#include "hitfilter_app.hpp"
(Private to src/app/hfilter.)

Inheritance diagram for CAppHitFilter:

Collaboration diagram for CAppHitFilter:

Classes
struct	SBuildIDs

Public Types
enum	EReciprocity { e_Other , e_SubjectDuplication , e_QueryDuplication , e_ReciprocalBest }

typedef CBlastTabular	THit

typedef CRef< THit >	THitRef

typedef vector< THitRef >	THitRefs

Public Types inherited from CNcbiApplicationAPI
enum	EAppNameType { eBaseName , eFullName , eRealName }

Public Member Functions
virtual void	Init ()
	Initialize the application. More...

virtual int	Run ()
	Run the application. More...

virtual void	Exit ()
	Cleanup on application exit. More...

Public Member Functions inherited from CNcbiApplication
virtual	~CNcbiApplication (void)
	Destructor. More...

	CNcbiApplication (const SBuildInfo &build_info=NCBI_SBUILDINFO_DEFAULT())
	Constructor. More...

Public Member Functions inherited from CNcbiApplicationAPI
	CNcbiApplicationAPI (const SBuildInfo &build_info)
	Constructor. More...

virtual	~CNcbiApplicationAPI (void)
	Destructor. More...

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. More...

virtual int	DryRun (void)
	Test run the application. More...

const CNcbiArguments &	GetArguments (void) const
	Get the application's cached unprocessed command-line arguments. More...

virtual const CArgs &	GetArgs (void) const
	Get parsed command line arguments. More...

const CNcbiEnvironment &	GetEnvironment (void) const
	Get the application's cached environment. More...

CNcbiEnvironment &	SetEnvironment (void)
	Get a non-const copy of the application's cached environment. More...

void	SetEnvironment (const string &name, const string &value)
	Set a specified environment variable by name. More...

bool	HasLoadedConfig (void) const
	Check if the config file has been loaded. More...

bool	FinishedLoadingConfig (void) const
	Check if the application has finished loading config file (successfully or not). More...

const CNcbiRegistry &	GetConfig (void) const
	Get the application's cached configuration parameters (read-only). More...

CNcbiRegistry &	GetConfig (void)

const string &	GetConfigPath (void) const
	Get the full path to the configuration file (if any) we ended up using. More...

bool	ReloadConfig (CMetaRegistry::TFlags flags=CMetaRegistry::fReloadIfChanged, IRegistry::TFlags reg_flags=IRegistry::fWithNcbirc)
	Reload the configuration file. More...

SIZE_TYPE	FlushDiag (CNcbiOstream *os, bool close_diag=false)
	Flush the in-memory diagnostic stream (for "eDS_ToMemory" case only). More...

const string &	GetProgramDisplayName (void) const
	Get the application's "display" name. More...

const string &	GetProgramExecutablePath (EFollowLinks follow_links=eIgnoreLinks) const
	Get the application's executable path. More...

CVersionInfo	GetVersion (void) const
	Get the program version information. More...

const CVersionAPI &	GetFullVersion (void) const
	Get the program version information. More...

bool	IsDryRun (void) const
	Check if it is a test run. More...

virtual bool	SetupDiag_AppSpecific (void)
	Setup application specific diagnostic stream. More...

template<class TFunc >
void	AddOnExitAction (TFunc func)
	Add callback to be executed from CNcbiApplicationAPI destructor. More...

Private Types
typedef list< CRef< objects::CSeq_align > >	TSeqAlignList

typedef map< string, string >	TMapIds

typedef map< string, SBuildIDs >	TMapIdPairs

Private Member Functions
void	x_ReadInputHits (THitRefs *phitrefs, bool one_pair=false)

void	x_IterateSeqAlignList (const TSeqAlignList &sa_list, THitRefs *phitrefs, bool parse_aln, const THit::TCoord &min_len, const double &min_idty) const

void	x_DumpOutput (const THitRefs &hitrefs)

void	x_LoadConstraints (CNcbiIstream &istr, THitRefs &all)

void	x_LoadIDs (CNcbiIstream &istr)

void	x_DoPairwise (THitRefs *pall)

void	x_DoMultiple (THitRefs *pall)

Private Attributes
TMapIds	m_IDs

TMapIdPairs	m_IDRevs

Additional Inherited Members
Static Public Member Functions inherited from CNcbiApplication
static CNcbiApplication *	Instance (void)
	Singleton method. More...

