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NCBI C++ ToolKit: src/algo/structure/struct_util/su_pssm.cpp Source File

(

Num)

((

)(Num + 0.5));

((

)(Num - 0.5));

score =

(((

) (matrix->

[pssmIndex][4] + matrix->

[pssmIndex][13])) / 2);

score =

(((

) (matrix->

[pssmIndex][5] + matrix->

[pssmIndex][15])) / 2);

score = matrix->

[pssmIndex][3];

score = matrix->

[pssmIndex][10];

score =

(((

) (matrix->

[pssmIndex][9] + matrix->

[pssmIndex][11])) / 2);

score = matrix->

[pssmIndex][blRes];

Char2UChar charMap;

(charMap.size() == 0) {

Char2UChar::const_iterator

= charMap.find(

((

)

));

(

!= charMap.end())

charMap.find(

)->second;

(

);

(

);

,

,

, masterStart, masterWidth, slaveStart, slaveWidth, left=0,

middle=0;

range->

< range->

- 1 ||

range->

!= ((

== 0) ? 0 : (

[

- 1]->GetRangeOfRow(0)->to + 1)) ||

(

);

masterStart = range->

;

masterWidth = range->

- range->

+ 1;

(range->

< 0 || range->

> (

)seq->

() || range->

< -1 || range->

>= (

)seq->

() ||

range->

< range->

- 1 ||

range->

!= ((

== 0) ? 0 : (

[

- 1]->GetRangeOfRow(

)->to + 1)) ||

(

==

.size() - 1 && range->

!= (

)seq->

() - 1))

(

);

slaveStart = range->

;

slaveWidth = range->

- range->

+ 1;

(slaveWidth == masterWidth) {

(slaveWidth > masterWidth) {

(

>= masterWidth - slaveWidth) {

(

==

.size() - 1) {

(slaveWidth > masterWidth) {

(

< slaveWidth) {

(slaveWidth < masterWidth) {

left = (slaveWidth + 1) / 2;

middle = masterWidth - slaveWidth;

(

< left + middle)

left = (masterWidth + 1) / 2;

CharDoubleMap standardProbabilities;

(standardProbabilities.size() == 0) {

(

);

(

=0;

<28; ++

) {

CharDoubleMap::const_iterator

= standardProbabilities.find(

((

) ch));

(

!= standardProbabilities.end())

(

<< ch);

infoContent = 0.0;

ColumnProfile profile;

ColumnProfile::iterator p, pe;

(

c=0; c<

->dimensions->query_length; ++c) {

(

=(ignoreMaster ? 1 : 0);

<=

->dimensions->num_seqs; ++

) {

(

->data[

][c].letter != gap) {

p = profile.find(

->data[

][c].letter);

(p == profile.end())

profile[

->data[

][c].letter] = 1;

ofs <<

<< (c+1) <<

<< nRes;

columnContent = 0.0;

ln2 =

(2.0), threshhold = 0.0001;

(p=profile.begin(), pe=profile.end(); p!=pe; ++p) {

(expFreq > threshhold) {

obsFreq = 1.0 * p->second / nRes,

freqRatio = obsFreq / expFreq;

(freqRatio > threshhold) {

infoContent += obsFreq *

(freqRatio) / ln2;

columnContent += obsFreq *

(freqRatio) / ln2;

<< setprecision(3) << (obsFreq *

(freqRatio) / ln2);

ofs <<

<< setprecision(6) << columnContent <<

;

ofs <<

<< setprecision(6) << infoContent <<

(

);

(

);

(

);

,

= 0, c = 0;

(

=0;

<nScores; ++

, ++s) {

ofs <<

<< (

) matrix->

<<

<<

<< (matrix->

? matrix->

:

) <<

<<

<< matrix->

<<

<<

<< matrix->

<<

;

(

=0; (

)r<matrix->rows; ++

) {

ofs << matrix->

[

][c] <<

;

}

(exception& e) {

(

<< e.what());

[

] =

[nColumns];

(

=0;

<

; ++

)

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent ...

PSIBlastOptions * PSIBlastOptionsFree(PSIBlastOptions *psi_options)

Deallocate PSI BLAST options.

Int2 PSIBlastOptionsNew(PSIBlastOptions **psi_options)

Initialize default options for PSI BLAST.

PSIMsa * PSIMsaFree(PSIMsa *msa)

Deallocates the PSIMsa structure.

PSIMsa * PSIMsaNew(const PSIMsaDimensions *dimensions)

Allocates and initializes the multiple sequence alignment data structure for use as input to the PSSM...

#define BLAST_SCORE_MIN

minimum allowed score (for one letter comparison).

double * BLAST_GetStandardAaProbabilities(void)

Get the standard amino acid probabilities.

