) {

segs_v.push_back(range);

vector<CRange<int> > masks_v;

aln_stop =

(query_seq.size()) - 1;

(ncbi::TMaskedQueryRegions, mask_iter, mask_info) {

((*mask_iter)->GetFrame() != query_frame)

(*mask_iter)->GetInterval().GetFrom());

(*mask_iter)->GetInterval().GetTo());

(query_frame < 0) {

masks_v.push_back(range);

(

seg_index = 0;

seg_index < (

) segs_v.size() && mask_index < (

) masks_v.size();

(segs_v[seg_index].

())

seg_start = segs_v[seg_index].GetFrom();

seg_stop = segs_v[seg_index].GetTo();

(mask_index < (

) masks_v.size() &&

(mask_pos =

(seg_start, masks_v[mask_index].GetFrom()))

mask_stop =

(seg_stop, masks_v[mask_index].GetTo());

( ; mask_pos <= mask_stop; ++mask_pos) {

( query_seq[mask_pos] ==

)

;

query_seq[mask_pos] =

;

query_seq[mask_pos]=

;

query_seq[mask_pos] =

((

)query_seq[mask_pos]);

(mask_pos < seg_stop)

objects::CDense_seg& ds,

objects::CScope& scope,

& masked_query,

objects::CDense_seg & ds,

objects::CScope & scope,

ncbi::TMaskedQueryRegions& mask_info,

align_format::CDisplaySeqalign::SeqLocCharOption mask_char,

masked_query =

;

(aln_vec, masked_query, mask_info, mask_char, query_frame);

(!org_align_set.

() || org_align_set.

().empty()) {

(

);

check_type = score_type;

(org_align_set.

().front()->GetNamedScore(

, dont_care)) {

(org_align_set.

().front()->GetNamedScore(

, dont_care)) {

(

);

list<CRef<CSeq_align> > & tmp_align_list = tmp_align_set.

();

list<CRef<CSeq_align> > & org_align_list = org_align_set.

();

list<CRef<CSeq_align> >::iterator left_it = org_align_list.begin();

list<CRef<CSeq_align> >::iterator right_it = org_align_list.begin();

(left_it != org_align_list.end())

& cur_id = (*left_it)->GetSeq_id(1);

(; right_it != org_align_list.end(); ++right_it)

&

= (*right_it)->GetSeq_id(1);

(!

.Match(cur_id))

tmp_align_list.assign(left_it, right_it);

master_coverage = align_format::CAlignFormatUtil::GetMasterCoverage(tmp_align_set);

subj_coverage = 100.0 * (double) master_coverage/ (

) query_len;

(subj_coverage < 99)

(*left_it)->SetNamedScore (

, (

) subj_coverage);

uniq_coverage = align_format::CAlignFormatUtil::GetUniqSeqCoverage(tmp_align_set);

uniq_subj_coverage = 100.0 * (double) uniq_coverage/ (

) query_len;

(uniq_subj_coverage < 99)

uniq_subj_coverage +=0.5;

(*left_it)->SetNamedScore (

, (

) uniq_subj_coverage);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

BLAST formatter utilities.

Boolean Blast_SubjectIsNucleotide(EBlastProgramType p)

Returns true if the subject is nucleotide.

#define BLAST_SCORE_MIN

minimum allowed score (for one letter comparison).

Definitions of special type used in BLAST.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

@ eDeltaBlast

Delta Blast.

CNcbiMatrix< int > TNcbiMatrixInt

static void s_MaskQuerySeq(CAlnVec &alnvec, string &query_seq, const ncbi::TMaskedQueryRegions &mask_info, align_format::CDisplaySeqalign::SeqLocCharOption mask_char, int query_frame)

Masks a query sequence string corresponding to an alignment, given a list of mask locations.

CNcbiMatrix< double > TNcbiMatrixDouble

static int RESIDUE_ORDER[]

Standard order of letters according to S.

static void s_GetQueryAndSubjectStrings(CAlnVec &aln_vec, string &query, string &subject, int master_gen_code, int slave_gen_code)

TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

TSeqPos GetAlnStop(TNumseg seg) const

TSeqPos GetAlnStart(TNumseg seg) const

TNumseg GetNumSegs(void) const

void SetGapChar(TResidue gap_char)

string & GetWholeAlnSeqString(TNumrow row, string &buffer, TSeqPosList *insert_aln_starts=0, TSeqPosList *insert_starts=0, TSeqPosList *insert_lens=0, unsigned int scrn_width=0, TSeqPosList *scrn_lefts=0, TSeqPosList *scrn_rights=0) const

void SetAaCoding(TCoding coding)

void SetGenCode(int gen_code, TNumrow row=-1)