Static Public Member Functions inherited from CNcbiApplicationAPI
static CNcbiApplicationAPI *	Instance (void)
	Singleton method. More...

static CNcbiApplicationGuard	InstanceGuard (void)
	Singleton method. More...

static SSystemMutex &	GetInstanceMutex (void)
	Mutex for application singleton object. More...

static string	GetAppName (EAppNameType name_type=eBaseName, int argc=0, const char const argv=NULL)

Protected Types inherited from CNcbiApplicationAPI
enum	EPreparseArgs { ePreparse_Continue , ePreparse_Exit }
	Result of PreparseArgs() More...

enum	EDisableArgDesc { fDisableStdArgs = 0x01 }
	Disable argument descriptions. More...

enum	EHideStdArgs { fHideLogfile = CArgDescriptions::fHideLogfile , fHideConffile = CArgDescriptions::fHideConffile , fHideVersion = CArgDescriptions::fHideVersion , fHideFullVersion = CArgDescriptions::fHideFullVersion , fHideDryRun = CArgDescriptions::fHideDryRun , fHideHelp = CArgDescriptions::fHideHelp , fHideFullHelp = CArgDescriptions::fHideFullHelp , fHideXmlHelp = CArgDescriptions::fHideXmlHelp , fHideAll = CArgDescriptions::fHideAll }
	Which standard flag's descriptions should not be displayed in the usage message. More...

enum	EStdioSetup { fNoSyncWithStdio = 0x01 , fDefault_CinBufferSize = 0x02 , fBinaryCin = 0x04 , fBinaryCout = 0x08 , fDefault_SyncWithStdio = 0x00 }
	Flags to adjust standard I/O streams' behaviour. More...

enum	EExitMode { eNoExits , eExceptionalExits , eAllExits }
	When to return a user-set exit code. More...

enum	EAppFlags { fSkipSafeStaticDestroy = 1 << 0 }

typedef int	TDisableArgDesc
	Binary OR of "EDisableArgDesc". More...

typedef int	THideStdArgs
	Binary OR of "EHideStdArgs". More...

typedef int	TStdioSetupFlags
	Binary OR of "EStdioSetup". More...

typedef int	TAppFlags

Protected Member Functions inherited from CNcbiApplicationAPI
virtual EPreparseArgs	PreparseArgs (int argc, const char const argv)
	Check the command line arguments before parsing them. More...

void	DisableArgDescriptions (TDisableArgDesc disable=fDisableStdArgs)

void	HideStdArgs (THideStdArgs hide_mask)
	Set the hide mask for the Hide Std Flags. More...

void	SetStdioFlags (TStdioSetupFlags stdio_flags)
	Adjust the behavior of standard I/O streams. More...

void	SetVersion (const CVersionInfo &version)
	Set the version number for the program. More...

void	SetVersion (const CVersionInfo &version, const SBuildInfo &build_info)

void	SetVersionByBuild (int major)

void	SetFullVersion (CRef< CVersionAPI > version)
	Set version data for the program. More...

virtual void	SetupArgDescriptions (CArgDescriptions *arg_desc)
	Setup the command line argument descriptions. More...

const CArgDescriptions *	GetArgDescriptions (void) const
	Get argument descriptions (set by SetupArgDescriptions) More...

bool	SetupDiag (EAppDiagStream diag)
	Setup the application diagnostic stream. More...

virtual bool	LoadConfig (CNcbiRegistry &reg, const string *conf, CNcbiRegistry::TFlags reg_flags)
	Load settings from the configuration file to the registry. More...

virtual bool	LoadConfig (CNcbiRegistry &reg, const string *conf)
	Load settings from the configuration file to the registry. More...

CNcbiRegistry &	GetRWConfig (void)
	Get the application's cached configuration parameters, accessible for read-write for an application's internal use only. More...

void	SetProgramDisplayName (const string &app_name)
	Set program's display name. More...

virtual void	AppStart (void)
	Method to be called before application start. More...

virtual void	AppStop (int exit_code)
	Method to be called before application exit. More...

void	SetExitCode (int exit_code, EExitMode when=eExceptionalExits)
	Force the program to return a specific exit code later, either when it exits due to an exception or unconditionally. More...

void	SetAppFlags (TAppFlags flags)

void	ExecuteOnExitActions ()
	Should only be called from the destructors of classes derived from CNcbiApplicationAPI - if it is necessary to access their data members and virtual methods; or to dynamic_cast<> from the base app class. More...

void	SetPhoneHomePolicy (IPhoneHomePolicy *policy, ENcbiOwnership ownership=eNoOwnership)
	Set Phone Home Policy. More...

