/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/blast/seqdb_reader/impl/ |
H A D | seqdbatlas.hpp | 179 : m_Atlas(atlas), in CSeqDBLockHold() 204 class CSeqDBAtlas & m_Atlas; member in CSeqDBLockHold 226 : m_Atlas(atlas), in CSeqDBMemReg() 246 class CSeqDBAtlas & m_Atlas; member in CSeqDBMemReg 276 CSeqDBAtlas & m_Atlas; member in CSeqDB_AtlasRegionHolder 661 static CSeqDBAtlas * m_Atlas; member in CSeqDBAtlasHolder 676 : m_Atlas(atlas), in CSeqDBFileMemMap() 685 : m_Atlas(atlas), in CSeqDBFileMemMap() 705 m_Atlas.Lock(locked); in Init() 712 m_Atlas.Unlock(locked); in Init() [all …]
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H A D | seqdbfile.hpp | 78 : m_Atlas(atlas) in CSeqDBRawFile() 98 bool success = m_Atlas.GetFileSizeL(name.GetPathS(), m_Length); in Open() 237 CSeqDBAtlas & m_Atlas; member in CSeqDBRawFile 372 CSeqDBAtlas & m_Atlas; member in CSeqDBExtFile
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H A D | seqdbcol.hpp | 202 CSeqDBAtlas & m_Atlas; member in CSeqDBColumn
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/blast/seqdb_reader/impl/ |
H A D | seqdbatlas.hpp | 179 : m_Atlas(atlas), in CSeqDBLockHold() 204 class CSeqDBAtlas & m_Atlas; member in CSeqDBLockHold 226 : m_Atlas(atlas), in CSeqDBMemReg() 246 class CSeqDBAtlas & m_Atlas; member in CSeqDBMemReg 276 CSeqDBAtlas & m_Atlas; member in CSeqDB_AtlasRegionHolder 661 static CSeqDBAtlas * m_Atlas; member in CSeqDBAtlasHolder 676 : m_Atlas(atlas), in CSeqDBFileMemMap() 685 : m_Atlas(atlas), in CSeqDBFileMemMap() 705 m_Atlas.Lock(locked); in Init() 712 m_Atlas.Unlock(locked); in Init() [all …]
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H A D | seqdbfile.hpp | 78 : m_Atlas(atlas) in CSeqDBRawFile() 98 bool success = m_Atlas.GetFileSizeL(name.GetPathS(), m_Length); in Open() 237 CSeqDBAtlas & m_Atlas; member in CSeqDBRawFile 372 CSeqDBAtlas & m_Atlas; member in CSeqDBExtFile
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H A D | seqdbcol.hpp | 202 CSeqDBAtlas & m_Atlas; member in CSeqDBColumn
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_reader/ |
H A D | seqdbimpl.cpp | 185 m_Atlas.Lock(locked); in SetIterationRange() 215 m_Atlas.Lock(locked); in ~CSeqDBImpl() 310 m_Atlas.Lock(locked); in GetNextOIDChunk() 451 m_Atlas.Lock(locked); in GetTaxIDs() 530 m_Atlas.Lock(locked); in GetLeafTaxIDs() 567 m_Atlas.Lock(locked); in GetLeafTaxIDs() 609 m_Atlas.Lock(locked); in GetBioseq() 742 m_Atlas.Lock(locked); in GetSeqData() 801 m_Atlas.Lock(locked); in GetSeqIDs() 896 m_Atlas.Lock(locked); in x_GetSeqGI() [all …]
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H A D | seqdbcol.cpp | 109 m_DataFile (m_Atlas), in CSeqDBColumn() 110 m_IndexLease (m_Atlas), in CSeqDBColumn() 111 m_DataLease (m_Atlas), in CSeqDBColumn() 117 CSeqDBLockHold locked2(m_Atlas); in CSeqDBColumn() 123 m_Atlas.Lock(*lockedp); in CSeqDBColumn() 141 m_Atlas.Unlock(*lockedp); in CSeqDBColumn() 149 CSeqDBLockHold locked(m_Atlas); in ~CSeqDBColumn() 150 m_Atlas.Lock(locked); in ~CSeqDBColumn() 210 m_Atlas.Lock(locked); in x_ReadFields() 275 m_Atlas.Lock(locked); in x_ReadMetaData() [all …]
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H A D | seqdbatlas.cpp | 296 m_Atlas = new CSeqDBAtlas(use_atlas_lock); in CSeqDBAtlasHolder() 311 m_Atlas = new CSeqDBAtlas(use_atlas_lock); in CSeqDBAtlasHolder() 327 delete m_Atlas; in ~CSeqDBAtlasHolder() 333 _ASSERT(m_Atlas); in Get() 334 return *m_Atlas; in Get() 341 m_Atlas.Unlock(*this); in ~CSeqDBLockHold() 346 CSeqDBAtlas * CSeqDBAtlasHolder::m_Atlas = NULL; member in CSeqDBAtlasHolder 351 : m_Atlas(atlas), m_Ptr(ptr) in CSeqDB_AtlasRegionHolder() 358 CSeqDBLockHold locked(m_Atlas); in ~CSeqDB_AtlasRegionHolder() 359 m_Atlas.Lock(locked); in ~CSeqDB_AtlasRegionHolder()
