seqannot_splicer_util.cpp File Reference

#include <ncbi_pch.hpp>
#include <stack>
#include <corelib/ncbiexpt.hpp>
#include <corelib/ncbimisc.hpp>
#include <corelib/ncbiobj.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <serial/objectio.hpp>
#include <serial/objistr.hpp>
#include <serial/serialdef.hpp>
#include "seqannot_splicer_stats.hpp"
#include "seqannot_splicer_util.hpp"

Include dependency graph for seqannot_splicer_util.cpp:

Go to the source code of this file.

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Classes
struct	SContext_tag

Macros
#define	ADDFLAG(flag)    if ((found_flag = find(fbegin,fend,#flag)) != fend) flags |= fSAMF_##flag;
#define	ADDFLAG(flag)    if ((found_flag = find(fbegin,fend,#flag)) != fend) flags |= fSIMF_##flag;

Typedefs
typedef list< TSeqRef >	TSeqRefCont
typedef list< CNcbiStreampos >	TPosCont
typedef CObjectFor< TSeqRefCont >	TSeqRefContOb
typedef CObjectFor< TPosCont >	TPosContOb
typedef CRef< TSeqRefContOb >	TSeqRefContRef
typedef CRef< TPosContOb >	TPosContRef
typedef set< TSeqRef, PPtrLess< TSeqRef > >	TContextSeqIds
typedef struct SContext_tag *	TContextPtr
typedef list< TContextPtr >	TContextList
typedef stack< TContextPtr >	TContextPtrStack
typedef map< CNcbiStreampos, TSeqRefContRef >	TAnnotToSeqIdMap
typedef map< TSeqRef, TPosContRef, PPtrLess< TSeqRef > >	TSeqIdToAnnotMap
typedef TAnnotToSeqIdMap::const_iterator	TAnnotToSeqIdMapCIter
typedef TAnnotToSeqIdMap::iterator	TAnnotToSeqIdMapIter
typedef TContextList::iterator	TContextListIter
typedef TPosCont::iterator	TPosContIter
typedef TSeqIdToAnnotMap::const_iterator	TSeqIdToAnnotMapCIter
typedef TSeqIdToAnnotMap::iterator	TSeqIdToAnnotMapIter
typedef TSeqRefCont::iterator	TSeqRefContIter
typedef struct SContext_tag	SContext

Functions
	USING_SCOPE (ncbi)
	USING_SCOPE (objects)
static void	s_DeleteContext (TContextPtr context)
static TSeqAnnotChoiceMaskFlags	s_GetSeqAnnotChoiceMask (const CSeq_annot *annot)
static TSeqIdChoiceMaskFlags	s_GetSeqIdChoiceMask (const CSeq_id *seqid)
static bool	s_RemoveAnnot (TAnnotToSeqIdMapIter annot_in_map_iter)
static bool	s_SpliceAnnot (unique_ptr< CObjectIStream > &sai, COStreamContainer &osc, TAnnotToSeqIdMapIter annot_in_map)
static void	s_SpliceAnnotsForSeqId (unique_ptr< CObjectIStream > &sai, COStreamContainer &osc, TSeqIdToAnnotMapIter seqid_iter)
void	AddSeqIdToCurrentContext (TSeqRef id)
void	ContextEnd (void)
void	ContextStart (CObjectIStream &in, EContextType type)
void	ContextEnter (void)
void	ContextLeave (void)
void	ContextInit (void)
void	CurrentContextContainsSeqAnnots (void)
ESerialDataFormat	GetFormat (const string &name)
bool	IsSeqAnnotChoiceSelected (TSeqAnnotChoiceMaskFlags flags)
bool	IsSeqAnnotChoiceSelected (const CSeq_annot *annot)
bool	IsSeqIdChoiceSelected (TSeqIdChoiceMaskFlags flags)
bool	IsSeqIdChoiceSelected (const CSeq_id *seqid)
void	ProcessSeqEntryAnnot (unique_ptr< CObjectIStream > &sai, COStreamContainer &osc)
void	ResetSeqEntryProcessing (void)
void	SeqAnnotMapSeqId (TSeqRef seqid_in_annot)
void	SeqAnnotSet_Pre (CObjectIStream &in)
void	SetSeqAnnotChoiceMask (const string &mask)
void	SetSeqAnnotChoiceMask (const TSeqAnnotChoiceMaskFlags mask)
void	SetSeqIdChoiceMask (const string &mask)
void	SetSeqIdChoiceMask (const TSeqIdChoiceMaskFlags mask)

