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NCBI C++ ToolKit: src/algo/structure/cd_utils/cuPssmMaker.cpp Source File

(

* filename,

* msa, vector<string>& seqIds)

= fopen(filename,

);

cerr <<

<< filename << endl;

fprintf(

,

, seqIds[

-startRow].c_str());

matrixName(

),

requestInformationContent(

),

requestResidueFrequencies(

),

requestWeightedResidueFrequencies(

),

requestFrequencyRatios(

),

requestNumIndepObs(

),

gaplessColumnWeights(

),

unalignedSegThreshold(-1),

inclusionThreshold(0.5),

: m_profiles(profiles),m_options(0), m_useConsensus(useConsensus), m_diagRequest(),

(

.pseudoCount > 0 ) {

(SumAInf > 84 ) iPseudo = 10;

(SumAInf > 55 ) iPseudo = 7;

(SumAInf > 43 ) iPseudo = 5;

(SumAInf > 41.5) iPseudo = 4;

(SumAInf > 40 ) iPseudo = 3;

(SumAInf > 39 ) iPseudo = 2;

vector<char> residuesOnColumn;

: m_conMaker(0), m_useConsensus(useConsensus), m_addQuery(addQueryToPssm),

m_masterSeqEntry(), m_trunctMaster(), m_cd(cd), m_pssmInput(0)

vector<int> seqIndice;

(seqIndice.size() > 0)

pssmRef = pssmEngine.

();

(pssmRef.

())

list< double >* freqs = 0;

list< int > & scores = pssm.

().SetScores();

(

col = 0; col < consensus.size(); col++)

c1 = consensus.at(col);

(

= 0;

< numRows;

++)

scores.push_back(score);

freqs->push_back(0.0);

commaSpace(

);

periodSpaceSpace(

);

list< CRef< CSeq_id > > & ids = bioseq.

();

list< CRef< CCdd_id > >& cdids =

->

().Set();

list< CRef< CCdd_id > >::iterator cit = cdids.begin();

(; cit != cdids.end(); cit++)

uid = (*cit)->GetUid();

dbtag.

(

);

dbtag.

(

);

ids.push_back(seqId);

list< CRef< CSeqdesc > >& descList = bioseq.

().Set();

(cdTitle.length() > 0) {

cdTitle = cdTitle.substr(0, cdTitle.length() - 1);

seqDescTitle += commaSpace;

(cdTitle.length() > 0) {

seqDescTitle += commaSpace + cdTitle + periodSpaceSpace;

list< CRef< CCdd_descr > >::iterator lit = cddescList.begin();

(; lit != cddescList.end(); lit++)

((*lit)->IsComment())

(cdTitle.length() == 0) {

seqDescTitle += commaSpace;

seqDescTitle += (*lit)->GetComment();

seqDescTitle +=

;

list< CRef< CSeqdesc > >::iterator it = descList.begin();

(; it != descList.end(); it++)

( (*it)->IsTitle() ) {

descList.push_back(desc);

.getSlave().setSeqId(seqId);

vector<string> seqIdStr;

seqIdStr.push_back(seqIds[0]->AsFastaString());

(

= 1;

< seqIds.size();

++)

seqIdStr.push_back(seqIds[

]->AsFastaString());

(fileName.length() == 0) {

, nCols;

vector<string> seqIdStr;

FILE*

= fopen(fileName.c_str(),

);

cerr <<

<< fileName << endl;

seqIdStr.push_back(seqIds[0]->AsFastaString());

(

k = 1; k < seqIds.size(); k++)

seqIdStr.push_back(seqIds[k]->AsFastaString());

(

= 0;

< seqIdStr.size(); ++

) {

fprintf(

,

,

,seqIdStr[

].c_str());

dash(

);

fprintf(

,

, nCols,

);

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

fprintf(

,

, j+1);

fprintf(

,

);

, j,

, nCols;

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

colResidues.assign(

+ 1,

);

colResidues[

] =

;

columnMap[j] = colResidues;

cd_utils::PssmMaker pm(ccd,

,

);

cd_utils::PssmMakerOptions

;

.requestFrequencyRatios =

;

.getSlave() =

.getMaster();

.remaster(guide);

score = ps.

(

,bioseq);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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...

bool GetSeqAlign(int Row, CRef< CSeq_align > &seqAlign)

bool GetSeqIDFromAlignment(int RowIndex, CRef< CSeq_id > &SeqID) const

bool FindConsensusInSequenceList(vector< int > *indices=NULL) const

bool GetSeqEntryForRow(int rowId, CRef< CSeq_entry > &seqEntry) const

bool GetBioseqForRow(int rowId, CRef< CBioseq > &bioseq)

string GetAccession(int &Version) const

bool GetSeqEntryForIndex(int seqIndex, CRef< CSeq_entry > &seqEntry) const

Computes a PSSM as specified in PSI-BLAST.

const char * GetMatrixName()

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

int countResiduesInRow(int row)

unsigned int GetQueryLength()

Get the query's length.

void copyRow(PSIMsaCell *src, PSIMsaCell *dest)

CdPssmInput(ResidueProfiles &profiles, PssmMakerOptions &config, bool useConsensus)

void unalignLeadingTrailingGaps()

PSIDiagnosticsRequest m_diagRequest

ResidueProfiles & m_profiles

void Process()

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

void read(ColumnResidueProfile &crp)

PSIMsa * GetData()

Obtain the multiple sequence alignment structure.

