NCBI C++ ToolKit
Functions | Variables
cn3d_tools.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbireg.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include "remove_header_conflicts.hpp"
#include <wx/wx.h>
#include <wx/file.h>
#include <wx/fileconf.h>
#include "cn3d_tools.hpp"
#include "asn_reader.hpp"
#include <memory>
+ Include dependency graph for cn3d_tools.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Functions

 USING_SCOPE (objects)
 
static void SetRegistryDefaults (void)
 
void LoadRegistry (void)
 
void SaveRegistry (void)
 
bool RegistryIsValidInteger (const string &section, const string &name)
 
bool RegistryIsValidDouble (const string &section, const string &name)
 
bool RegistryIsValidBoolean (const string &section, const string &name)
 
bool RegistryIsValidString (const string &section, const string &name)
 
bool RegistryGetInteger (const string &section, const string &name, int *value)
 
bool RegistryGetDouble (const string &section, const string &name, double *value)
 
bool RegistryGetBoolean (const string &section, const string &name, bool *value)
 
bool RegistryGetString (const string &section, const string &name, string *value)
 
bool RegistrySetInteger (const string &section, const string &name, int value)
 
bool RegistrySetDouble (const string &section, const string &name, double value)
 
bool RegistrySetBoolean (const string &section, const string &name, bool value, bool useYesOrNo)
 
bool RegistrySetString (const string &section, const string &name, const string &value)
 
const stringGetWorkingDir (void)
 
const stringGetProgramDir (void)
 
const stringGetDataDir (void)
 
const stringGetPrefsDir (void)
 
void SetUpWorkingDirectories (const char *argv0)
 
void LaunchWebPage (const char *url)
 
CRef< CBioseqFetchSequenceViaHTTP (const string &id)
 
static const string NCBIStdaaResidues ("-ABCDEFGHIKLMNPQRSTVWXYZU*OJ")
 
unsigned char LookupNCBIStdaaNumberFromCharacter (char r)
 
char LookupCharacterFromNCBIStdaaNumber (unsigned char n)
 
bool Prosite2Regex (const string &prosite, string *regex, int *nGroups)
 
unsigned int PrositePatternLength (const string &prosite)
 

Variables

 USING_NCBI_SCOPE
 
static CMemoryRegistry registry
 
static string registryFile
 
static bool registryChanged = false
 
static string workingDir
 
static string programDir
 
static string dataDir
 
static string prefsDir
 

Function Documentation

◆ FetchSequenceViaHTTP()

CRef< CBioseq > FetchSequenceViaHTTP ( const string id)

◆ GetDataDir()

const string& GetDataDir ( void  )

◆ GetPrefsDir()

const string& GetPrefsDir ( void  )

Definition at line 331 of file cn3d_tools.cpp.

References prefsDir.

Referenced by GetFavoritesFile(), LoadRegistry(), StructureWindow::OnHelp(), and SetRegistryDefaults().

◆ GetProgramDir()

const string& GetProgramDir ( void  )

Definition at line 329 of file cn3d_tools.cpp.

References programDir.

Referenced by LoadRegistry(), StructureWindow::OnHelp(), and SetRegistryDefaults().

◆ GetWorkingDir()

const string& GetWorkingDir ( void  )

Definition at line 328 of file cn3d_tools.cpp.

References workingDir.

Referenced by LoadDataOnly(), and StructureWindow::OnSave().

◆ LaunchWebPage()

void LaunchWebPage ( const char *  url)

◆ LoadRegistry()

void LoadRegistry ( void  )

◆ LookupCharacterFromNCBIStdaaNumber()

char LookupCharacterFromNCBIStdaaNumber ( unsigned char  n)

◆ LookupNCBIStdaaNumberFromCharacter()

unsigned char LookupNCBIStdaaNumberFromCharacter ( char  r)

◆ NCBIStdaaResidues()

static const string NCBIStdaaResidues ( "-ABCDEFGHIKLMNPQRSTVWXYZU*OJ"  )
static

◆ Prosite2Regex()

bool Prosite2Regex ( const string prosite,
string regex,
int nGroups 
)

Definition at line 519 of file cn3d_tools.cpp.