TSeqPos GetLength(void) const

bool IsSetLength(void) const

void Resize(size_t i, size_t j, int val=int())

resize this matrix, filling the empty cells with a known value

void AddUserObject(CUser_object &obj)

static TSeqPos Convert(const CSeq_data &in_seq, CSeq_data *out_seq, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx=0, TSeqPos uLength=0, bool bAmbig=false, Uint4 seed=17734276)

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

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

main entry point for tests

bool Empty(const CNcbiOstrstream &src)

static const char * str(char *buf, int n)

EBlastProgramType EProgramToEBlastProgramType(EProgram p)

Convert EProgram to EBlastProgramType.

const Uint1 AMINOACID_TO_NCBISTDAA[]

Translates between ncbieaa and ncbistdaa.

string EProgramToTaskName(EProgram p)

Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries...

const char NCBISTDAA_TO_AMINOACID[]

Translates between ncbieaa and ncbistdaa.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SBlastXMLIncremental()

Default ctor()

static void PrintAsciiPssm(const objects::CPssmWithParameters &pssm, CConstRef< blast::CBlastAncillaryData > ancillary_data, CNcbiOstream &out)

Prints the PSSM in ASCII format (as in blastpgp's -Q option)

static void BlastPrintVersionInfo(const string program, bool html, CNcbiOstream &out)

Print out blast engine version.

static void PrintDbInformation(size_t line_len, string definition_line, int nNumSeqs, Uint8 nTotalLength, bool html, bool with_links, CNcbiOstream &out)

static void BlastPrintReference(bool html, size_t line_len, CNcbiOstream &out, blast::CReference::EPublication publication=blast::CReference::eGappedBlast, bool is_psiblast=false)

Print out blast reference.

static void InsertSubjectScores(objects::CSeq_align_set &org_align_set, const objects::CBioseq_Handle &query_handle, TSeqRange query_range=TSeqRange(), ESubjectScores score_type=eQueryCovPerSubj)

string m_SerialXmlEnd

tag to be printed at end.

static CRef< objects::CSeq_annot > CreateSeqAnnotFromSeqAlignSet(const objects::CSeq_align_set &alnset, blast::EProgram program, const string &db_name, const string &db_title, bool vdb_search=false)

static void GetWholeAlnSeqStrings(string &query, string &subject, const objects::CDense_seg &ds, objects::CScope &scope, int master_gen_code, int slave_gen_code)

static string BlastGetVersion(const string program)

Returns the version and release date, e.g.

CBlastFormattingMatrix(int **data, unsigned int nrows, unsigned int ncols)

Constructor - allocates the matrix with appropriate size and populates with the values retrieved from...

const TPrim & Get(void) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

bool Empty(void) const THROWS_NONE

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

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

position_type GetLength(void) const

bool NotEmpty(void) const

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

virtual bool HasEntry(const string &section, const string &name=kEmptyStr, TFlags flags=0) const

bool Empty(TFlags flags=fAllLayers) const

Verify if Registry is empty.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

NCBI_NS_STD::string::size_type SIZE_TYPE

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

static string UInt8ToString(Uint8 value, TNumToStringFlags flags=0, int base=10)

Convert UInt8 to string.

@ fWithCommas

Use commas as thousands separator.

TFrom GetFrom(void) const

Get the From member data.

void SetType(TType &value)

Assign a value to Type data member.

Tdata & Set(void)

Assign a value to data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

const TIupacaa & GetIupacaa(void) const

Get the variant data.

void SetData(TData &value)

Assign a value to Data data member.

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Ncbistdaa

consecutive codes for std aas

@ e_Iupacaa

IUPAC 1 letter amino acid code.

unsigned int

A callback function used to compare two keys in a database.

constexpr auto sort(_Init &&init)

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

const GenericPointer< typename T::ValueType > T2 value

#define DIM(A)

dimension of an array.

C++ API for the PSI-BLAST PSSM engine.

Defines BLAST database access classes.

#define row(bind, expected)

Structure to hold the Karlin-Altschul parameters.

double K

K value used in statistics.

double Lambda

Lambda value used in statistics.

Auxiliary structure used for sorting CRange<int> objects in increasing order of starting positions.

bool operator()(CRange< int > const &range1, CRange< int > const &range2)

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