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.

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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 string &	GetWorkingDir (void)
const string &	GetProgramDir (void)
const string &	GetDataDir (void)
const string &	GetPrefsDir (void)
void	SetUpWorkingDirectories (const char *argv0)
void	LaunchWebPage (const char *url)
CRef< CBioseq >	FetchSequenceViaHTTP (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

)

Definition at line 463 of file cn3d_tools.cpp.

References CRef< C, Locker >::Empty(), GetAsnDataViaHTTPS(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), INFOMSG, CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), ok, CRef< C, Locker >::Reset(), round(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), string, and WARNINGMSG.

Referenced by CreateMimeFromBiostruc(), and UpdateViewer::FetchSequencesViaHTTP().

GetDataDir()

const string& GetDataDir

(

void

)

Definition at line 330 of file cn3d_tools.cpp.

References dataDir.

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

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

)

Definition at line 432 of file cn3d_tools.cpp.

References command, ERRORMSG, i, INFOMSG, l(), REG_ADVANCED_SECTION, RegistryGetString(), and TRACEMSG.

Referenced by IBISAnnotateDialog::LaunchIbisWebPage(), Sequence::LaunchWebBrowserWithInfo(), CDDRefDialog::OnButton(), CDDBookRefDialog::OnClick(), StructureWindow::OnHelp(), and CDDAnnotateDialog::ShowEvidence().

LoadRegistry()

void LoadRegistry

(

void

)

Definition at line 171 of file cn3d_tools.cpp.

References CNcbiRegistry::eOverride, CNcbiRegistry::ePersistent, GetPrefsDir(), GetProgramDir(), in(), IRWRegistry::Read(), registry, registryChanged, registryFile, SetRegistryDefaults(), ncbi::grid::netcache::search::fields::size, and TRACEMSG.

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

LookupCharacterFromNCBIStdaaNumber()

char LookupCharacterFromNCBIStdaaNumber

(

unsigned char

n

)

Definition at line 511 of file cn3d_tools.cpp.

References ERROR_MESSAGE, ERRORMSG, n, and NCBIStdaaResidues().

Referenced by PSSMWrapper::GetPSSMScore(), GetStandardProbability(), ScreenResidueCharacter(), and StringFromStdaa().

LookupNCBIStdaaNumberFromCharacter()

unsigned char LookupNCBIStdaaNumberFromCharacter

(

char

r

)

Definition at line 494 of file cn3d_tools.cpp.

References i, n, NCBIStdaaResidues(), r(), and toupper().

Referenced by ConservationColorer::CalculateFitConservationColors(), Threader::CreateSeqMtf(), CreateTruncatedSequence(), dpScoreFunction(), LookupNCBIStdaaNumberFromThreaderResidueNumber(), ScreenResidueCharacter(), and UpdateViewer::SortByPSSM().

NCBIStdaaResidues()

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

static

Referenced by LookupCharacterFromNCBIStdaaNumber(), and LookupNCBIStdaaNumberFromCharacter().

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

)

Definition at line 598 of file cn3d_tools.cpp.

References NStr::fConvErr_NoThrow, i, isalpha(), NStr::StringToInt(), and toupper().

Referenced by CDDAnnotateDialog::HighlightMotif(), and CDDAnnotateDialog::NewOrEditMotif().

RegistryGetBoolean()

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

Definition at line 250 of file cn3d_tools.cpp.

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

Referenced by CDDRefDialog::CDDRefDialog(), OpenGLRenderer::Construct(), OpenGLRenderer::Display(), GetStructureViaHTTPAndAddToCache(), LoadStructureViaCache(), Cn3DApp::OnInit(), CDDAnnotateDialog::SetupGUIControls(), IBISAnnotateDialog::SetupGUIControls(), CDDBookRefDialog::SetWidgetStates(), and StructureWindow::StructureWindow().

RegistryGetDouble()

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

Definition at line 240 of file cn3d_tools.cpp.

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

Referenced by OpenGLRenderer::Display(), and StructureWindow::OnAnimate().

RegistryGetInteger()

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

Definition at line 228 of file cn3d_tools.cpp.