Variables
static TAnnotToSeqIdMap	s_AnnotToSeqIdMap
static TSeqIdToAnnotMap	s_SeqIdToAnnotMap
static TContextPtr	s_CurrentContextPtr = NULL
static TContextPtr	s_RootContextPtr = NULL
static TContextList	s_ContextSequence
static TContextListIter	s_ContextSequenceIter
static TContextPtrStack	s_ContextPtrStack
static TSeqAnnotChoiceMaskFlags	s_SeqAnnotChoiceMask = fSAMF_Default
static TSeqIdChoiceMaskFlags	s_SeqIdChoiceMask = fSIMF_Default
static CNcbiStreampos	s_AnnotPos

Macro Definition Documentation

ADDFLAG [1/2]

#define ADDFLAG

(

flag

)

if ((found_flag = find(fbegin,fend,#flag)) != fend) flags |= fSAMF_##flag;

ADDFLAG [2/2]

#define ADDFLAG

(

flag

)

if ((found_flag = find(fbegin,fend,#flag)) != fend) flags |= fSIMF_##flag;

Typedef Documentation

SContext

typedef struct SContext_tag SContext

TAnnotToSeqIdMap

typedef map<CNcbiStreampos,TSeqRefContRef> TAnnotToSeqIdMap

Definition at line 73 of file seqannot_splicer_util.cpp.

TAnnotToSeqIdMapCIter

typedef TAnnotToSeqIdMap::const_iterator TAnnotToSeqIdMapCIter

Definition at line 76 of file seqannot_splicer_util.cpp.

TAnnotToSeqIdMapIter

typedef TAnnotToSeqIdMap::iterator TAnnotToSeqIdMapIter

Definition at line 77 of file seqannot_splicer_util.cpp.

TContextList

typedef list<TContextPtr> TContextList

Definition at line 70 of file seqannot_splicer_util.cpp.

TContextListIter

typedef TContextList::iterator TContextListIter

Definition at line 78 of file seqannot_splicer_util.cpp.

TContextPtr

typedef struct SContext_tag* TContextPtr

Definition at line 69 of file seqannot_splicer_util.cpp.

TContextPtrStack

typedef stack<TContextPtr> TContextPtrStack

Definition at line 71 of file seqannot_splicer_util.cpp.

TContextSeqIds

typedef set<TSeqRef,PPtrLess<TSeqRef> > TContextSeqIds

Definition at line 68 of file seqannot_splicer_util.cpp.

TPosCont

typedef list<CNcbiStreampos> TPosCont

Definition at line 60 of file seqannot_splicer_util.cpp.

TPosContIter

typedef TPosCont::iterator TPosContIter

Definition at line 79 of file seqannot_splicer_util.cpp.

TPosContOb

typedef CObjectFor<TPosCont> TPosContOb

Definition at line 63 of file seqannot_splicer_util.cpp.

TPosContRef

typedef CRef<TPosContOb> TPosContRef

Definition at line 66 of file seqannot_splicer_util.cpp.

TSeqIdToAnnotMap

typedef map<TSeqRef,TPosContRef,PPtrLess<TSeqRef> > TSeqIdToAnnotMap

Definition at line 74 of file seqannot_splicer_util.cpp.

TSeqIdToAnnotMapCIter

typedef TSeqIdToAnnotMap::const_iterator TSeqIdToAnnotMapCIter

Definition at line 80 of file seqannot_splicer_util.cpp.

TSeqIdToAnnotMapIter

typedef TSeqIdToAnnotMap::iterator TSeqIdToAnnotMapIter

Definition at line 81 of file seqannot_splicer_util.cpp.

TSeqRefCont

typedef list<TSeqRef> TSeqRefCont

Definition at line 59 of file seqannot_splicer_util.cpp.

TSeqRefContIter

typedef TSeqRefCont::iterator TSeqRefContIter

Definition at line 82 of file seqannot_splicer_util.cpp.

TSeqRefContOb

typedef CObjectFor<TSeqRefCont> TSeqRefContOb

Definition at line 62 of file seqannot_splicer_util.cpp.

TSeqRefContRef

typedef CRef<TSeqRefContOb> TSeqRefContRef

Definition at line 65 of file seqannot_splicer_util.cpp.

