src/app/cn3d/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.

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)

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

CRef< CBioseq > FetchSequenceViaHTTP (  const string &  id  ) 
 

Definition at line 467 of file cn3d_tools.cpp.

References CRef< C, Locker >::Empty(), ERRORMSG, GetAsnDataViaHTTP(), CSeq_entry_Base::GetSet(), INFOMSG, CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CRef< C, Locker >::Reset(), CSeq_entry_Base::SetSeq(), and CSeq_entry_Base::SetSet().

Referenced by UpdateViewer::FetchSequencesViaHTTP().

const string& GetDataDir (  void   ) 
 

Definition at line 334 of file cn3d_tools.cpp.

References dataDir.

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

const string& GetPrefsDir (  void   ) 
 

Definition at line 335 of file cn3d_tools.cpp.

References prefsDir.

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

const string& GetProgramDir (  void   ) 
 

Definition at line 333 of file cn3d_tools.cpp.

References programDir.

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

const string& GetWorkingDir (  void   ) 
 

Definition at line 332 of file cn3d_tools.cpp.

References workingDir.

Referenced by LoadDataOnly().

void LaunchWebPage (  const char *  url  ) 
 

Definition at line 436 of file cn3d_tools.cpp.

References ERRORMSG, INFOMSG, pos, REG_ADVANCED_SECTION, RegistryGetString(), and TRACEMSG.

Referenced by CDDAnnotateDialog::ShowEvidence().

void LoadRegistry (  void   ) 
 

Definition at line 171 of file cn3d_tools.cpp.

References CNcbiRegistry::eOverride, CNcbiRegistry::ePersistent, GetPrefsDir(), GetProgramDir(), IRWRegistry::Read(), registry, registryChanged, registryFile, SetRegistryDefaults(), size, and TRACEMSG.

Referenced by Cn3DNoWin::Run().

char LookupCharacterFromNCBIStdaaNumber (  unsigned char  n  ) 
 

Definition at line 510 of file cn3d_tools.cpp.

References ERROR_MESSAGE, ERRORMSG, and NCBIStdaaResidues().

unsigned char LookupNCBIStdaaNumberFromCharacter (  char  r  ) 
 

Definition at line 493 of file cn3d_tools.cpp.

References NCBIStdaaResidues().

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

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

Definition at line 250 of file cn3d_tools.cpp.

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

Referenced by CDDRefDialog::CDDRefDialog(), OpenGLRenderer::Construct(), OpenGLRenderer::Display(), CDDAnnotateDialog::SetupGUIControls(), and StructureWindow::StructureWindow().

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

Definition at line 240 of file cn3d_tools.cpp.

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

Referenced by OpenGLRenderer::Display().

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

Definition at line 228 of file cn3d_tools.cpp.

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

Referenced by BLASTer::CalculateSelfHitScores(), OpenGLRenderer::Construct(), LoadDataOnly(), MultiTextDialog::MultiTextDialog(), and BlockMultipleAlignment::OptimizeBlock().

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

Definition at line 263 of file cn3d_tools.cpp.

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

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

bool RegistryIsValidBoolean (  const string &  section,
const string &  name
) 
 

Definition at line 214 of file cn3d_tools.cpp.

References IRegistry::Get(), and registry.

bool RegistryIsValidDouble (  const string &  section,
const string &  name
) 
 

Definition at line 207 of file cn3d_tools.cpp.

References IRegistry::Get(), and registry.

bool RegistryIsValidInteger (  const string &  section,
const string &  name
) 
 

Definition at line 200 of file cn3d_tools.cpp.

References IRegistry::Get(), and registry.

bool RegistryIsValidString (  const string &  section,
const string &  name
) 
 

Definition at line 222 of file cn3d_tools.cpp.

References IRegistry::Get(), and registry.

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

Definition at line 298 of file cn3d_tools.cpp.

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

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

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

Definition at line 286 of file cn3d_tools.cpp.

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

Referenced by SetRegistryDefaults().

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

Definition at line 274 of file cn3d_tools.cpp.

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

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

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

Definition at line 313 of file cn3d_tools.cpp.

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

Referenced by GetFavoritesFile(), LoadFavorites(), and SetRegistryDefaults().

void SaveRegistry (  void   ) 
 

Definition at line 189 of file cn3d_tools.cpp.

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

Referenced by Cn3DApp::OnExit().

static void SetRegistryDefaults (  void   )  [static]
 

Definition at line 83 of file cn3d_tools.cpp.

References endif, 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(), and size.