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

Referenced by UpdateViewer::BlastNeighbor(), BLASTer::CalculateSelfHitScores(), OpenGLRenderer::Construct(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), GetStructureViaHTTPAndAddToCache(), LoadDataOnly(), MultiTextDialog::MultiTextDialog(), StructureWindow::OnAnimate(), and BlockMultipleAlignment::OptimizeBlock().

RegistryGetString()

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

Definition at line 263 of file cn3d_tools.cpp.

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

Referenced by OpenGLRenderer::Construct(), CreateCacheFolder(), GetCacheFilePath(), GetFavoritesFile(), LaunchWebPage(), LoadFavorites(), StructureWindow::OnSetFont(), Cn3DGLCanvas::SetGLFontFromRegistry(), ViewerWindowBase::SetupFontFromRegistry(), and TruncateCache().

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
	)

Definition at line 294 of file cn3d_tools.cpp.

References CNcbiRegistry::ePersistent, ERRORMSG, registry, registryChanged, IRWRegistry::Set(), and rapidjson::value.

Referenced by StructureWindow::OnShowWindow(), and SetRegistryDefaults().

RegistrySetDouble()

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

Definition at line 284 of file cn3d_tools.cpp.

References NStr::DoubleToString(), CNcbiRegistry::ePersistent, ERRORMSG, registry, registryChanged, IRWRegistry::Set(), and rapidjson::value.

Referenced by SetRegistryDefaults().

RegistrySetInteger()

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

Definition at line 274 of file cn3d_tools.cpp.

References CNcbiRegistry::ePersistent, ERRORMSG, NStr::IntToString(), registry, registryChanged, IRWRegistry::Set(), and rapidjson::value.

Referenced by SetRegistryDefaults(), and MultiTextDialog::~MultiTextDialog().

RegistrySetString()

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

Definition at line 309 of file cn3d_tools.cpp.

References CNcbiRegistry::ePersistent, ERRORMSG, registry, registryChanged, IRWRegistry::Set(), and rapidjson::value.

Referenced by GetFavoritesFile(), LoadFavorites(), StructureWindow::OnEditFavorite(), StructureWindow::OnSetFont(), and SetRegistryDefaults().

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

Definition at line 85 of file cn3d_tools.cpp.

References ERRORMSG, GetPrefsDir(), GetProgramDir(), IsWindowedMode(), NO_FAVORITES_FILE, REG_ADVANCED_SECTION, REG_ANIMATION_SECTION, REG_CACHE_ENABLED, REG_CACHE_FOLDER, REG_CACHE_MAX_SIZE, REG_CACHE_SECTION, REG_CDD_ANNOT_READONLY, REG_CONFIG_SECTION, REG_FAVORITES_NAME, REG_FONT_NATIVE_FONT_INFO, REG_FOOTPRINT_RES, REG_FRAME_DELAY, REG_HIGHLIGHTS_ON, REG_MAX_N_STRUCTS, REG_MT_DIALOG_POS_X, REG_MT_DIALOG_POS_Y, REG_MT_DIALOG_SIZE_H, REG_MT_DIALOG_SIZE_W, REG_OPENGL_FONT_SECTION, REG_PROJECTION_TYPE, REG_PROXIMAL_STEREO, REG_QUALITY_ATOM_SLICES, REG_QUALITY_ATOM_STACKS, REG_QUALITY_BOND_SIDES, REG_QUALITY_HELIX_SIDES, REG_QUALITY_SECTION, REG_QUALITY_WORM_SEGMENTS, REG_QUALITY_WORM_SIDES, REG_SEQUENCE_FONT_SECTION, REG_SHOW_LOG_ON_START, REG_SPIN_DELAY, REG_SPIN_INCREMENT, REG_STEREO_SEPARATION, RegistrySetBoolean(), RegistrySetDouble(), RegistrySetInteger(), RegistrySetString(), ncbi::grid::netcache::search::fields::size, and WX_TO_STD.

Referenced by LoadRegistry().

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_ReadLMDBProcessorSection(), 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

Definition at line 83 of file cn3d_tools.cpp.

Referenced by LoadRegistry(), RegistrySetBoolean(), RegistrySetDouble(), RegistrySetInteger(), RegistrySetString(), and SaveRegistry().

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().