PSIMsaDimensions m_msaDimensions

Multiple sequence alignment dimensions.

const PSIDiagnosticsRequest * GetDiagnosticsRequest()

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

PSIBlastOptions * SetOptions()

Obtain the options for the PSSM engine.

PSIBlastOptions * m_options

unsigned char * GetQuery()

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

const PSIBlastOptions * GetOptions()

Obtain the options for the PSSM engine.

static int getResiduesStringSize()

int getIndexByConsensus() const

void getResiduesByRow(vector< char > &residues, bool byNcbiStd=true) const

static unsigned char getNcbiStdCode(char eaa)

static char getEaaCode(char stdCode)

const string & getConsensus()

CRef< CSeq_entry > getConsensusSeqEntry()

ResidueProfiles & getResidueProfiles()

const BlockModelPair & getGuideAlignment() const

void skipUnalignedSeg(int threshold)

const string & getConsensus()

void setOptions(const PssmMakerOptions &option)

CRef< CPssmWithParameters > m_pssmMade

PssmMaker(CCdCore *cd, bool useConsensus=true, bool addQueryToPssm=true)

ConsensusMaker * m_conMaker

CdPssmInput * m_pssmInput

vector< char > m_trunctMaster

bool getTrunctMaster(CRef< CSeq_entry > &seqEntry)

CRef< CPssmWithParameters > makeDefaultPssm()

CRef< CPssmWithParameters > make()

PssmMakerOptions m_config

void printAlignment(string &fileName)

void getPssmColumnResidues(map< unsigned int, string > &columnMap)

void modifyQuery(CRef< CSeq_entry > query)

const BlockModelPair & getGuideAlignment()

void printAlignmentByColumn(string &fileName)

CRef< CSeq_entry > m_masterSeqEntry

int score(const CRef< CSeq_align > align, const CRef< CBioseq > bioseq)

const vector< CRef< CSeq_id > > getSeqIdsByRow() const

void traverseColumnsOnMaster(ColumnReader &cr)

double calcInformationContent(bool byConsensus=true)

const string getConsensus(bool inNcbieaa=true)

int countColumnsOnMaster(string &seq)

void traverseColumnsOnConsensus(ColumnReader &cr)

int GetScore(char i, char j)

The NCBI C++ standard methods for dealing with std::string.

int findHighestScoringRowByPssm(CCdCore *ccd)

static void printMsa(const char *filename, const PSIMsa *msa, vector< string > &seqIds)

string GetScoringMatrixName(EScoreMatrixType type)

void NcbistdaaToNcbieaaString(const vector< char > &vec, string *str)

bool IsConsensus(const CRef< CSeq_id > &seqId)

thread_local unique_ptr< FtaMsgPost > bmp

CRef< objects::CPssmWithParameters > Run()

Runs the PSSM engine to compute the PSSM.

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

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

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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.

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 bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

void SetId(TId &value)

Assign a value to Id data member.

void SetDescription(TDescription &value)

Assign a value to Description data member.

const TName & GetName(void) const

Get the Name member data.

void SetTag(TTag &value)

Assign a value to Tag data member.

TStr & SetStr(void)

Select the variant.

void SetDb(const TDb &value)

Assign a value to Db data member.

TId & SetId(void)

Select the variant.

void SetPssm(TPssm &value)

Assign a value to Pssm data member.

void SetIntermediateData(TIntermediateData &value)

Assign a value to IntermediateData data member.

void SetFinalData(TFinalData &value)

Assign a value to FinalData data member.

void SetNumColumns(TNumColumns value)

Assign a value to NumColumns data member.

void SetNumRows(TNumRows value)

Assign a value to NumRows data member.

TGeneral & SetGeneral(void)

Select the variant.

TSeq & SetSeq(void)

Select the variant.

TId & SetId(void)

Assign a value to Id data member.

void ResetId(void)

Reset Id data member.

TTitle & SetTitle(void)

Select the variant.

void SetInst(TInst &value)

Assign a value to Inst data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

void SetLength(TLength value)

Assign a value to Length data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

void ResetSeq_data(void)

Reset Seq_data data member.

@ e_Ncbieaa

extended ASCII 1 letter aa codes

unsigned int

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

#define ASSERT

macro for assert.

Declares the CPSIBlastOptionsHandle class.

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

#define row(bind, expected)

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.

Int4 pseudo_count

Pseudocount constant.

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 independent_observations

request number of independent observations

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.

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

bool IsRequestingIntermediateData()

double inclusionThreshold

bool requestFrequencyRatios

request frequency ratios

int unalignedSegThreshold

bool requestWeightedResidueFrequencies

request observed weighted residue frequencies

bool gaplessColumnWeights

bool requestResidueFrequencies

request observed residue frequencies

bool requestInformationContent

request information content

bool requestNumIndepObs

request number of independent observations per position

voidp calloc(uInt items, uInt size)

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