NCBI C++ ToolKit
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#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>
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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 | |
#define NCBI_USE_ERRCODE_X Objtools_CAV_Func |
Definition at line 59 of file cav_function.cpp.
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(), and NULL.
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 | ||
) |
Definition at line 280 of file cav_function.cpp.
References CAV_CONDENSED, CAV_DEBUG, CAV_ERROR_BAD_PARAMS, CAV_ERROR_DISPLAY, CAV_FASTA, CAV_FASTA_LOWERCASE, CAV_HTML, CAV_HTML_HEADER, CAV_IGNORE_BAD_ALN, CAV_LEFTTAILS, CAV_NO_CHANGE_DIAG, CAV_RIGHTTAILS, CAV_SHOW_IDENTITY, CAV_SUCCESS, CAV_TEXT, Critical(), defaultDiagPostLevel, eDiag_Error, eDiag_Info, ERR_POST_X, Error(), Info(), NcbiCerr, NcbiCout, SetDiagPostLevel(), SetDiagStream(), AlignmentDisplay::SHOW_IDENTITY, and VerifyAlignmentData().
Referenced by CAV_DisplayMultiple().
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 | ||
) |
Definition at line 385 of file cav_function.cpp.
References CAV_DisplayMultiple(), CAV_ERROR_BAD_ASN, CAV_SUCCESS, Critical(), ERR_POST_X, and LoadASNFromIstream().
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(), and NULL.
Referenced by CAVApp::Run().
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static |
Definition at line 67 of file cav_function.cpp.
References CAV_ERROR_BAD_ASN, CAV_SUCCESS, defaultDiagPostLevel, eDiag_Fatal, ERR_POST_X, Error(), NULL, ReadASNFromIstream(), CRef< C, Locker >::Reset(), and SetDiagPostLevel().
Referenced by CAV_DisplayMultiple().
USING_SCOPE | ( | objects | ) |
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static |
Definition at line 158 of file cav_function.cpp.
References AlignmentSet::alignments, ERR_POST_X, Error(), AlignmentDisplay::GetCharAt(), AlignmentDisplay::GetWidth(), i, int, IsAligned(), IsGap(), IsUnaligned(), MasterSlaveAlignment::master, MasterSlaveAlignment::masterToSlave, Sequence::sequenceString, MasterSlaveAlignment::slave, and toupper().
Referenced by CAV_DisplayMultiple().
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static |
Definition at line 65 of file cav_function.cpp.
Referenced by CAV_DisplayMultiple(), and LoadASNFromIstream().
USING_NCBI_SCOPE |
Definition at line 278 of file cav_function.cpp.