IPhoneHomePolicy *	GetPhoneHomePolicy () const
	Return pointer to current Phone Home Policy or NULL. More...

Static Protected Member Functions inherited from CNcbiApplicationAPI
static CRWLock &	GetInstanceLock (void)

static string	FindProgramExecutablePath (int argc, const char const argv, string *real_path=0)
	Find the application's executable file. More...

Detailed Description

Definition at line 71 of file hitfilter_app.hpp.

Member Typedef Documentation

◆ THit

typedef CBlastTabular CAppHitFilter::THit

Definition at line 79 of file hitfilter_app.hpp.

◆ THitRef

typedef CRef<THit> CAppHitFilter::THitRef

Definition at line 80 of file hitfilter_app.hpp.

◆ THitRefs

typedef vector<THitRef> CAppHitFilter::THitRefs

Definition at line 81 of file hitfilter_app.hpp.

◆ TMapIdPairs

typedef map<string,SBuildIDs> CAppHitFilter::TMapIdPairs

private

Definition at line 113 of file hitfilter_app.hpp.

◆ TMapIds

typedef map<string,string> CAppHitFilter::TMapIds

private

Definition at line 107 of file hitfilter_app.hpp.

◆ TSeqAlignList

typedef list<CRef<objects::CSeq_align> > CAppHitFilter::TSeqAlignList

private

Definition at line 92 of file hitfilter_app.hpp.

Member Enumeration Documentation

◆ EReciprocity

enum CAppHitFilter::EReciprocity

Enumerator
e_Other
e_SubjectDuplication
e_QueryDuplication
e_ReciprocalBest

Definition at line 83 of file hitfilter_app.hpp.

Member Function Documentation

◆ Exit()

void CAppHitFilter::Exit ( void )

virtual

Cleanup on application exit.

Perform cleanup before exiting. The default behavior of this is "do nothing". If you have special cleanup logic that needs to be performed, then you must override this method with your own logic.

Reimplemented from CNcbiApplicationAPI.

Definition at line 751 of file hitfilter_app.cpp.

◆ Init()

void CAppHitFilter::Init ( void )

virtual

Initialize the application.

The default behavior of this is "do nothing". If you have special initialization logic that needs to be peformed, then you must override this method with your own logic.

Reimplemented from CNcbiApplicationAPI.

Definition at line 71 of file hitfilter_app.cpp.

References CArgAllow_Strings::Allow(), CArgDescriptions::eDouble, CArgDescriptions::eInputFile, CArgDescriptions::eInteger, CArgDescriptions::eOutputFile, CArgDescriptions::eString, CArgDescriptions::fBinary, CNcbiApplicationAPI::fHideConffile, CNcbiApplicationAPI::fHideLogfile, CNcbiApplicationAPI::fHideVersion, CNcbiApplicationAPI::GetArguments(), GetProgramName, CNcbiApplicationAPI::HideStdArgs(), and CNcbiApplicationAPI::SetupArgDescriptions().

◆ Run()

int CAppHitFilter::Run ( )

virtual

Run the application.

It is defined as a pure virtual method – so you must(!) supply the Run() method to implement the application-specific logic.

Returns: Exit code.

Implements CNcbiApplicationAPI.

Definition at line 501 of file hitfilter_app.cpp.

References all, eUnknown, CNcbiApplicationAPI::GetArgs(), NCBI_THROW, CHitFilter< THit >::s_MergeAbutting(), x_DoMultiple(), x_DoPairwise(), and x_DumpOutput().

◆ x_DoMultiple()

void CAppHitFilter::x_DoMultiple ( THitRefs * pall )

private

Definition at line 593 of file hitfilter_app.cpp.

References all, copy(), CNcbiApplicationAPI::GetArgs(), LOG_POST, min(), remove_if(), s_PHitRefScore(), CHitFilter< THit >::s_RunGreedy(), ct::sort(), x_LoadConstraints(), x_LoadIDs(), and x_ReadInputHits().

Referenced by Run().

◆ x_DoPairwise()

void CAppHitFilter::x_DoPairwise ( THitRefs * pall )

private

Definition at line 548 of file hitfilter_app.cpp.

