Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__aligner_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/ngalign/blast_aligner.cpp Source File

blast::CGenericSearchArgs search_args(

,

blast::CFilteringArgs filter_args(

);

blast::CNuclArgs nucl_args;

blast::CGappedArgs gapped_args;

blast::CHspFilteringArgs cull_args;

blast::CBlastDatabaseArgs blastdb_args;

blast::CWindowSizeArg window_args;

blast::CFormattingArgs format_args;

blast::CRemoteArgs remote_args;

search_args.SetArgumentDescriptions(ArgDesc);

filter_args.SetArgumentDescriptions(ArgDesc);

nucl_args.SetArgumentDescriptions(ArgDesc);

gapped_args.SetArgumentDescriptions(ArgDesc);

cull_args.SetArgumentDescriptions(ArgDesc);

blastdb_args.SetArgumentDescriptions(ArgDesc);

window_args.SetArgumentDescriptions(ArgDesc);

format_args.SetArgumentDescriptions(ArgDesc);

remote_args.SetArgumentDescriptions(ArgDesc);

blast::CGenericSearchArgs search_args(

,

blast::CFilteringArgs filter_args(

);

blast::CNuclArgs nucl_args;

blast::CGappedArgs gapped_args;

blast::CHspFilteringArgs cull_args;

blast::CBlastDatabaseArgs blastdb_args;

blast::CWindowSizeArg window_args;

blast::CFormattingArgs format_args;

blast::CRemoteArgs remote_args;

NucOptions->SetTraditionalMegablastDefaults();

search_args.ExtractAlgorithmOptions(Args, Options->

());

filter_args.ExtractAlgorithmOptions(Args, Options->

());

nucl_args.ExtractAlgorithmOptions(Args, Options->

());

gapped_args.ExtractAlgorithmOptions(Args, Options->

());

cull_args.ExtractAlgorithmOptions(Args, Options->

());

window_args.ExtractAlgorithmOptions(Args, Options->

());

format_args.ExtractAlgorithmOptions(Args, Options->

());

remote_args.ExtractAlgorithmOptions(Args, Options->

());

vector<string> Tokens;

Tokens.push_back(

);

unique_ptr<CArgs> Args(ArgDesc.

(Tokens.size(), Tokens));

Delims =

;

Quotes =

;

InQuotes =

;

(

Index = 0; Index < Params.length(); Index++) {

(Quotes.find(Params[Index]) !=

) {

Tokens.push_back(Curr);

Curr.push_back(Params[Index]);

(Delims.find(Params[Index]) !=

) {

Tokens.push_back(Curr);

(Quotes.find(Params[Index]) !=

) {

Tokens.push_back(Curr);

Curr.push_back(Params[Index]);

(Subjects.

()) {

(

<<

);

BlastResults = Blast.

();

(SetIter->IsNull())

TSubjectMap SubjectMap;

SubjectMap[SubjectIdH].push_back(*AlignIter);

(TSubjectMap, SubjectIter, SubjectMap) {

list<CRef<CSeq_align> > Filtered;

(!Filtered.empty()) {

FilteredResults.

().insert(FilteredResults.

().end(),

Filtered.begin(), Filtered.end());

scores.push_back(Score);

(AlignCount == 0) {

(

);

(

<< AlignCount <<

);

Results->Insert(FilteredResults);

list<CBlastAligner::TBlastAlignerRef>

list<TBlastAlignerRef> Aligners;

Aligners.push_back(CurrAligner);

list<CBlastAligner::TBlastAlignerRef>

list<TBlastOptionsRef> BlastOptions;

(list<string>, ParamsIter, Params) {

BlastOptions.push_back(CurrOptions);

(

<<

);

TSubjectMap SubjectMap;

SubjectMap[SubjectIdH].push_back(*AlignIter);

(TSubjectMap, SubjectIter, SubjectMap) {

list<CRef<CSeq_align> > Filtered;

(!Filtered.empty()) {

FilteredResults.

().insert(FilteredResults.

().end(),

Filtered.begin(), Filtered.end());

(AlignCount == 0) {

Results->Insert(FilteredResults);

list<CRemoteBlastAligner::TBlastAlignerRef>

list<TBlastAlignerRef> Aligners;

Aligners.push_back(CurrAligner);

list<CRemoteBlastAligner::TBlastAlignerRef>

list<TBlastOptionsRef> BlastOptions;

(list<string>, ParamsIter, Params) {

BlastOptions.push_back(CurrOptions);

Declares the CBl2Seq (BLAST 2 Sequences) class.