#define WARNING_MESSAGE(s)

BLAST_Matrix(int nRows, int nColumns)

const Sequence * GetMaster(void) const

const Sequence * GetSequenceOfRow(unsigned int row) const

unsigned int NRows(void) const

void GetBlockList(ConstBlockList &cbl) const

std::vector< ncbi::CConstRef< Block > > ConstBlockList

const Range * GetRangeOfRow(int row) const

Computes a PSSM as specified in PSI-BLAST.

unsigned int masterLength

const PSIDiagnosticsRequest * GetDiagnosticsRequest(void)

Obtain the diagnostics data that is requested from the PSSM engine Its results will be populated in t...

PSIMsa * GetData(void)

Obtain the multiple sequence alignment structure.

PSIDiagnosticsRequest diag

PSIBlastOptions * options

SU_PSSMInput(const BlockMultipleAlignment *b)

unsigned char * GetQuery(void)

Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding.

const char * GetMatrixName(void)

Obtain the name of the underlying matrix to use when building the PSSM.

unsigned int GetQueryLength(void)

Get the query's length.

void Process(void)

Algorithm to produce multiple sequence alignment structure should be implemented in this method.

const BlockMultipleAlignment * bma

unsigned char * masterNCBIStdaa

const PSIBlastOptions * GetOptions(void)

Obtain the options for the PSSM engine.

std::string m_sequenceString

unsigned int Length(void) const

Include a standard set of the NCBI C++ Toolkit most basic headers.

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

main entry point for tests

static const char * column

static const column_t columns[]

CRef< objects::CPssmWithParameters > Run()

Runs the PSSM engine to compute the PSSM.

#define BLASTAA_SIZE

Size of aminoacid alphabet.

@ eNoOwnership

No ownership is assumed.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

TNumRows GetNumRows(void) const

Get the NumRows member data.

bool IsSetFinalData(void) const

Final representation for the PSSM Check if a value has been assigned to FinalData data member.

TKappa GetKappa(void) const

Get the Kappa member data.

const TScores & GetScores(void) const

Get the Scores member data.

TIsProtein GetIsProtein(void) const

Get the IsProtein member data.

const TFinalData & GetFinalData(void) const

Get the FinalData member data.

TNumColumns GetNumColumns(void) const

Get the NumColumns member data.

TByRow GetByRow(void) const

Get the ByRow member data.

bool IsSetKappa(void) const

Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned...

const TPssm & GetPssm(void) const

Get the Pssm member data.

unsigned int

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

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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

Defines interface for a sequence alignment processor that can populate a multiple alignment data stru...

#define row(bind, expected)

Abstract base class to encapsulate the source(s) and pre-processing of PSSM input data as well as opt...

Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should...

Boolean nsg_compatibility_mode

Compatibility option for the NCBI's structure group (note nsg_ prefix, stands for NCBI's structure gr...

double impala_scaling_factor

Scaling factor as used in IMPALA to do the matrix rescaling.

double inclusion_ethresh

Minimum evalue for inclusion in PSSM calculation.

Int4 pseudo_count

Pseudocount constant.

Boolean use_best_alignment

If set to TRUE, use the best alignment when multiple HSPs are found in a query-subject alignment (i....

Structure to allow requesting various diagnostics data to be collected by PSSM engine.

Boolean information_content

request information content

Boolean frequency_ratios

request frequency ratios

Boolean weighted_residue_frequencies

request observed weighted residue frequencies

Boolean gapless_column_weights

request gapless column weights

Boolean residue_frequencies

request observed residue frequencies

Structure to describe the characteristics of a position in the multiple sequence alignment data struc...

Boolean is_aligned

Is this letter part of the alignment?

Uint1 letter

Preferred letter at this position, in ncbistdaa encoding.

Structure representing the dimensions of the multiple sequence alignment data structure.

Uint4 num_seqs

Number of distinct sequences aligned with the query (does not include the query)

Uint4 query_length

Length of the query.

Multiple sequence alignment (msa) data structure containing the raw data needed by the PSSM engine to...

PSIMsaCell ** data

actual data, dimensions are (dimensions->num_seqs+1) by (dimensions->query_length)

PSIMsaDimensions * dimensions

dimensions of the msa

static DP_BlockInfo * blocks

static int Round(double Num)

unsigned char LookupNCBIStdaaNumberFromCharacter(char r)

double GetStandardProbability(char ch)

BLAST_Matrix * CreateBlastMatrix(const BlockMultipleAlignment *bma)

static const string NCBIStdaaResidues("-ABCDEFGHIKLMNPQRSTVWXYZU*OJ")

static double CalculateInformationContent(const PSIMsa *data, bool ignoreMaster)

int GetPSSMScoreOfCharWithAverageOfBZ(const BLAST_Matrix *matrix, unsigned int pssmIndex, char resChar)

static void FillInAlignmentData(const BlockMultipleAlignment *bma, PSIMsa *data)

char LookupCharacterFromNCBIStdaaNumber(unsigned char n)

static BLAST_Matrix * ConvertPSSMToBLASTMatrix(const CPssmWithParameters &pssm)

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