Function Documentation

AddSeqIdToCurrentContext()

void AddSeqIdToCurrentContext

(

TSeqRef

id

)

Definition at line 140 of file seqannot_splicer_util.cpp.

References set< Key, Compare >::insert(), IsSeqIdChoiceSelected(), s_CurrentContextPtr, and SContext_tag::seqids.

Referenced by CHookSeq_entry__Skip__Seq_id::SkipObject().

ContextEnd()

void ContextEnd

(

void

)

Definition at line 151 of file seqannot_splicer_util.cpp.

References NULL, s_ContextPtrStack, and s_CurrentContextPtr.

Referenced by CHookSeq_entry__Skip::SkipObject().

ContextEnter()

void ContextEnter

(

void

)

Definition at line 194 of file seqannot_splicer_util.cpp.

References s_ContextSequence, s_ContextSequenceIter, and s_CurrentContextPtr.

Referenced by CHookSeq_entry__Copy::CopyObject().

ContextInit()

void ContextInit

(

void

)

Definition at line 215 of file seqannot_splicer_util.cpp.

References NULL, s_ContextSequence, s_ContextSequenceIter, and s_CurrentContextPtr.

Referenced by s_PreprocessSeqEntry().

ContextLeave()

void ContextLeave

(

void

)

Definition at line 208 of file seqannot_splicer_util.cpp.

Referenced by CHookSeq_entry__Copy::CopyObject().

ContextStart()

void ContextStart	(	CObjectIStream &	in,
		EContextType	type
	)

Definition at line 163 of file seqannot_splicer_util.cpp.

References context, NULL, s_ContextPtrStack, s_ContextSequence, s_CurrentContextPtr, s_RootContextPtr, SContext_tag::sub_contexts, and type.

Referenced by CHookSeq_entry__Skip::SkipObject().

CurrentContextContainsSeqAnnots()

void CurrentContextContainsSeqAnnots

(

void

)

Definition at line 224 of file seqannot_splicer_util.cpp.

References SContext_tag::has_annots, and s_CurrentContextPtr.

Referenced by CHookSeq_entry__Skip__Seq_annot::SkipObject().

GetFormat()

ESerialDataFormat GetFormat

(

const string &

name

)

Definition at line 231 of file seqannot_splicer_util.cpp.

References eSerial_AsnBinary, eSerial_AsnText, eSerial_Json, eSerial_Xml, eUnknown, and NCBI_THROW.

Referenced by CSeqAnnotSplicerApp::Run(), CRPCClient< TRequest, TReply >::x_ConnectURL(), and CRPCClient< TRequest, TReply >::x_FillConnNetInfo().

IsSeqAnnotChoiceSelected() [1/2]

bool IsSeqAnnotChoiceSelected

(

const CSeq_annot *

annot

)

Definition at line 255 of file seqannot_splicer_util.cpp.

References s_GetSeqAnnotChoiceMask(), and s_SeqAnnotChoiceMask.

IsSeqAnnotChoiceSelected() [2/2]

bool IsSeqAnnotChoiceSelected

(

TSeqAnnotChoiceMaskFlags

flags

)

Definition at line 251 of file seqannot_splicer_util.cpp.

References flags, and s_SeqAnnotChoiceMask.

Referenced by CSeqAnnotSplicerApp::Run().

IsSeqIdChoiceSelected() [1/2]

bool IsSeqIdChoiceSelected

(

const CSeq_id *

seqid

)

Definition at line 267 of file seqannot_splicer_util.cpp.

References s_GetSeqIdChoiceMask(), and s_SeqIdChoiceMask.

IsSeqIdChoiceSelected() [2/2]

bool IsSeqIdChoiceSelected

(

TSeqIdChoiceMaskFlags

flags

)

Definition at line 263 of file seqannot_splicer_util.cpp.

References flags, and s_SeqIdChoiceMask.

Referenced by AddSeqIdToCurrentContext(), and SeqAnnotMapSeqId().

ProcessSeqEntryAnnot()

void ProcessSeqEntryAnnot	(	unique_ptr< CObjectIStream > &	sai,
		COStreamContainer &	osc
	)

Definition at line 276 of file seqannot_splicer_util.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), g_Stats, s_CurrentContextPtr, s_SeqIdToAnnotMap, s_SpliceAnnotsForSeqId(), CSeqAnnotSplicerStats::SeqEntry_Changed(), and SContext_tag::seqids.

Referenced by CHookSeq_entry__Copy__Seq_annot::CopyClassMember().

