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NCBI C++ ToolKit: src/app/blastdb/convert2blastmask.cpp Source File

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unique_ptr<CMaskFromFasta> reader(

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unique_ptr<CMaskWriterBlastDbMaskInfo> writer(

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void AddParam(EUsageParams p, int val)

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

static const char *const USAGE_LINE

Contains the description of this application.

CConvert2BlastMaskApplication()

virtual void Init(void)

Initialize the application.

CMaskWriterBlastDbMaskInfo * x_GetWriter()

CMaskFromFasta * x_GetReader()

virtual void Exit(void)

Cleanup on application exit.

virtual int Run(void)

Run the application.

CBlastUsageReport m_UsageReport

~CConvert2BlastMaskApplication()

Base class for reading FASTA sequences.

CMaskFromFasta(CNcbiIstream &input, bool parse_seqids)

virtual void x_OpenMask(void)

const CMaskWriter::TMaskList & GetMask() const

virtual void x_CloseMask(void)

virtual void ParseDataLine(const TStr &s, ILineErrorListener *pMessageListener)

CMaskWriter::TMaskList m_mask

Output filter to print masked sequence locations as Blast-db-mask-info objects.

pair< TSeqPos, TSeqPos > TMaskedInterval

Type representing a masked interval within a sequence.

vector< TMaskedInterval > TMaskList

A type representing the total of masking information about a sequence.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

void Print(const CCompactSAMApplication::AlignInfo &ai)

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

Operators to edit gaps in sequences.

static SQLCHAR output[256]

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.

unsigned int TSeqPos

Type for sequence locations and lengths.

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.

CVersionInfo GetVersion(void) const

Get the program version information.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

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.

CArgAllow_Strings * Allow(const string &value)

Add allowed string values.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

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

Set diagnostic stream.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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

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

virtual void x_CloseMask(void)

CRef< CSeq_loc > SaveMask(void)

Directs the *following* call to ReadOneSeq to note the locations of lowercase letters.

TSeqPos GetCurrentPos(EPosType pos_type)

virtual void x_OpenMask(void)

virtual void ParseDataLine(const TStr &s, ILineErrorListener *pMessageListener)

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

@ fNoParseID

Generate an ID (whole defline -> title)

bool IsEnabled(void)

Indicates whether application usage statistics collection is enabled for a current reporter instance.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

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

Convert string to unsigned int.

size_type find(const CTempString match, size_type pos=0) const

Find the first instance of the entire matching string within the current string, beginning at an opti...

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

double Elapsed(void) const

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

void Start(void)

Start the timer.

EBlast_filter_program

This defines the possible sequence filtering algorithms to be used in a BLAST database.

@ eBlast_filter_program_dust

@ eBlast_filter_program_repeat

@ eBlast_filter_program_seg

@ eBlast_filter_program_windowmasker

@ eBlast_filter_program_not_set

@ eBlast_filter_program_other

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

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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