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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seedtop__app_8cpp_source.html below:

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

44 #ifndef SKIP_DOXYGEN_PROCESSING 73 in

.getline(line, 128);

74 int len

.gcount();

75 if

(

len

< 4 || line[0]!=

'I'

|| line[1]!=

'D'

|| line[2]!=

' '

)

return

retv;

78 in

.getline(line, 100);

80 if

(

len

< 4 || line[0]!=

'P'

|| line[1]!=

'A'

|| line[2]!=

' '

)

return

retv;

81 while

(line[

len

-2] ==

' '

)

len

-= 1;

82 if

(line[

len

-2] ==

'>'

) line[

len

-2] =

'-'

;

83 else if

(line[

len

-2] ==

'.'

)

len

-= 1;

100 virtual void Init

();

106 static const string kDb

(

"db"

);

116

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

117 "Application to find pattern in BLAST databases or subject sequences, version " 120

arg_desc->AddDefaultKey(

kPattern

"input_file"

121 "File containing the patterns to be searched"

124

arg_desc->AddOptionalKey(

kDb

"database_name"

125 "Name of BLAST database to be searched"

128

arg_desc->AddOptionalKey(

kSubject

"input_file"

129 "File containing the subject sequences in FASTA format"

132

arg_desc->AddDefaultKey(

kOutput

"output_file"

133 "Output file to include results of the search"

184 "Either a BLAST database or subject sequence(s) must be specified"

);

191 if

(

pattern

.pattern ==

""

)

break

;

197 const CSeq_id

*sid = (*it)->GetId();

202

f_output << endl << '>

'; 203 ITERATE(CBioseq_Handle::TId, id, ids) { 204 string idst((*id).AsString()); 205 int index = idst.find_last_not_of('

'); 206 f_output << string(idst, 0, index + 1) << "|" ; 209 f_output << sequence::CDeflineGenerator().GenerateDefline(bhl) << endl << endl; 210 f_output << "ID " << pattern.name << endl;; 211 f_output << "PA " << pattern.pattern << endl; 216 ITERATE(CPacked_seqint_Base::Tdata, range, (*it)->GetPacked_int().Get()) { 217 static const ESeqLocExtremes ex = eExtreme_Positional; 218 f_output << " (" << (*range)->GetStart(ex)+1 << " " 219 << (*range)->GetStop(ex)+1 << ")"; 222 CSeqVector sv = bhl.GetSeqVector(CBioseq_Handle::eCoding_Iupac); 224 CSeq_loc::TRange tot_range = (*it)->GetTotalRange(); 225 sv.GetSeqData(tot_range.GetFrom(), tot_range.GetTo()+1, sq); 226 f_output << "SQ " << sq << endl; 229 db_adapter->ResetBlastSeqSrcIteration(); 236 #ifndef SKIP_DOXYGEN_PROCESSING 237 int main(int argc, const char* argv[] /*, const char* envp[]*/) 239 return CSeedTopApp().AppMain(argc, argv); 241 #endif /* SKIP_DOXYGEN_PROCESSING */

Produce formatted blast output for command line applications.

string RegisterOMDataLoader(CRef< CSeqDB > db_handle)

Utility functions for BLAST command line applications.

#define BLAST_EXIT_SUCCESS

Command line binary exit code: success.

Interface for reading SRA sequences into blast input.

@ eBlastp

Protein-Protein.

Main argument class for BLASTP application.

Class representing a text file containing sequences in fasta format.

Class that centralizes the configuration data for sequences to be converted.

Generalized converter from an abstract source of biological sequence data to collections of blast inp...

Keeps track of the version of the BLAST engine in the NCBI C++ toolkit.

Defines user input exceptions.

Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/s...

virtual void Init()

@inheritDoc

virtual int Run()

@inheritDoc

CSeedTopApp()

@inheritDoc

void Print(const CCompactSAMApplication::AlignInfo &ai)

TSeedTopResults Run(CRef< CLocalDbAdapter > db)

CRef< CSeqDB > GetSeqDb() const

Obtain a reference to the database.

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested program,...

vector< CConstRef< CSeq_loc > > TSeedTopResults

@ eBlastDbIsProtein

protein

void SetFullVersion(CRef< CVersionAPI > version)

Set version data for the program.

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

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.

@ fHideXmlHelp

Hide XML help description.

@ fHideLogfile

Hide log file description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

bool Exist(const string &name) const

Check existence of argument description.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

void SetDiagPostPrefix(const char *prefix)

Specify a string to prefix all subsequent error postings with.

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

@ eDiag_Warning

Warning message.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string AsFastaString(void) const

void AddDataLoader(const string &loader_name, TPriority pri=kPriority_Default)

Add data loader by name.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

vector< CSeq_id_Handle > TId

const TId & GetId(void) const

void Reset(void)

Reset reference object.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

std::istream & in(std::istream &in_, double &x_)

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Declares the CSeedTop class.

static struct SSeedTopPattern s_ReadPattern(CNcbiIstream &in)

static const string kOutput("out")

static const string kSubject("subject")

static const string kPattern("pattern")

static const string kDb("db")

Configuration structure for the CBlastScopeSource.

void OptimizeForWholeLargeSequenceRetrieval(bool value=true)

Configures the BLAST database data loader to optimize the retrieval of *entire* large sequences.

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