References ERRORMSG, i, isalpha(), and toupper().

◆ PrositePatternLength()

unsigned int PrositePatternLength ( const string prosite)

◆ RegistryGetBoolean()

bool RegistryGetBoolean ( const string section,
const string name,
bool value 
)

◆ RegistryGetDouble()

bool RegistryGetDouble ( const string section,
const string name,
double *  value 
)

◆ RegistryGetInteger()

bool RegistryGetInteger ( const string section,
const string name,
int value 
)

◆ RegistryGetString()

bool RegistryGetString ( const string section,
const string name,
string value 
)

◆ RegistryIsValidBoolean()

bool RegistryIsValidBoolean ( const string section,
const string name 
)

Definition at line 214 of file cn3d_tools.cpp.

References IRegistry::Get(), registry, and toupper().

◆ RegistryIsValidDouble()

bool RegistryIsValidDouble ( const string section,
const string name 
)

Definition at line 207 of file cn3d_tools.cpp.

References IRegistry::Get(), registry, and rapidjson::value.

◆ RegistryIsValidInteger()

bool RegistryIsValidInteger ( const string section,
const string name 
)

Definition at line 200 of file cn3d_tools.cpp.

References IRegistry::Get(), registry, and rapidjson::value.

◆ RegistryIsValidString()

bool RegistryIsValidString ( const string section,
const string name 
)

Definition at line 222 of file cn3d_tools.cpp.

References IRegistry::Get(), and registry.

◆ RegistrySetBoolean()

bool RegistrySetBoolean ( const string section,
const string name,
bool  value,
bool  useYesOrNo 
)

◆ RegistrySetDouble()

bool RegistrySetDouble ( const string section,
const string name,
double  value 
)

◆ RegistrySetInteger()

bool RegistrySetInteger ( const string section,
const string name,
int  value 
)

◆ RegistrySetString()

bool RegistrySetString ( const string section,
const string name,
const string value 
)

◆ SaveRegistry()

void SaveRegistry ( void  )

Definition at line 189 of file cn3d_tools.cpp.

References out(), registry, registryChanged, registryFile, and IRegistry::Write().

Referenced by Cn3DApp::OnExit().

◆ SetRegistryDefaults()

static void SetRegistryDefaults ( void  )
static

◆ SetUpWorkingDirectories()

void SetUpWorkingDirectories ( const char *  argv0)

Definition at line 333 of file cn3d_tools.cpp.

References dataDir, NULL, prefsDir, programDir, TRACEMSG, WARNINGMSG, workingDir, and WX_TO_STD.

Referenced by Cn3DApp::OnInit(), and Cn3DNoWin::Run().

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ dataDir

string dataDir
static

Definition at line 326 of file cn3d_tools.cpp.

Referenced by GetDataDir(), and SetUpWorkingDirectories().

◆ prefsDir

string prefsDir
static

Definition at line 327 of file cn3d_tools.cpp.

Referenced by GetPrefsDir(), and SetUpWorkingDirectories().

◆ programDir

string programDir
static

Definition at line 325 of file cn3d_tools.cpp.

Referenced by GetProgramDir(), and SetUpWorkingDirectories().

◆ registry

CMemoryRegistry registry
static

Definition at line 81 of file cn3d_tools.cpp.