ResetSeqEntryProcessing()

void ResetSeqEntryProcessing

(

void

)

Definition at line 307 of file seqannot_splicer_util.cpp.

References _ASSERT, NULL, s_ContextPtrStack, s_ContextSequence, s_CurrentContextPtr, s_DeleteContext(), and s_RootContextPtr.

Referenced by CSeqAnnotSplicerApp::Run().

s_DeleteContext()

static void s_DeleteContext ( TContextPtr  context )

static

Definition at line 506 of file seqannot_splicer_util.cpp.

References context.

Referenced by ResetSeqEntryProcessing().

s_GetSeqAnnotChoiceMask()

static TSeqAnnotChoiceMaskFlags s_GetSeqAnnotChoiceMask ( const CSeq_annot *  annot )

static

Definition at line 550 of file seqannot_splicer_util.cpp.

References CSeq_annot_Base::CanGetData(), CSeq_annot_Base::C_Data::e_Align, CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, CSeq_annot_Base::C_Data::e_Ids, CSeq_annot_Base::C_Data::e_Locs, CSeq_annot_Base::C_Data::e_not_set, CSeq_annot_Base::C_Data::e_Seq_table, eUnknown, fSAMF_Align, fSAMF_Ftable, fSAMF_Graph, fSAMF_Ids, fSAMF_Locs, fSAMF_NotSet, fSAMF_Seq_table, CSeq_annot_Base::GetData(), CSeq_annot_Base::IsSetData(), NCBI_THROW, and CSeq_annot_Base::C_Data::Which().

Referenced by IsSeqAnnotChoiceSelected().

s_GetSeqIdChoiceMask()

static TSeqIdChoiceMaskFlags s_GetSeqIdChoiceMask ( const CSeq_id *  seqid )

static

Definition at line 571 of file seqannot_splicer_util.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, eUnknown, fSIMF_Ddbj, fSIMF_Embl, fSIMF_Genbank, fSIMF_General, fSIMF_Gi, fSIMF_Gibbmt, fSIMF_Gibbsq, fSIMF_Giim, fSIMF_Gpipe, fSIMF_Local, fSIMF_Named_annot_track, fSIMF_NotSet, fSIMF_Other, fSIMF_Patent, fSIMF_Pdb, fSIMF_Pir, fSIMF_Prf, fSIMF_Swissprot, fSIMF_Tpd, fSIMF_Tpe, fSIMF_Tpg, NCBI_THROW, and CSeq_id_Base::Which().

Referenced by IsSeqIdChoiceSelected().

s_RemoveAnnot()

static bool s_RemoveAnnot ( TAnnotToSeqIdMapIter  annot_in_map_iter )

static

Definition at line 603 of file seqannot_splicer_util.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), s_AnnotToSeqIdMap, and s_SeqIdToAnnotMap.

Referenced by s_SpliceAnnot().

s_SpliceAnnot()

static bool s_SpliceAnnot ( unique_ptr< CObjectIStream > &  sai, COStreamContainer &  osc, TAnnotToSeqIdMapIter  annot_in_map  )

static

Definition at line 649 of file seqannot_splicer_util.cpp.

References CObjectIStream::eNoFileHeader, g_Stats, s_RemoveAnnot(), and CSeqAnnotSplicerStats::SeqAnnot_Spliced().

Referenced by s_SpliceAnnotsForSeqId().

s_SpliceAnnotsForSeqId()

static void s_SpliceAnnotsForSeqId ( unique_ptr< CObjectIStream > &  sai, COStreamContainer &  osc, TSeqIdToAnnotMapIter  seqid_iter  )

static

Definition at line 674 of file seqannot_splicer_util.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), s_AnnotToSeqIdMap, and s_SpliceAnnot().

Referenced by ProcessSeqEntryAnnot().

SeqAnnotMapSeqId()

void SeqAnnotMapSeqId

(

TSeqRef

seqid_in_annot

)

Definition at line 322 of file seqannot_splicer_util.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), map_checker< Container >::insert(), IsSeqIdChoiceSelected(), s_AnnotPos, s_AnnotToSeqIdMap, and s_SeqIdToAnnotMap.

Referenced by CHookSeq_annot__Seq_id::SkipObject().

SeqAnnotSet_Pre()

void SeqAnnotSet_Pre

(

CObjectIStream &

in

)

Definition at line 398 of file seqannot_splicer_util.cpp.