References all, copy(), CNcbiApplicationAPI::GetArgs(), remove_if(), s_PHitRefScore(), CHitFilter< THit >::s_RunGreedy(), ct::sort(), and x_ReadInputHits().

Referenced by Run().

◆ x_DumpOutput()

void CAppHitFilter::x_DumpOutput ( const THitRefs & hitrefs )

private

Definition at line 356 of file hitfilter_app.cpp.

References CSeq_annot::AddComment(), e_QueryDuplication, e_ReciprocalBest, e_SubjectDuplication, eNa_strand_minus, eNa_strand_plus, CSeq_align_Base::eType_partial, CDense_seg::FromTranscript(), CNcbiApplicationAPI::GetArgs(), CDense_seg_Base::GetDim(), CAlignShadow::GetId(), CDense_seg_Base::GetNumseg(), CAlignShadow::GetQueryStart(), CAlignShadow::GetQueryStrand(), CBlastTabular::GetScore(), CDense_seg_Base::GetStarts(), CAlignShadow::GetSubjStart(), CAlignShadow::GetSubjStrand(), CAlignShadow::GetTranscript(), i, ITERATE, kQuery, MSerial_AsnBinary, MSerial_AsnText, CDense_seg_Base::ResetStrands(), CAlignShadow::s_RunLengthDecode(), CSeq_annot_Base::SetData(), CDense_seg_Base::SetIds(), CSeq_align_Base::SetScore(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::SetType().

Referenced by Run().

◆ x_IterateSeqAlignList()

void CAppHitFilter::x_IterateSeqAlignList	(	const TSeqAlignList &	sa_list,
		THitRefs *	phitrefs,
		bool	parse_aln,
		const THit::TCoord &	min_len,
		const double &	min_idty
	)		const

private

Definition at line 333 of file hitfilter_app.cpp.

References ITERATE, and r().

Referenced by x_ReadInputHits().

◆ x_LoadConstraints()

void CAppHitFilter::x_LoadConstraints	(	CNcbiIstream &	istr,
		THitRefs &	all
	)

private

◆ x_LoadIDs()

void CAppHitFilter::x_LoadIDs ( CNcbiIstream & istr )

private

Definition at line 183 of file hitfilter_app.cpp.

References map_checker< Container >::clear(), map_checker< Container >::end(), map_checker< Container >::find(), CAppHitFilter::SBuildIDs::m_id, m_IDRevs, and m_IDs.

Referenced by x_DoMultiple().

◆ x_ReadInputHits()

void CAppHitFilter::x_ReadInputHits	(	THitRefs *	phitrefs,
		bool	one_pair = `false`
	)

private

Definition at line 213 of file hitfilter_app.cpp.

References eSerial_AsnBinary, eSerial_AsnText, eUnknown, CSeq_align_set_Base::Get(), CSeq_annot_Base::C_Data::GetAlign(), CNcbiApplicationAPI::GetArgs(), CSeq_annot_Base::GetData(), CSeq_align_Base::C_Segs::GetDisc(), CSeq_align_Base::GetSegs(), in(), CConstRef< C, Locker >::IsNull(), ITERATE, NCBI_THROW, CObjectIStream::Open(), tag, NStr::TruncateSpaces(), and x_IterateSeqAlignList().

Referenced by x_DoMultiple(), and x_DoPairwise().

Member Data Documentation

◆ m_IDRevs

TMapIdPairs CAppHitFilter::m_IDRevs

private

Definition at line 114 of file hitfilter_app.hpp.

Referenced by x_LoadConstraints(), and x_LoadIDs().

◆ m_IDs

TMapIds CAppHitFilter::m_IDs

private

Definition at line 108 of file hitfilter_app.hpp.

Referenced by x_LoadIDs().

The documentation for this class was generated from the following files:

src/app/hfilter/hitfilter_app.hpp
src/app/hfilter/hitfilter_app.cpp

Classes

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ THit

◆ THitRef

◆ THitRefs

◆ TMapIdPairs

◆ TMapIds

◆ TSeqAlignList

Member Enumeration Documentation

◆ EReciprocity

Member Function Documentation

◆ Exit()

◆ Init()

◆ Run()

◆ x_DoMultiple()

◆ x_DoPairwise()

◆ x_DumpOutput()

◆ x_IterateSeqAlignList()

◆ x_LoadConstraints()

◆ x_LoadIDs()

◆ x_ReadInputHits()

Member Data Documentation

◆ m_IDRevs

◆ m_IDs