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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/ngalign__app_8cpp_source.html below:

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

()

{

; }

= In.tellg();

NewResults->Insert(Temp);

cerr <<

<< endl;

NewResults->Insert(*Temp);

cerr <<

<< Temp->

().size() <<

<< endl;

TempSet->

().insert(TempSet->

().end(), Temp->

().SetAlign().begin(), Temp->

().SetAlign().end());

NewResults->Insert(*TempSet);

cerr <<

<< TempSet->

().size() <<

<< endl;

& Category);

& Category,

);

arg_desc->AddFlag(

,

);

arg_desc->AddDefaultKey(

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

(args[

].

()) {

Orig = args[

].AsString();

(vector<string>, DBIter, DBs) {

cerr << *DBIter << endl;

(args[

].

()) {

vector<string> Tokens;

(args[

].AsString(),

, Tokens);

(vector<string>, CacheIter, Tokens) {

CacheFile( *CacheIter +

);

(CacheFile.

()) {

AllowDupes =

;

(RunRegistry.

(

,

) ==

)

(args[

].

() && args[

].AsBoolean())

cerr <<

<< endl;

CurrAligns = NgAligner.

();

Alignments->

().insert(Alignments->

().end(),

CurrAligns->

().begin(),

CurrAligns->

().end());

(!Alignments.

()) {

(args[

].

() && args[

].AsBoolean())

cerr <<

<< endl;

& Category)

= RunRegistry->

(Category,

);

Source = RunRegistry->

(Category,

);

Mask = RunRegistry->

(Category,

);

NMer =

+ Mask;

0, 1, 1, 0, 0, 0, 0, 0, 0,

, 0, 0, 0, 0,

, 0,

, 0,

);

(

==

) {

(Args[

].

() && Source.empty() && Category ==

) {

& Id = Args[

].AsString();

IdList->SetIdList().push_back(QueryId);

(Args[

].

() && Source.empty() && Category ==

) {

& Id = Args[

].AsString();

IdList->SetIdList().push_back(SubjectId);

(Args[

].

() && Source.empty() && Category ==

) {

(!

.AtEOF()) {

(!

.empty() &&

[0] !=

) {

IdList->SetIdList().push_back(QueryId);

(Args[

].

() && Source.empty() && Category ==

) {

(!

.AtEOF()) {

(!

.empty() &&

[0] !=

) {

IdList->SetIdList().push_back(SubjectId);

(!

.AtEOF()) {

(!

.empty() &&

[0] !=

) {

(IdList->SetIdList().empty() && !

.empty()) {

BatchSize = Args[

].AsInteger();

IdList->SetSeqMasker(Masker);

(

==

) {

(Args[

].

() && Source.empty() && Category ==

) {

QueryString = Args[

].AsString();

= QueryString;

(!

.empty() &&

[0] !=

) {

vector<string> Tokens;

->SetInt().SetId().Set(Tokens[0]);

(

->GetInt().GetId().IsGi() &&

->GetInt().GetId().GetGi() <

(50)) {

LocList->SetLocList().push_back(

);

(Args[

].

() && Source.empty() && Category ==

) {

(!

.AtEOF()) {

(!

.empty() &&

[0] !=

) {

vector<string> Tokens;

->SetInt().SetId().Set(Tokens[0]);

(

->GetInt().GetId().IsGi() &&

->GetInt().GetId().GetGi() <

(50)) {

LocList->SetLocList().push_back(

);

(Args[

].

() && Source.empty() && Category ==

) {

SubjectString = Args[

].AsString();

= SubjectString;

(!

.empty() &&

[0] !=

) {

vector<string> Tokens;

->SetInt().SetId().Set(Tokens[0]);

(

->GetInt().GetId().IsGi() &&

->GetInt().GetId().GetGi() <

(50)) {

LocList->SetLocList().push_back(

);

(Args[

].

() && Source.empty() && Category ==

) {

(!

.AtEOF()) {

(!

.empty() &&

[0] !=

) {

vector<string> Tokens;

->SetInt().SetId().Set(Tokens[0]);

(

->GetInt().GetId().IsGi() &&

->GetInt().GetId().GetGi() <

(50)) {

LocList->SetLocList().push_back(

);

LocList->SetSeqMasker(Masker);

(

==

) {

Orig = Args[

].AsString();

(vector<string>, DBIter, DBs) {

(Args[

].

