gc_cli.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <serial/serial.hpp>
#include <serial/objostr.hpp>
#include <objects/genomecoll/genomic_collections_cli.hpp>
#include <objects/genomecoll/GC_Assembly.hpp>
#include <objects/genomecoll/GC_AssemblySet.hpp>
#include <objects/genomecoll/GC_AssemblyUnit.hpp>
#include <objects/genomecoll/GC_AssemblyDesc.hpp>
#include <objects/genomecoll/GCClient_ValidateChrTypeLo.hpp>
#include <objects/genomecoll/GCClient_AssemblyInfo.hpp>
#include <objects/genomecoll/GCClient_AssemblySequenceI.hpp>
#include <objects/genomecoll/GCClient_AssembliesForSequ.hpp>
#include <objects/genomecoll/GCClient_EquivalentAssembl.hpp>
#include <objects/genomecoll/GCClient_GetEquivalentAsse.hpp>
#include <objects/genomecoll/GCClient_GetAssemblyBlobRe.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <sstream>
#include <numeric>

Include dependency graph for gc_cli.cpp:

Go to the source code of this file.

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Classes
class	CGencollService
class	CDirectCGIExec
class	CClientGenomicCollectionsSvcApplication

Functions
static CGC_AssemblyDesc *	GetAssebmlyDesc (CRef< CGC_Assembly > &assembly)
static bool	isVersionsObject (CRef< CSeqdesc > desc)
static CRef< CGC_Assembly >	RemoveVersions (CRef< CGC_Assembly > assembly)
static list< string >	GetIDs (const string &ids)
static list< string >	GetIDsFromFile (CNcbiIstream &istr)
static list< string >	GetAccessions (const CArgs &args)
static list< string >	GetReleaseIds (const CArgs &args)
int	main (int argc, const char *argv[])

Function Documentation

GetAccessions()

static list<string> GetAccessions ( const CArgs &  args )

static

Definition at line 348 of file gc_cli.cpp.

References GetIDs(), and GetIDsFromFile().

Referenced by CClientGenomicCollectionsSvcApplication::RunWithService().

GetAssebmlyDesc()

static CGC_AssemblyDesc* GetAssebmlyDesc ( CRef< CGC_Assembly > &  assembly )

static

Definition at line 286 of file gc_cli.cpp.

References CGC_Assembly_Base::GetAssembly_set(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsAssembly_set(), CGC_AssemblySet_Base::IsSetDesc(), CGC_AssemblyUnit_Base::IsSetDesc(), CGC_Assembly_Base::IsUnit(), NULL, CGC_Assembly_Base::SetAssembly_set(), CGC_AssemblySet_Base::SetDesc(), CGC_AssemblyUnit_Base::SetDesc(), and CGC_Assembly_Base::SetUnit().

Referenced by RemoveVersions().

GetIDs()

static list<string> GetIDs ( const string &  ids )

static

Definition at line 318 of file gc_cli.cpp.

References NStr::fSplit_Tokenize, and NStr::Split().

Referenced by GetAccessions(), GetIDsFromFile(), and GetReleaseIds().

GetIDsFromFile()

static list<string> GetIDsFromFile ( CNcbiIstream &  istr )

static

Definition at line 327 of file gc_cli.cpp.

References GetIDs(), NcbiGetlineEOL(), and NStr::TruncateSpacesInPlace().

Referenced by GetAccessions(), and GetReleaseIds().

GetReleaseIds()

static list<string> GetReleaseIds ( const CArgs &  args )

static

Definition at line 354 of file gc_cli.cpp.

References GetIDs(), and GetIDsFromFile().

Referenced by CClientGenomicCollectionsSvcApplication::RunWithService().

isVersionsObject()

static bool isVersionsObject ( CRef< CSeqdesc >  desc )

static

Definition at line 295 of file gc_cli.cpp.

References CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), and CSeqdesc_Base::IsUser().

Referenced by RemoveVersions().

main()

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

Definition at line 408 of file gc_cli.cpp.

References CNcbiApplicationAPI::AppMain(), GetDiagContext(), and CDiagContext::SetOldPostFormat().

RemoveVersions()

static CRef<CGC_Assembly> RemoveVersions ( CRef< CGC_Assembly >  assembly )

static

Definition at line 304 of file gc_cli.cpp.

References CGC_AssemblyDesc_Base::CanGetDescr(), GetAssebmlyDesc(), isVersionsObject(), l(), remove_if(), and CGC_AssemblyDesc_Base::SetDescr().

Referenced by CClientGenomicCollectionsSvcApplication::RunWithService().