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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/speedtest_8cpp_source.html below:

NCBI C++ ToolKit: src/app/speedtest/speedtest.cpp Source File

70 virtual void Init

(

void

);

71 virtual int Run

(

void

);

72 virtual void Exit

(

void

);

127

arg_desc->SetUsageContext

129 "C++ speed test program"

);

132

(

"i"

"InputFile"

136

arg_desc->AddDefaultKey

137

(

"o"

"OutputFile"

141

arg_desc->AddDefaultKey

145

arg_desc->SetConstraint

148

arg_desc->AddDefaultKey

149

(

"X"

"Repetitions"

153

arg_desc->AddOptionalKey

155 "b Basic, s Serious"

157

arg_desc->SetConstraint

160

arg_desc->AddOptionalKey

162 "f Feature Indexing"

164

arg_desc->SetConstraint

167

arg_desc->AddOptionalKey

169 "s FASTA, S FASTA(no_scope mode), r No Defline, d Defline only, D Defline only(no_scope mode), " 170 "f By Feature, t Translation, v Visit, o Ostream"

172

arg_desc->SetConstraint

173

(

"S"

, &(*

new CArgAllow_Strings

"S"

"s"

"r"

"D"

"d"

"f"

"t"

"v"

"o"

));

175

arg_desc->AddOptionalKey

177 "v Visit, g Gene Overlap Print, h Gene Overlap Speed, x Xref, o Operon s Suggest"

179

arg_desc->SetConstraint

310 switch

(se->

Which

()) {

440

list< CConstRef<CSeq_id> > proteins;

444 for

( ; seq_iter; ++seq_iter ) {

452 else if

(bs.

IsAa

()) {

453

proteins.push_back( bs.

GetSeqId

() );

458

list< CConstRef<CSeq_id> >::iterator it = proteins.begin();

459 for

( ; it != proteins.end(); ++it ) {

476 string

asntype =

GetArgs

()[

"a"

].AsString();

478

is->SetStreamPos( 0 );

480 if

( asntype ==

"a"

|| asntype ==

"m"

) {

488

is->SetStreamPos( 0 );

491 if

( asntype ==

"a"

|| asntype ==

"e"

) {

497

is->SetStreamPos( 0 );

500 if

( asntype ==

"a"

|| asntype ==

"b"

) {

508

is->SetStreamPos( 0 );

511 if

( asntype ==

"a"

|| asntype ==

"s"

) {

534 string

tp = args[

"a"

].AsString();

536 int

mx = args[

"X"

].AsInteger();

563 string

km = args[

"K"

].AsString();

573 string

im = args[

"I"

].AsString();

580 string

sm = args[

"S"

].AsString();

615 string

fm = args[

"F"

].AsString();

639 double

lastInterval( 0 );

646 if

str

.empty ()) {

651

lastInterval =

Elapsed

() - lastInterval;

652 NcbiCout

"Read by line time is "

<< lastInterval <<

" seconds"

<< endl;

675

lastInterval =

Elapsed

() - lastInterval;

676 NcbiCout

"Internal processing time is "

<< lastInterval <<

" seconds"

<< endl;

682

lastInterval =

Elapsed

() - lastInterval;

683 NcbiCout

"ASN reading time is "

<< lastInterval <<

" seconds"

<< endl;

685 for

(

= 0;

< mx;

++) {

689

lastInterval =

Elapsed

() - lastInterval;

690 NcbiCout

"Internal processing time is "

<< lastInterval <<

" seconds"

<< endl;

720 int main

(

int

argc,

const char

* argv[])

User-defined methods of the data storage class.

TChanges BasicCleanup(CSeq_entry &se, Uint4 options=0)

FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>

void GetSeqEntry(CNcbiIstream &, CRef< CSeq_entry > &se)

int DoProcessFeatureSuggest(CNcbiIstream &, CNcbiOstream &, CScope &, CRef< CSeq_entry > &, bool do_format)

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

int TestFeatureGeneOverlap(CNcbiIstream &, CNcbiOstream &, CScope &, CBioseq &, bool do_format)

int PlayAroundWithSuggestIntervals(CNcbiIstream &, CNcbiOstream &, CScope &, CRef< CSeq_entry > &)

void DoProcessStreamDefline(CNcbiIstream &ip, CNcbiOstream &op, CRef< CSeq_entry > &se, CScope &i)

void DoProcessStreamFasta(CNcbiIstream &ip, CNcbiOstream &op, CRef< CSeq_entry > &se)

void DumpAlignment(CNcbiOstream &, CRef< CSeq_align > &)

void DoProcess(CNcbiIstream &ip, CNcbiOstream &op, CScope &, CRef< CSeq_entry > &se)

virtual void Exit(void)

Cleanup on application exit.

int DoProcessFeatureGeneOverlap(CNcbiIstream &, CNcbiOstream &, CScope &, CRef< CSeq_entry > &, bool do_format)

spliced protein to genomic alignment

CRef< objects::CSeq_align > FindAlignment(objects::CScope &scope, const objects::CSeq_id &protein, const objects::CSeq_loc &genomic, CProSplignOutputOptions output_options=CProSplignOutputOptions())

Aligns protein to a region on genomic sequence.

namespace ncbi::objects::

Template class for iteration on objects of class C (non-medifiable version)

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

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 NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

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)

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

@ eDS_Default

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

#define MSerial_AsnText

I/O stream manipulators â.

@ eSerial_AsnText

ASN.1 text.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

CConstRef< CSeq_feat > GetOverlappingGene(const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)

virtual void WriteTitle(const CBioseq_Handle &handle, const CSeq_loc *location=0, const string &custom_title=kEmptyStr)

virtual void Write(const CSeq_entry_Handle &handle, const CSeq_loc *location=0)

Unspecified locations designate complete sequences; non-empty custom titles override the usual title ...

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...

CSeq_entry_Handle GetSeq_entryHandle(CDataLoader *loader, const TBlobId &blob_id, EMissing action=eMissing_Default)

Get Seq-entry handle by its blob-id, with possible loading.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

TClass GetClass(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

TInst_Length GetInst_Length(void) const

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

@ eLevel_Mains

Main bioseq only.

void Reset(void)

Reset reference object.

TObjectType & GetObject(void)

Get object.

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

const TLocation & GetLocation(void) const

Get the Location member data.

TSet & SetSet(void)

Select the variant.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

bool IsSetAnnot(void) const

Check if a value has been assigned to Annot data member.

bool IsSetSeq_set(void) const

Check if a value has been assigned to Seq_set data member.

E_Choice Which(void) const

Which variant is currently selected.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

@ eClass_nuc_prot

nuc acid and coded proteins

@ e_not_set

No variant selected.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetAnnot(void) const

Check if a value has been assigned to Annot data member.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

bool IsSetData(void) const

Check if a value has been assigned to Data data member.

EMol

molecule class in living organism

list< CRef< CSeq_feat > > TFtable

bool IsFtable(void) const

Check if variant Ftable is selected.

const TData & GetData(void) const

Get the Data member data.

list< CRef< CSeq_annot > > TAnnot

@ eMol_not_set

> cdna = rna

void SetData(TData &value)

Assign a value to Data data member.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

The NCBI C++/STL use hints.

Defines: CTimeFormat - storage class for time format.

int main(int argc, const char *argv[])

string SeqLocString(const CSeq_loc &loc)

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