()) {

BlastDb->SetSoftFiltering(Args[

].AsString());

(

==

) {

FileName = RunRegistry->

(Category,

);

FileName = Args[

].AsString();

Batch = Args[

].AsInteger();

(

= 0;

< Batch;

++) {

(

==

) {

& Id = Args[

].AsString();

IdList->AddSeqId(QueryId);

(!

.AtEOF()) {

(!

.empty() &&

[0] !=

) {

cerr << __LINE__ << endl;

BatchSize = Args[

].AsInteger();

cerr << __LINE__ << (*LoadedIdsIter)->AsFastaString() << endl;

(IdList->

()) {

(

<<

);

IdList->SetSeqMasker(Masker);

(

==

) {

(Args[

].

() && Source.empty() && Category ==

) {

(!

.AtEOF()) {

(!

.empty() &&

[0] !=

) {

vector<string> Tokens;

(Tokens.size() >= 3) {

->SetInt().SetId().Set(Tokens[0]);

->SetWhole().Set(Tokens[0]);

LocList->AddSeqLoc(

);

(Args[

].

() && Source.empty() && Category ==

) {

(!

.AtEOF()) {

(!

.empty() &&

[0] !=

) {

vector<string> Tokens;

(Tokens.size() >= 3) {

->SetInt().SetId().Set(Tokens[0]);

->SetWhole().Set(Tokens[0]);

LocList->AddSeqLoc(

);

(LocList->

()) {

(

<<

);

LocList->SetSeqMasker(Masker);

& Category,

(!FastaReader.

()) {

LoadedIds.push_back(

->GetSeq().GetId().front() );

cerr << __LINE__ <<

<< LoadedIds.size() << endl;

(Args[

].

()) {

= In.tellg();

cerr <<

<< endl;

vector< CRef< CSeq_entry > > SeqEntries;

SeqEntries =

.GetResult();

cerr <<

<< e.

() << endl;

LoadedIds.push_back( (*SeqEntryIter)->GetSeq().GetId().front() );

(Top->

()) {

}

(Top->

()) {

ScorerNames =

()[

].AsString();

ScorerNames = RunRegistry->

(

,

);

vector<string> Names;

(vector<string>, NameIter, Names) {

(*NameIter ==

)

(*NameIter ==

)

(*NameIter ==

)

(*NameIter ==

)

(*NameIter ==

)

(*NameIter ==

) {

K = RunRegistry->

(

,

, 0.04);

(*NameIter ==

)

(*NameIter ==

)

(*NameIter ==

) {

K = RunRegistry->

(

,

, 0.04);

(args[

].

()) {

OrigFilters = args[

].AsString();

vector<string> SplitFilters;

(vector<string>, FilterIter, SplitFilters) {

FilterStr = *FilterIter;

cerr <<

<<

<< Rank <<

<< FilterStr << endl;

FilterNames = RunRegistry->

(

,

);

vector<string> Names;

(vector<string>, NameIter, Names) {

FilterStr = RunRegistry->

(

, *NameIter);

cerr <<

<<

<< *NameIter <<

<< FilterStr << endl;

FilterNames = RunRegistry->

(

,

);

vector<string> Names;

(vector<string>, NameIter, Names) {

= RunRegistry->

(*NameIter,

);

(

==

)

(

==

)

(

==

)

(

==

)

(

==

)

(

==

)

Params = RunRegistry->

(Name,

);

Threshold = RunRegistry->

(Name,

, 0);

= RunRegistry->

(Name,

);

UseNegatives = RunRegistry->

(Name,

,

);

(Args[

].

())

= Args[

].AsString();

Blaster->SetSoftFiltering(

);

Blaster->SetUseNegativeGiList(UseNegatives);

Params = RunRegistry->

(Name,

);

Threshold = RunRegistry->

(Name,

, 0);

Threshold = RunRegistry->

(Name,

, 0);

Clip = RunRegistry->

(Name,

, 3.0);

ModeStr = RunRegistry->

(Name,

);

(ModeStr ==

)

(ModeStr ==

)

Threshold = RunRegistry->

(Name,

, 0);

FileNameStr = RunRegistry->

(Name,

);

cerr <<

<< FileNameStr << endl;

(Found != GivenIds.

())

GivenIds.