Referenced by CSynRegistry::Add(), BOOST_AUTO_TEST_CASE(), NWinHook::CApiHookMgr::CApiHookMgr(), CBlastDBExtractor::CBlastDBExtractor(), CBlastFormat::CBlastFormat(), CDBConnectionFactory::CDBConnectionFactory(), CDBLB_ServiceMapper::CDBLB_ServiceMapper(), CDBUDPriorityMapper::CDBUDPriorityMapper(), CDBUDRandomMapper::CDBUDRandomMapper(), CDBUniversalMapper::CDBUniversalMapper(), CFastaBioseqSource::CFastaBioseqSource(), CDBLB_ServiceMapper::Configure(), CDBConnectionFactory::Configure(), CDBServiceMapperCoR::Configure(), CDBUDRandomMapper::Configure(), CDBUDPriorityMapper::Configure(), CDBUniversalMapper::Configure(), CDBLB_ServiceMapper::ConfigureFromRegistry(), CDBConnectionFactory::ConfigureFromRegistry(), CDBServiceMapperCoR::ConfigureFromRegistry(), CDBUDRandomMapper::ConfigureFromRegistry(), CDBUDPriorityMapper::ConfigureFromRegistry(), CDBUniversalMapper::ConfigureFromRegistry(), CPluginManager< TClass >::CPluginManager(), CPSGS_CDDProcessor::CPSGS_CDDProcessor(), SNetServiceImpl::Create(), CSynRegistryBuilder::CSynRegistryBuilder(), CSeqFormatter::DumpAll(), CIgBlastArgs::ExtractAlgorithmOptions(), CDBLB_ServiceMapper::Factory(), CDBUDRandomMapper::Factory(), CDBUDPriorityMapper::Factory(), FindBlastDbPath(), CSeqDBAtlas::GenerateSearchPath(), CSynRegistry::CInclude::Get(), CFeatGlyph::GetCustomColor(), CVcfGlyph::GetCustomColor(), GetDllsList(), GetHostedLibs(), CVcfTrackFactory::GetMatchedAnnots(), GetOpt(), SPubseqGatewaySettings::GetProcessorMaxConcurrency(), CSequenceTrackFactory::GetSettings(), CSixFramesTransTrackFactory::GetSettings(), CAlignmentTrackFactory::GetSettings(), CAggregateFeatureTrack::GetSubtypeListAsString(), SNetCacheAPIImpl::Init(), SNetICacheClientImpl::Init(), SNetServerPoolImpl::Init(), SThrottleParams::SIOFailureThreshold::Init(), SThrottleParams::Init(), SNetScheduleAPIImpl::Init(), SNetServiceImpl::Init(), SNetScheduleAPIImpl::InitAffinities(), CUIDataSourceService::InitService(), CCassConnectionFactory::LoadConfig(), LoadConfigInfoByNames(), CFeaturePanel::LoadDefaultTracks(), CTempTrackProxy::LoadFromRegistry(), LoadRegistry(), CGeneModelConfig::LoadSettings(), CRulerPanel::LoadSettings(), CHistParamsManager::LoadSettings(), CGeneModelConfig::LoadSettingsPartial(), MakeCassConnection(), MakeCDBUniversalMapper(), CGenBankUIDataSource::Open(), CPubseqGatewayApp::OpenCass(), CPubseqGatewayApp::ParseArgs(), CGetStatisticsProcessor::Process(), CGetConfProcessor::Process(), CAckAlertProcessor::Process(), CCassConnectionFactory::ProcessParams(), SPubseqGatewaySettings::Read(), RegisterTooManyVariantsOfSameMaskingAlgorithm(), RegistryGetBoolean(), RegistryGetDouble(), RegistryGetInteger(), RegistryGetString(), RegistryIsValidBoolean(), RegistryIsValidDouble(), RegistryIsValidInteger(), RegistryIsValidString(), RegistrySetBoolean(), RegistrySetDouble(), RegistrySetInteger(), RegistrySetString(), CCassConnectionFactory::ReloadConfig(), s_CreateISynRegistry(), NDirectNetStorageImpl::s_GetFTConfig(), NDirectNetStorageImpl::s_GetICClient(), NDirectNetStorageImpl::s_GetRelocateChunk(), NDirectNetStorageImpl::s_GetSection(), s_LoadTempTrackRecursive(), SaveRegistry(), CGeneModelConfig::SaveSettings(), CHistParamsManager::SaveSettings(), CTempTrackProxy::SaveToRegistry(), CVcfFeatureDS::SetNonAsnDataRegistry(), CSeqGraphicPane::SetNonAsnInput(), CUIDataSourceService::ShutDownService(), CSatInfoSchema::x_AddSatInfoEntry(), CSnpTrack::x_AddSnpsLayout(), CMakeBlastDBApp::x_BuildDatabase(), CBlastUsageReport::x_CheckBlastUsageEnv(), CBinsGlyph::x_Draw(), CGeneMarkerGlyph::x_Draw(), CScatterPlotGlyph::x_Draw(), SPubseqGatewaySettings::x_GetDataSize(), CODBC_Connection::x_GetDriverName(), CAggregateFeatureTrack::x_GetSubkeyStringVec(), SDataLoaderConfig::x_Init(), CAlignmentTrack::x_LoadAlignmentSettings(), SDataLoaderConfig::x_LoadBlastDbDataLoaderConfig(), CPSGS_SNPProcessor::x_LoadConfig(), CPSGS_WGSProcessor::x_LoadConfig(), SDataLoaderConfig::x_LoadDataLoadersConfig(), CAlignmentTrack::x_LoadMatePairSettings(), CFeaturePanel::x_LoadSettings(), CFeatureTrack::x_LoadSettings(), CSnpTrack::x_LoadSettings(), CSegmentMapTrack::x_LoadSettings(), CSequenceTrack::x_LoadSettings(), CAlignmentTrack::x_LoadSettings(), CSixFramesTransTrack::x_LoadSettings(), SPubseqGatewaySettings::x_ReadAdminSection(), SPubseqGatewaySettings::x_ReadAutoExcludeSection(), SPubseqGatewaySettings::x_ReadCassandraProcessorSection(), SPubseqGatewaySettings::x_ReadCDDProcessorSection(), CNcbiTestApplication::x_ReadConfiguration(), SPubseqGatewaySettings::x_ReadCountersSection(), SPubseqGatewaySettings::x_ReadDebugSection(), SPubseqGatewaySettings::x_ReadHealthSection(), SPubseqGatewaySettings::x_ReadIPGSection(), SPubseqGatewaySettings::x_ReadLmdbCacheSection(), SPubseqGatewaySettings::x_ReadMyNCBISection(), SPubseqGatewaySettings::x_ReadServerSection(), SPubseqGatewaySettings::x_ReadSNPProcessorSection(), SPubseqGatewaySettings::x_ReadSSLSection(), SPubseqGatewaySettings::x_ReadStatisticsSection(), SPubseqGatewaySettings::x_ReadWGSProcessorSection(), CSatInfoSchema::x_ResolveConnectionByServiceName(), CAlignmentTrack::x_SaveAlignmentSettings(), CAlignmentTrack::x_SaveConfiguration(), CSegmentMapTrack::x_SaveConfiguration(), CSequenceTrack::x_SaveConfiguration(), CAlignmentTrack::x_SaveMatePairSettings(), CFeaturePanel::x_SaveSettings(), CODBCContext::x_SetRegistry(), CTLibContext::x_SetRegistry(), CSequenceSearchForm::x_UpdateFileList(), COrfSearchForm::x_UpdateKozak(), and CBlastDBCmdApp::x_UseLongSeqIds().

◆ registryChanged

bool registryChanged = false
static

◆ registryFile

string registryFile
static

Definition at line 82 of file cn3d_tools.cpp.

Referenced by LoadRegistry(), and SaveRegistry().

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 73 of file cn3d_tools.cpp.

◆ workingDir

string workingDir
static

Definition at line 324 of file cn3d_tools.cpp.

Referenced by GetWorkingDir(), and SetUpWorkingDirectories().

Modified on Thu May 30 12:23:38 2024 by modify_doxy.py rev. 669887