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

;

OpenInputFile(

& filename,

binary);

OpenOutputFile(

& filename,

binary);

ProcessAsnInput(

);

ProcessSeqSubmit(

);

ProcessSeqEntry(

);

ProcessSet(

);

unique_ptr<CObjectIStream>

;

header = m_In->ReadFileHeader();

unhandled =

;

(header ==

) {

}

(header ==

) {

}

(header ==

) {

ProcessSeqEntry(*se);

ProcessSeqEntry(*se);

(

& consensus) { m_Consensus = consensus; m_CalculateConsensus =

; }

(m_CalculateConsensus) {

(

& consensus) { m_Consensus = consensus; }

(

);

(

);

Setup(

& args);

arg_desc->AddKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddOptionalKey(

,

,

,

prog_description =

;

arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),

prog_description,

);

SetupArgDescriptions(arg_desc.release());

(args[

]) {

m_ContigHandler.SetConsensus(args[

].AsString());

dir_name =

;

(args[

]) {

dir_name = args[

].AsString();

suffix =

;

(args[

]) {

suffix = args[

].AsString();

suffix = suffix.substr(1, suffix.length() - 2);

suffix = suffix.substr(1);

outdir = dir_name;

(args[

]) {

outdir = args[

].AsString();

outsuffix =

;

(args[

]) {

outsuffix = args[

].AsString();

=

+ suffix;

m_ContigHandler.OpenInputFile(fname, args[

]);

m_ContigHandler.OpenOutputFile(oname, args[

]);

m_ContigHandler.ProcessAsnInput();

& consensus = m_ContigHandler.GetConsensus();

m_MasterHandler.SetConsensus(consensus);

& master_file = args[

].AsString();

m_MasterHandler.OpenInputFile(master_file, args[

]);

m_MasterHandler.OpenOutputFile(args[

] ? args[

].AsString() : master_file +

, args[

]);

m_MasterHandler.ProcessAsnInput();

(

argc,

* argv[])

User-defined methods of the data storage class.

ncbi::TMaskedQueryRegions mask

CTLSMasterHandler m_MasterHandler

CTLSContigHandler m_ContigHandler

void Setup(const CArgs &args)

void SetConsensus(const string &consensus)

virtual ~CTLSContigHandler()

const string & GetConsensus()

bool m_CalculateConsensus

virtual void ProcessBioseq(CBioseq_Handle bh)

virtual void ProcessBioseq(CBioseq_Handle bh)

CRef< CBioseq_set > ReadBioseqSet(void)

unique_ptr< CObjectIStream > m_In

void StreamFile(const string &infile, const string &outfile, bool binary)

void ProcessSeqSubmit(void)

void OpenOutputFile(const string &filename, bool binary)

CRef< CSeq_entry > ReadSeqEntry(void)

void ProcessSeqEntry(void)

unique_ptr< CObjectOStream > m_Out

void ProcessAsnInput(void)

void OpenInputFile(const string &filename, bool binary)

CRef< CObjectManager > m_ObjMgr

CRef< CScope > BuildScope(void)

virtual void ProcessBioseq(CBioseq_Handle bh)

virtual ~CTLSMasterHandler()

void SetConsensus(const string &consensus)

Include a standard set of the NCBI C++ Toolkit most basic headers.

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eDirectory

Name of file directory.

@ eDS_Default

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

#define NCBI_THROW(exception_class, err_code, message)

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

TEntries GetEntries(const string &mask=kEmptyStr, TGetEntriesFlags flags=0) const

Get directory entries based on the specified "mask".

static string MakePath(const string &dir=kEmptyStr, const string &base=kEmptyStr, const string &ext=kEmptyStr)

Assemble a path from basic components.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

pair< TObjectPtr, TTypeInfo > ObjectInfo(C &obj)

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

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

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

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.

void RemoveTopLevelSeqEntry(const CTSE_Handle &entry)

Revoke TSE previously added using AddTopLevelSeqEntry() or AddBioseq().

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

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

void Run(void)

Enter the main loop.

LOG LOG_cxx2c(void)

Create LOG on top of C++ Toolkit CNcbiDiag.

void CORE_SetREG(REG rg)

Set the registry (no registry if "rg" is passed zero) – to be used by the core internals.

REG REG_cxx2c(IRWRegistry *reg, bool pass_ownership=false)

Convert a C++ Toolkit registry object to a REG registry.

void CORE_SetLOG(LOG lg)

Set the log handle (no logging if "lg" is passed zero) – to be used by the core internals (CORE LOG).

bool IsSetSeq_set(void) const

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

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

@ eMol_na

just a nucleic acid

list< CRef< CSeq_entry > > TEntrys

const TEntrys & GetEntrys(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool IsEntrys(void) const

Check if variant Entrys is selected.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

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

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

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

#define GetArgs

Avoid preprocessor name clash with the NCBI C Toolkit.

Defines command line argument related classes.

Defines unified interface to application:

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

Useful/utility classes and methods.

void SetTargetedLocusName(CBioseq_Handle seq, const string &tls)

string GetTargetedLocusNameConsensus(const string &tls1, const string &tls2)

string GenerateTargetedLocusName(CBioseq_Handle seq)

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

CRef< CScope > BuildScope(void)

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