Declares the CBlastNucleotideOptionsHandle class.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

Definitions of special type used in BLAST.

Main argument class for BLASTN application.

static void FilterBothRows(const list< CRef< objects::CSeq_align > > &Input, list< CRef< objects::CSeq_align > > &Output, size_t DepthCutoff=5, double PctIdentRescue=95.0)

TAlignResultsRef GenerateAlignments(objects::CScope &Scope, ISequenceSet *QuerySet, ISequenceSet *SubjectSet, TAlignResultsRef AccumResults)

CRef< blast::CBlastOptionsHandle > m_BlastOptions

static list< TBlastAlignerRef > CreateBlastAligners(list< TBlastOptionsRef > &Options, int Threshold)

TInterruptFnPtr m_InterruptFunc

CBlastAligner(blast::CBlastOptionsHandle &Options, int Threshold)

static void x_ParseOptionsString(const string &Params, vector< string > &Tokens)

static CRef< blast::CBlastOptionsHandle > s_CreateBlastOptions(const string &Params)

static void s_CreateBlastArgDescriptions(CArgDescriptions &ArgDesc)

static CRef< blast::CBlastOptionsHandle > s_ExtractBlastArgs(CArgs &Args)

void SetSoftFiltering(int Filter)

void SetNegativeGiList(const vector< TGi > &GiList)

Handle to the nucleotide-nucleotide options to the BLAST algorithm.

@ eRemote

To be used when running BLAST remotely.

Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this cl...

static list< TBlastAlignerRef > CreateBlastAligners(list< TBlastOptionsRef > &Options, int Threshold)

CRef< blast::CBlastOptionsHandle > m_BlastOptions

TAlignResultsRef GenerateAlignments(objects::CScope &Scope, ISequenceSet *QuerySet, ISequenceSet *SubjectSet, TAlignResultsRef AccumResults)

CRemoteBlastAligner(blast::CBlastOptionsHandle &Options, int Threshold)

API for Remote Blast Requests.

Search Results for All Queries.

Search Results for One Query.

void GetGiList(vector< TGi > &GiList, objects::CScope &Scope, const CAlignResultsSet &Alignments, int Threshold)

void SetNamedScore(const string &id, int score)

bool GetNamedScore(const string &id, int &score) const

Get score.

virtual CRef< blast::IQueryFactory > CreateQueryFactory(objects::CScope &Scope, const blast::CBlastOptionsHandle &BlastOpts)=0

virtual CRef< blast::CLocalDbAdapter > CreateLocalDbAdapter(objects::CScope &Scope, const blast::CBlastOptionsHandle &BlastOpts)=0

Class for the messages for an individual query sequence.

Declares the CDiscNucleotideOptionsHandle class.

bool HasErrors() const

Returns true if there are errors among the results for this object.

CConstRef< objects::CSeq_align_set > GetSeqAlign() const

Accessor for the Seq-align results.

CRef< CSearchResultSet > Run()

Executes the search.

CBlastOptions & SetOptions()

Returns a reference to the internal options class which this object is a handle for.

TInterruptFnPtr SetInterruptCallback(TInterruptFnPtr fnptr, void *user_data=NULL)

Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in pr...

bool HasWarnings() const

Returns true if there are warnings among the results for this object.

string GetWarningStrings() const

Retrieve a string with the query identifier followed by the warnings produced, returns a empty string...

CRef< CSearchResultSet > GetResultSet()

Submit the search (if necessary) and return the results.

TQueryMessages GetErrors(int min_severity=eBlastSevError) const

Accessor for the error/warning messsages for this query.

string GetErrorStrings() const

Retrieve a string with the query identifier followed by the errors produced, returns a empty string i...

@ eBlastDbIsNucleotide

nucleotide

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

virtual string & PrintUsage(string &str, bool detailed=false) const

Print usage message to end of specified string.

CArgs * CreateArgs(TSize argc, TArray argv) const

Create parsed arguments in CArgs object.

CDiagContext_Extra & Print(const string &name, const string &value)

The method does not print the argument, but adds it to the string.

CDiagContext & GetDiagContext(void)

Get diag context instance.

CDiagContext_Extra Extra(void) const

Create a temporary CDiagContext_Extra object.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

void Warning(CExceptionArgs_Base &args)

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

void Info(CExceptionArgs_Base &args)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

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

Convert int to string.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

Main class to perform a BLAST search on the local machine.

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

Defines NCBI C++ exception handling.

Declares the CRemoteBlast class.

Predicate for sorting CSeq_id_Handles in a defined order.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4