51 arg_desc.SetCurrentGroup(
"General search options");
53 arg_desc.AddOptionalKey(
kArgDb,
"database_name",
"SRA or WGS database name",
56 arg_desc.SetCurrentGroup(
"");
58 vector<string> database_args;
59 database_args.push_back(
kArgDb);
62 arg_desc.SetCurrentGroup(
"Statistical options");
63 arg_desc.AddOptionalKey(
kArgDbSize,
"num_letters",
64 "Effective length of the database ",
67 arg_desc.SetCurrentGroup(
"");
74 string kSRASearchMode =
string(
76 "0 = unaligned reads only\n"
77 "1 = aligned reference seqs only\n"
78 "2 = both unaligned reads and aligned reference seqs n");
82 string kIncludeFilteredReads =
string (
"Include filtered reads\n");
89 static const string kProgram(
"blastn");
91 "Nucleotide-Nucleotide BLAST"));
92 const bool kQueryIsProtein =
false;
96 static const string kDefaultTask =
"megablast";
100 tasks.
erase(
"vecscreen");
Declares singleton objects to store the version and reference for the BLAST engine.
Declares the BLAST exception class.
const string kArgIncludeFilteredReads("include_filtered_reads")
const string kArgSRASearchMode("sra_mode")
Main argument class for BLASTN_VDB application.
CRef< CRemoteArgs > m_RemoteArgs
remote vs. local execution options
string GetTask() const
Get the task for this object.
CRef< CQueryOptionsArgs > m_QueryOptsArgs
query options object
CRef< CBlastDatabaseArgs > m_BlastDbArgs
database/subject object
CRef< CDebugArgs > m_DebugArgs
Debugging arguments.
CRef< CMTArgs > m_MTArgs
multi-threaded options
CRef< CFormattingArgs > m_FormattingArgs
formatting options
bool m_IsUngapped
Is this application being run ungapped.
TBlastCmdLineArgs m_Args
Set of command line argument objects.
void SetTask(const string &task)
Set the task for this object.
CRef< CStdCmdLineArgs > m_StdCmdLineArgs
standard command line arguments class
CRef< CHspFilteringArgs > m_HspFilteringArgs
HSP filtering arguments.
string m_ClientId
Client ID used for remote BLAST submissions, must be populated by subclasses.
void SetDatabaseMaskingSupport(bool val)
Turns on/off database masking support.
EAPILocality
Enumerates the possible contexts in which objects of this type can be used.
Argument class to collect database/subject arguments.
Keeps track of the version of the BLAST engine in the NCBI C++ toolkit.
virtual int GetQueryBatchSize() const
@inheritDoc
CBlastnVdbAppArgs()
Constructor.
virtual CRef< CBlastOptionsHandle > x_CreateOptionsHandle(CBlastOptions::EAPILocality locality, const CArgs &args)
@inheritDoc
CRef< CSRASearchModeArgs > m_VDBSearchModeArgs
Argument class to collect debugging options.
Argument class to retrieve discontiguous megablast arguments.
Argument class for collecting filtering options.
Argument class for collecting gapped options.
Argument class for general search BLAST algorithm options: evalue, gap penalties, query filter string...
Argument class to retrieve options for filtering HSPs (e.g.
Argument class to collect multi-threaded arguments.
Defines values for match and mismatch in nucleotide comparisons as well as non-greedy extension.
Argument class to retrieve and set the off-diagonal range used in 2-hit algorithm.
Argument class to populate an application's name and description.
Argument class to collect query options.
Argument class to collect remote vs. local execution.
bool ExecuteRemotely() const
Return whether the search should be executed remotely or not.
Argument class to collect database/subject arguments.
virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)
Sets the command line descriptions in the CArgDescriptions object relevant to the subclass.
Argument class to retrieve input and output streams for a command line program.
Argument class to specify the supported tasks a given program.
Argument class to retrieve and set the window size BLAST algorithm option.
const string kArgDbSize
Effective length of BLAST database.
const string kTask
Task to perform.
const string kArgDb
BLAST database name.
Declares the CDiscNucleotideOptionsHandle class.
static set< string > GetTasks(ETaskSets choice=eAll)
Retrieve the set of supported tasks.
EProgram ProgramNameToEnum(const std::string &program_name)
Map a string into an element of the ncbi::blast::EProgram enumeration (except eBlastProgramMax).
virtual string Print(void) const
Print version information.
static CBlastOptionsHandle * CreateTask(string task, EAPILocality locality=CBlastOptions::eLocal)
Creates an options handle object configured with default options for the requested task,...
@ eNuclNucl
Nucleotide-nucleotide tasks.
void AddFlag(const string &name, const string &comment, CBoolEnum< EFlagValue > set_value=eFlagHasValueIfSet, TFlags flags=0)
Add description for flag argument.
void SetCurrentGroup(const string &group)
Set current arguments group name.
void AddDefaultKey(const string &name, const string &synopsis, const string &comment, EType type, const string &default_value, TFlags flags=0, const string &env_var=kEmptyStr, const char *display_value=nullptr)
Add description for optional key with default value.
@ eInt8
Convertible into an integer number (Int8 only)
@ eString
An arbitrary string.
@ eInteger
Convertible into an integer number (int or Int8)
void Reset(void)
Reset reference object.
bool NotEmpty(void) const THROWS_NONE
Check if CRef is not empty – pointing to an object and has a non-null value.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define END_SCOPE(ns)
End the previously defined scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define BEGIN_SCOPE(ns)
Define a new scope.