References in(), and s_AnnotPos.

Referenced by CHookSeq_annot__Seq_annot::SkipObject().

SetSeqAnnotChoiceMask() [1/2]

void SetSeqAnnotChoiceMask

(

const string &

mask

)

Definition at line 410 of file seqannot_splicer_util.cpp.

References ADDFLAG, flags, fSAMF_All, fSAMF_Default, fSAMF_NotSet, NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, mask, and NStr::Split().

Referenced by CSeqAnnotSplicerApp::Run().

SetSeqAnnotChoiceMask() [2/2]

void SetSeqAnnotChoiceMask

(

const TSeqAnnotChoiceMaskFlags

mask

)

Definition at line 441 of file seqannot_splicer_util.cpp.

References mask, and s_SeqAnnotChoiceMask.

SetSeqIdChoiceMask() [1/2]

void SetSeqIdChoiceMask

(

const string &

mask

)

Definition at line 448 of file seqannot_splicer_util.cpp.

References ADDFLAG, flags, fSIMF_All, fSIMF_AllButLocal, fSIMF_Default, fSIMF_NotSet, NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, mask, and NStr::Split().

Referenced by CSeqAnnotSplicerApp::Run().

SetSeqIdChoiceMask() [2/2]

void SetSeqIdChoiceMask

(

const TSeqIdChoiceMaskFlags

mask

)

Definition at line 496 of file seqannot_splicer_util.cpp.

References mask, and s_SeqIdChoiceMask.

USING_SCOPE() [1/2]

USING_SCOPE

(

ncbi

)

USING_SCOPE() [2/2]

USING_SCOPE

(

objects

)

Variable Documentation

s_AnnotPos

CNcbiStreampos s_AnnotPos

static

Definition at line 132 of file seqannot_splicer_util.cpp.

Referenced by SeqAnnotMapSeqId(), and SeqAnnotSet_Pre().

s_AnnotToSeqIdMap

TAnnotToSeqIdMap s_AnnotToSeqIdMap

static

Definition at line 120 of file seqannot_splicer_util.cpp.

Referenced by s_RemoveAnnot(), s_SpliceAnnotsForSeqId(), and SeqAnnotMapSeqId().

s_ContextPtrStack

TContextPtrStack s_ContextPtrStack

static

Definition at line 127 of file seqannot_splicer_util.cpp.

Referenced by ContextEnd(), ContextStart(), and ResetSeqEntryProcessing().

s_ContextSequence

TContextList s_ContextSequence

static

Definition at line 125 of file seqannot_splicer_util.cpp.

Referenced by ContextEnter(), ContextInit(), ContextStart(), and ResetSeqEntryProcessing().

s_ContextSequenceIter

TContextListIter s_ContextSequenceIter

static

Definition at line 126 of file seqannot_splicer_util.cpp.

Referenced by ContextEnter(), and ContextInit().

s_CurrentContextPtr

TContextPtr s_CurrentContextPtr = NULL

static

Definition at line 123 of file seqannot_splicer_util.cpp.

Referenced by AddSeqIdToCurrentContext(), ContextEnd(), ContextEnter(), ContextInit(), ContextStart(), CurrentContextContainsSeqAnnots(), ProcessSeqEntryAnnot(), and ResetSeqEntryProcessing().

s_RootContextPtr

TContextPtr s_RootContextPtr = NULL

static

Definition at line 124 of file seqannot_splicer_util.cpp.

Referenced by ContextStart(), and ResetSeqEntryProcessing().

s_SeqAnnotChoiceMask

TSeqAnnotChoiceMaskFlags s_SeqAnnotChoiceMask = fSAMF_Default

static

Definition at line 129 of file seqannot_splicer_util.cpp.

Referenced by IsSeqAnnotChoiceSelected(), and SetSeqAnnotChoiceMask().

s_SeqIdChoiceMask

TSeqIdChoiceMaskFlags s_SeqIdChoiceMask = fSIMF_Default

static

Definition at line 130 of file seqannot_splicer_util.cpp.

Referenced by IsSeqIdChoiceSelected(), and SetSeqIdChoiceMask().

s_SeqIdToAnnotMap

TSeqIdToAnnotMap s_SeqIdToAnnotMap

static

Definition at line 121 of file seqannot_splicer_util.cpp.

Referenced by ProcessSeqEntryAnnot(), s_RemoveAnnot(), and SeqAnnotMapSeqId().