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NCBI C++ ToolKit: src/serial/datatool/fileutil.cpp File Reference

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Definition at line 159 of file fileutil.cpp.

Definition at line 156 of file fileutil.cpp.

Definition at line 157 of file fileutil.cpp.

Definition at line 158 of file fileutil.cpp.

Definition at line 42 of file fileutil.cpp.

Definition at line 523 of file fileutil.cpp.

References IsOssEmpty().

Referenced by CGeneModel::AddExon(), CGeneModel::AddNormalExon(), CDiscrepancyContext::AddTest(), CAlignMap::CAlignMap(), CAlnStats< _TAlnIdVec >::CAlnStats(), CGeneModel::CdsInvariant(), CCDSInfo::Clip(), CChain::ClipChain(), CChain::ClipLowCoverageUTR(), CLocalRange< TOffset >::Contains(), ConvertStdsegToPairwiseAln(), CVDBBlastUtil::CreateBioseqFromOid(), CCDSInfo::Cut(), rapidjson::PrettyWriter< OutputStream, SourceEncoding, TargetEncoding, StackAllocator, writeFlags >::EndArray(), rapidjson::PrettyWriter< OutputStream, SourceEncoding, TargetEncoding, StackAllocator, writeFlags >::EndObject(), CClassCode::GenerateHPP(), AlignmentCollection::GetBioseqForRow(), CGeneModel::GetCdsDnaSequence(), CApplyQualTreeItemData::GetFunction(), CAddRNAFeatTreeItemData::GetFunction(), CAddCDSFeatTreeItemData::GetFunction(), CAddFeatureTreeItemData::GetFunction(), CApplyDOIToEntryTreeItemData::GetFunction(), CApplyDOILookupTreeItemData::GetFunction(), CCopyFeatQualTreeItemData::GetFunction(), CEditRNAQualTreeItemData::GetFunction(), CSetExceptionsTreeItemData::GetFunction(), CConvertGapsTreeItemData::GetFunction(), CParseQualTreeItemData::GetFunction(), CParseBsrcTreeItemData::GetFunction(), CParseToBsrcTreeItemData::GetFunction(), CParseToDBLinkTreeItemData::GetFunction(), CParseToCdsGeneProtTreeItemData::GetFunction(), CParseProteinQualTreeItemData::GetFunction(), CParseFeatQualTreeItemData::GetFunction(), CParseCdsGeneProtTreeItemdata::GetFunction(), CParseBsrcToStructCommTreeItemData::GetFunction(), CRmvRNAQualTreeItemData::GetFunction(), CRemoveDescrTreeItemData::GetFunction(), CRemoveDbXrefTreeItemData::GetFunction(), CRmvOutsideBsrcTreeItemData::GetFunction(), CSwapRNAQualTreeItemData::GetFunction(), CSwapFeatQualTreeItemData::GetFunction(), CAlignFormatUtil::GetGiForSeqIdList(), CApplyRNAQualTreeItemData::GetMacroDescription(), CAddRNAFeatTreeItemData::GetMacroDescription(), CConvertRNAQualTreeItemData::GetMacroDescription(), CCopyRNAQualTreeItemData::GetMacroDescription(), CEditRNAQualTreeItemData::GetMacroDescription(), CAutodefTreeItemData::GetMacroDescription(), CParseRNAQualTreeItemData::GetMacroDescription(), CRmvRNAQualTreeItemData::GetMacroDescription(), CRmvOutsideRNAQualTreeItemData::GetMacroDescription(), CSwapRNAQualTreeItemData::GetMacroDescription(), CBioseq::GetNonLocalId(), CVDBBlastUtil::GetOidsFromSeqIds_WGS(), CAddRNAFeatTreeItemData::GetVariables(), CAddCDSFeatTreeItemData::GetVariables(), CAddFeatureTreeItemData::GetVariables(), CGeneModel::GoodEnoughToBeAnnotation(), CChain::HarborsNested(), CClassCode::HaveInitializers(), CCDSInfo::Invariant(), CGeneModel::isNMD(), CGeneModel::MaxCdsLimits(), CPSGDataLoader_Impl::CGetRequests::ProcessResult(), CChain::RestoreReasonableConfirmedStart(), CChain::RestoreTrimmedEnds(), s_BestLocalRank(), s_BestNonLocalRank(), s_MaskQuerySeq(), SeqIdHasMatchInBioseq(), CClassTypeInfo::SetParentClass(), rapidjson::internal::Stack< StackAllocator >::ShrinkToFit(), CAlignModel::TargetAccession(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CFeatGlyph::x_Draw(), CGeneGroup::x_Draw(), CLinkedFeatsGroup::x_Draw(), CLayoutGroup::x_Draw(), CVcfGlyph::x_Draw(), CSGSegmentSmearJob::x_Execute(), CSeqDBAliasNode::x_ExpandAliases(), CMultiAligner::x_FindConservedColumns(), CEditMolinfoFieldsTreeItemData::x_GetDescrChangeFrom(), CEditMolinfoFieldsTreeItemData::x_GetDescrChangeTo(), CEditMolinfoFieldsTreeItemData::x_GetFunctionFor(), CParseQualTreeItemData::x_GetParsedTextDescription(), CBlastInputReader::x_ValidateMoleculeType(), CCSraShortReadIterator::x_ValidRead(), CGff3Writer::xWriteNucleotideFeature(), and CGff3Writer::xWriteProteinFeature().

Definition at line 233 of file fileutil.cpp.

References CDir::GetCwd(), CDirEntry::IsAbsolutePath(), CDirEntry::NormalizePath(), and Path().

Referenced by CCodeGenerator::GenerateCombiningFile(), CCodeGenerator::GenerateCvsignore(), CCodeGenerator::GenerateDoxygenGroupDescription(), CCodeGenerator::GenerateFileList(), CCodeGenerator::IsGitRepository(), CDelayedOfstream::open(), CFileModules::PrintDTDModular(), CFileModules::PrintSampleDEF(), CFileModules::PrintXMLSchemaModular(), CCodeGenerator::UndoGenerateCode(), and CFileCode::WriteSpecRefs().

Definition at line 243 of file fileutil.cpp.

References _TRACE, DIR_SEPARATOR_CHAR, file, and IsDirSeparator().

Referenced by Threader::CreateRcxPtl(), CDataType::FileName(), CCodeGenerator::GenerateClientCode(), CCodeGenerator::GenerateCode(), CCodeGenerator::GenerateCombiningFile(), CFileCode::GenerateCPP(), CCodeGenerator::GenerateCvsignore(), CCodeGenerator::GenerateDoxygenGroupDescription(), CCodeGenerator::GenerateFileList(), CFileCode::GenerateHPP(), CCodeGenerator::GenerateModuleCPP(), CCodeGenerator::GenerateModuleHPP(), CDataTypeModule::GetFileNamePrefix(), CFileModules::GetFileNamePrefix(), CCodeGenerator::IsGitRepository(), MakeAbsolutePath(), CTreeAlignMerger::Merge_AllAtOnce(), CTreeAlignMerger::Merge_Pairwise(), CFileModules::PrintSampleDEF(), CDataTool::ProcessModules(), CSearchHelper::ReadModFiles(), s_FindBestSubRange(), CMergeTree::Score(), CMergeTree::Search(), SourceFile::SourceFile(), CCodeGenerator::UndoGenerateCode(), CFileCode::WriteSpecRefs(), CFileCode::WriteUserFile(), and CTreeAlignMerger::x_Merge_Dist_Impl().

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