Referenced by LoadRegistry().

void SetUpWorkingDirectories (  const char *  argv0  ) 
 

Definition at line 337 of file cn3d_tools.cpp.

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

Referenced by Cn3DNoWin::Run().

USING_SCOPE (  objects   ) 
 

Variable Documentation

string dataDir [static]
 

Definition at line 328 of file cn3d_tools.cpp.

Referenced by GetDataDir(), and SetUpWorkingDirectories().

string prefsDir [static]
 

Definition at line 328 of file cn3d_tools.cpp.

Referenced by GetPrefsDir(), and SetUpWorkingDirectories().

string programDir [static]
 

Definition at line 328 of file cn3d_tools.cpp.

Referenced by GetProgramDir(), and SetUpWorkingDirectories().

CMemoryRegistry registry [static]
 

Definition at line 79 of file cn3d_tools.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), CDBConnectionFactory::CDBConnectionFactory(), CDBUDPriorityMapper::CDBUDPriorityMapper(), CDBUDRandomMapper::CDBUDRandomMapper(), CDBUniversalMapper::Configure(), CDBUDPriorityMapper::Configure(), CDBUDRandomMapper::Configure(), CDBServiceMapperCoR::Configure(), CDBConnectionFactory::Configure(), CDBUniversalMapper::ConfigureFromRegistry(), CDBUDPriorityMapper::ConfigureFromRegistry(), CDBUDRandomMapper::ConfigureFromRegistry(), CDBServiceMapperCoR::ConfigureFromRegistry(), CDBConnectionFactory::ConfigureFromRegistry(), CPluginManager< TClass >::CPluginManager(), CDBUDPriorityMapper::Factory(), CDBUDRandomMapper::Factory(), GetDllsList(), GetHostedLibs(), GetOpt(), CUIDataSourceService::InitService(), LoadConfigInfoByNames(), LoadRegistry(), CGeneModelConfig::LoadSettings(), CHistParamsManager::LoadSettings(), MakeCDBUniversalMapper(), CGenBankUIDataSource::Open(), RegisterTooManyVariantsOfSameMaskingAlgorithm(), RegistryGetBoolean(), RegistryGetDouble(), RegistryGetInteger(), RegistryGetString(), RegistryIsValidBoolean(), RegistryIsValidDouble(), RegistryIsValidInteger(), RegistryIsValidString(), RegistrySetBoolean(), RegistrySetDouble(), RegistrySetInteger(), RegistrySetString(), SaveRegistry(), CGeneModelConfig::SaveSettings(), CHistParamsManager::SaveSettings(), CUIDataSourceService::ShutDownService(), CNcbiTestApplication::x_CalcConfigValue(), CODBC_Connection::x_GetDriverName(), CAlignmentTrack::x_LoadAlignmentSettings(), CAlignmentTrack::x_LoadMatePairSettings(), CFeaturePanel::x_LoadSettings(), CFeaturePanel::x_LoadTempTrackRecursive(), CFeaturePanel::x_LoadTrackSettingsRecursive(), CNcbiTestApplication::x_ReadConfiguration(), CGBenchGUI::x_RegisterCommands(), CAlignmentTrack::x_SaveAlignmentSettings(), CSequenceTrack::x_SaveConfiguration(), CSegmentMapTrack::x_SaveConfiguration(), CAlignmentTrack::x_SaveConfiguration(), CAlignmentTrack::x_SaveMatePairSettings(), CFeaturePanel::x_SaveSettings(), CFeaturePanel::x_SaveTrackSettingsRecursive(), CODBCContext::x_SetRegistry(), CDBLibContext::x_SetRegistry(), CTLibContext::x_SetRegistry(), CGBenchApplication::x_TestGuiRegistry(), CSequenceSearchForm::x_UpdateFileList(), and COrfSearchForm::x_UpdateKozak().

bool registryChanged = false [static]
 

Definition at line 81 of file cn3d_tools.cpp.

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

string registryFile [static]
 

Definition at line 80 of file cn3d_tools.cpp.

Referenced by LoadRegistry(), and SaveRegistry().

USING_NCBI_SCOPE
 

Definition at line 71 of file cn3d_tools.cpp.

string workingDir [static]
 

Definition at line 328 of file cn3d_tools.cpp.

Referenced by GetWorkingDir(), and SetUpWorkingDirectories().

Generated on Wed Dec 9 07:42:33 2009 for NCBI C++ ToolKit by  doxygen 1.4.6
Modified on Wed Dec 09 08:18:32 2009 by modify_doxy.py rev. 173732