NCBI C++ ToolKit
Macros | Functions | Variables
cav_function.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistl.hpp>
#include <corelib/ncbistre.hpp>
#include <corelib/ncbi_limits.h>
#include <corelib/ncbidiag.hpp>
#include <list>
#include <memory>
#include <objects/cdd/Cdd.hpp>
#include <objects/ncbimime/Ncbi_mime_asn1.hpp>
#include <objects/ncbimime/Biostruc_seqs.hpp>
#include <objects/ncbimime/Biostruc_align.hpp>
#include <objects/ncbimime/Biostruc_align_seq.hpp>
#include <objects/ncbimime/Biostruc_seqs_aligns_cdd.hpp>
#include <objects/ncbimime/Bundle_seqs_aligns.hpp>
#include <objtools/cddalignview/cddalignview.h>
#include <objtools/cddalignview/cav_seqset.hpp>
#include <objtools/cddalignview/cav_alignset.hpp>
#include <objtools/cddalignview/cav_asnio.hpp>
#include <objtools/cddalignview/cav_alndisplay.hpp>
#include <objtools/error_codes.hpp>
+ Include dependency graph for cav_function.cpp:

Go to the source code of this file.

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Macros

#define NCBI_USE_ERRCODE_X   Objtools_CAV_Func
 

Functions

 USING_SCOPE (objects)
 
static int LoadASNFromIstream (CNcbiIstream &asnIstream, const SeqEntryList **sequences, const SeqAnnotList **alignments)
 
static bool VerifyAlignmentData (const AlignmentSet *alignmentSet, const AlignmentDisplay *display)
 
int CAV_DisplayMultiple (const SeqEntryList &sequences, const SeqAnnotList &alignments, unsigned int options, unsigned int paragraphWidth, double conservationThreshhold, const char *title, int nFeatures, const AlignmentFeature *alnFeatures, CNcbiOstream *outputStream, CNcbiOstream *diagnosticStream)
 
int CAV_DisplayMultiple (const void *asnDataBlock, int asnSize, unsigned int options, unsigned int paragraphWidth, double conservationThreshhold, const char *title, int nFeatures, const AlignmentFeature *alnFeatures, CNcbiOstream *outputStream, CNcbiOstream *diagnosticStream)
 
int CAV_DisplayMultiple (const void *asnDataBlock, int asnSize, unsigned int options, unsigned int paragraphWidth, double conservationThreshhold, const char *title, int nFeatures, const AlignmentFeature *features)
 
int CAV_DisplayMultiple (const ncbi::objects::CNcbi_mime_asn1 &mime, unsigned int options, unsigned int paragraphWidth, double conservationThreshhold, const char *title, int nFeatures, const AlignmentFeature *features, ncbi::CNcbiOstream *outputStream, ncbi::CNcbiOstream *diagnosticStream)
 

Variables

static EDiagSev defaultDiagPostLevel
 
 USING_NCBI_SCOPE
 

Macro Definition Documentation

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   Objtools_CAV_Func

Definition at line 59 of file cav_function.cpp.

Function Documentation

◆ CAV_DisplayMultiple() [1/4]

int CAV_DisplayMultiple ( const ncbi::objects::CNcbi_mime_asn1 &  mime,
unsigned int  options,
unsigned int  paragraphWidth,
double  conservationThreshhold,
const char *  title,
int  nFeatures,
const AlignmentFeature features,
ncbi::CNcbiOstream outputStream,
ncbi::CNcbiOstream diagnosticStream 
)

Definition at line 436 of file cav_function.cpp.

References CAV_DisplayMultiple(), CAV_ERROR_BAD_ASN, ERR_POST_X, Error(), features, and NULL.

◆ CAV_DisplayMultiple() [2/4]

int CAV_DisplayMultiple ( const SeqEntryList sequences,
const SeqAnnotList alignments,
unsigned int  options,
unsigned int  paragraphWidth,
double  conservationThreshhold,
const char *  title,
int  nFeatures,
const AlignmentFeature alnFeatures,
CNcbiOstream outputStream,
CNcbiOstream diagnosticStream 
)

◆ CAV_DisplayMultiple() [3/4]

int CAV_DisplayMultiple ( const void *  asnDataBlock,
int  asnSize,
unsigned int  options,
unsigned int  paragraphWidth,
double  conservationThreshhold,
const char *  title,
int  nFeatures,
const AlignmentFeature alnFeatures,
CNcbiOstream outputStream,
CNcbiOstream diagnosticStream 
)

◆ CAV_DisplayMultiple() [4/4]

int CAV_DisplayMultiple ( const void *  asnDataBlock,
int  asnSize,
unsigned int  options,
unsigned int  paragraphWidth,
double  conservationThreshhold,
const char *  title,
int  nFeatures,
const AlignmentFeature features 
)

Definition at line 422 of file cav_function.cpp.

References CAV_DisplayMultiple(), features, and NULL.

Referenced by CAVApp::Run().

◆ LoadASNFromIstream()

static int LoadASNFromIstream ( CNcbiIstream asnIstream,
const SeqEntryList **  sequences,
const SeqAnnotList **  alignments 
)
static

◆ USING_SCOPE()

USING_SCOPE ( objects  )

◆ VerifyAlignmentData()

static bool VerifyAlignmentData ( const AlignmentSet alignmentSet,
const AlignmentDisplay display 
)
static

Variable Documentation

◆ defaultDiagPostLevel

EDiagSev defaultDiagPostLevel
static

Definition at line 65 of file cav_function.cpp.

Referenced by CAV_DisplayMultiple(), and LoadASNFromIstream().

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 278 of file cav_function.cpp.

Modified on Thu Feb 29 12:19:31 2024 by modify_doxy.py rev. 669887