(Found);

<< IdIter->AsString() << endl;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eAgpVersion_1_1

AGP spec 1.1.

Data loader implementation that uses the blast databases.

vector< CRef< CSeq_id > > SeqIdList

This class is used to turn an AGP file into a vector of Seq-entry's.

@ fSetSeqGap

Found gaps will not be given Seq-data such as Type and Linkage.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const string &db_path, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const string &dbname="nr", const EDbType dbtype=eUnknown, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

@ eNucleotide

nucleotide database

@ eSkipUnsupportedAlignments

Base class for reading FASTA sequences.

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

CFileLoadAligner(const string &name)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

@ eAlignCleanup

Use the older (CAlignCleanup) merge algorithm.

@ eTreeAlignMerger

Use the new (CTreeAlignMerger) merge algorithm.

void Init()

Initialize the application.

void x_AddAligners(CNgAligner &NgAligner, IRegistry *RunRegistry)

unique_ptr< CUnorderedSplitter > m_Splitter

list< CRef< CSeq_id > >::const_iterator LoadedIdsIter

void x_AddScorers(CNgAligner &NgAligner, IRegistry *RunRegistry)

CRef< CInversionMergeAligner > x_CreateInversionMergeAligner(IRegistry *RunRegistry, const string &Name)

CRef< ISequenceSet > x_CreateSequenceSet(IRegistry *RunRegistry, const string &Category)

list< CRef< CSeq_id > > m_LoadedIds

void x_RecurseSeqEntry(CRef< CSeq_entry > Top, list< CRef< CSeq_id > > &SeqIdList)

CRef< CSplitSeqAlignMerger > x_CreateSplitSeqMergeAligner(IRegistry *RunRegistry, const string &Name)

CRef< CMergeAligner > x_CreateMergeAligner(IRegistry *RunRegistry, const string &Name)

void x_LoadExternalSequences(IRegistry *RunRegistry, const string &Category, list< CRef< CSeq_id > > &LoadedIds)

CRef< CGC_Assembly > x_LoadAssembly(CNcbiIstream &In)

void x_AddFilters(CNgAligner &NgAligner, IRegistry *RunRegistry)

void x_PrintNoHitList(CNcbiOstream &Out, const CSeq_align_set &Alignments)

int Run()

Run the application.

CRef< CRemoteBlastAligner > x_CreateRemoteBlastAligner(IRegistry *RunRegistry, const string &Name)

bool x_CreateNgAlignRun(CNgAligner &NgAligner, IRegistry *RunRegistry)

CRef< CFileLoadAligner > x_CreateFileLoadAligner(IRegistry *RunRegistry, const string &Name)

CRef< CBlastAligner > x_CreateBlastAligner(IRegistry *RunRegistry, const string &Name)

void SetQuery(ISequenceSet *Set)

void SetSubject(ISequenceSet *Set)

void AddFilter(IAlignmentFilter *Filter)

void AddAligner(IAlignmentFactory *Aligner)

void AddScorer(IAlignmentScorer *Scorer)

Main interface to window based masker functionality.

Simple implementation of ILineReader for i(o)streams.

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

Operators to edit gaps in sequences.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define ERR_POST(message)

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

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

@ eDiag_Info

Informational message.

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)

virtual bool Exists(void) const

Check existence of file.

#define MSerial_AsnBinary

#define MSerial_AsnText

I/O stream manipulators –.

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

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

bool Empty(void) const THROWS_NONE

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

virtual bool GetBool(const string &section, const string &name, bool default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get boolean value of specified parameter name.

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

Get the parameter value.

virtual int GetInt(const string &section, const string &name, int default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get integer value of specified parameter name.

virtual double GetDouble(const string &section, const string &name, double default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get double value of specified parameter name.

#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::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

const TSeq & GetSeq(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

void SetData(TData &value)

Assign a value to Data data member.

const TId & GetId(void) const

Get the Id member data.

Lightweight interface for getting lines of data with minimal memory copying.

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

GenericReader< UTF8< char >, UTF8< char >, CrtAllocator > Reader

Reader with UTF8 encoding and default allocator.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

#define GetProgramName

Avoid name clash with the NCBI C Toolkit.

void Filter(TTimeline &timeline, TServers &servers)

int main(int argc, char **argv)

void Out(T t, int w, CNcbiOstream &to=cout)

CRef< objects::CObjectManager > om

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