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H A D | seqdbgimask.cpp | 46 : m_Atlas (atlas), in CSeqDBGiMask() 51 m_IndexFile (m_Atlas), in CSeqDBGiMask() 52 m_OffsetFile (m_Atlas) in CSeqDBGiMask() 155 m_DataFile.push_back(new CSeqDBRawFile(m_Atlas)); in x_Open() 156 m_DataLease.push_back(new CSeqDBFileMemMap(m_Atlas)); in x_Open() 166 m_DataFile.push_back(new CSeqDBRawFile(m_Atlas)); in x_Open() 167 m_DataLease.push_back(new CSeqDBFileMemMap(m_Atlas)); in x_Open()
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H A D | seqdbalias.cpp | 103 : m_Atlas (atlas), in CSeqDBAliasNode() 162 : m_Atlas (atlas), in CSeqDBAliasNode() 193 m_Atlas); in x_FindBlastDBPath() 308 m_Atlas); in x_ResolveNames() 550 CSeqDBFileMemMap lease(m_Atlas,aset_path.GetPathS()); in x_ReadAliasSetFile() 553 m_Atlas.GetFileSizeL(aset_path.GetPathS(), length); in x_ReadAliasSetFile() 609 if (! m_Atlas.DoesFileExist(aset_path)) { in ReadAliasFile() 673 CSeqDBFileMemMap lease(m_Atlas,path.GetPathS()); in x_ReadValues() 719 subnode( new CSeqDBAliasNode(m_Atlas, in x_AppendSubNode() 842 if (m_Atlas.DoesFileExist(new_vol_path)) { in x_ExpandAliases() [all …]
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H A D | seqdbalias.hpp | 233 : m_Atlas(atlas) in CSeqDBAliasSets() 382 CSeqDBAtlas & m_Atlas; member in CSeqDBAliasSets 921 CSeqDBAtlas & m_Atlas; member in CSeqDBAliasNode
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H A D | seqdbgilistset.hpp | 172 CSeqDBAtlas & m_Atlas; member in CSeqDBGiListSet
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H A D | seqdbvol.cpp | 79 : m_Atlas (atlas), in CSeqDBVol() 117 m_Seq.Reset(new CSeqDBSeqFile(m_Atlas, m_VolName, (m_IsAA?'p':'n'))); in x_OpenSeqFile() 126 m_Hdr.Reset(new CSeqDBHdrFile(m_Atlas, m_VolName, (m_IsAA?'p':'n'))); in x_OpenHdrFile() 139 m_IsamPig = new CSeqDBIsam(m_Atlas, m_VolName, (m_IsAA?'p':'n'), 'p', ePigId); in x_OpenPigFile() 164 m_IsamGi = new CSeqDBIsam(m_Atlas, m_VolName, (m_IsAA?'p':'n'), 'n', eGiId); in x_OpenGiFile() 214 m_IsamTi = new CSeqDBIsam(m_Atlas, m_VolName, (m_IsAA?'p':'n'), 't', eTiId); in x_OpenTiFile() 239 new CSeqDBIsam(m_Atlas, in x_OpenHashFile() 256 new CSeqDBGiIndex(m_Atlas, in x_OpenOidFile() 3296 if (CSeqDBColumn::ColumnExists(m_VolName, ei, m_Atlas)) { in x_OpenAllColumns() 3298 bool big = CSeqDBColumn::ColumnExists(m_VolName, ed, m_Atlas); in x_OpenAllColumns() [all …]
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H A D | seqdboidlist.cpp | 50 : m_Atlas (atlas), in CSeqDBOIDList() 84 CSeqDBGiListSet gi_list_set(m_Atlas, in x_Setup() 455 CSeqDBRawFile volmask(m_Atlas); in x_GetOidMask() 456 CSeqDBFileMemMap lease(m_Atlas); in x_GetOidMask()
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H A D | seqdboidlist.hpp | 285 CSeqDBAtlas & m_Atlas; member in CSeqDBOIDList
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_reader/ |
H A D | seqdbimpl.cpp | 185 m_Atlas.Lock(locked); in SetIterationRange() 215 m_Atlas.Lock(locked); in ~CSeqDBImpl() 310 m_Atlas.Lock(locked); in GetNextOIDChunk() 451 m_Atlas.Lock(locked); in GetTaxIDs() 530 m_Atlas.Lock(locked); in GetLeafTaxIDs() 567 m_Atlas.Lock(locked); in GetLeafTaxIDs() 609 m_Atlas.Lock(locked); in GetBioseq() 742 m_Atlas.Lock(locked); in GetSeqData() 801 m_Atlas.Lock(locked); in GetSeqIDs() 896 m_Atlas.Lock(locked); in x_GetSeqGI() [all …]
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H A D | seqdbcol.cpp | 109 m_DataFile (m_Atlas), in CSeqDBColumn() 110 m_IndexLease (m_Atlas), in CSeqDBColumn() 111 m_DataLease (m_Atlas), in CSeqDBColumn() 117 CSeqDBLockHold locked2(m_Atlas); in CSeqDBColumn() 123 m_Atlas.Lock(*lockedp); in CSeqDBColumn() 141 m_Atlas.Unlock(*lockedp); in CSeqDBColumn() 149 CSeqDBLockHold locked(m_Atlas); in ~CSeqDBColumn() 150 m_Atlas.Lock(locked); in ~CSeqDBColumn() 210 m_Atlas.Lock(locked); in x_ReadFields() 275 m_Atlas.Lock(locked); in x_ReadMetaData() [all …]
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H A D | seqdbatlas.cpp | 309 m_Atlas = new CSeqDBAtlas(use_atlas_lock); in CSeqDBAtlasHolder() 324 m_Atlas = new CSeqDBAtlas(use_atlas_lock); in CSeqDBAtlasHolder() 340 delete m_Atlas; in ~CSeqDBAtlasHolder() 346 _ASSERT(m_Atlas); in Get() 347 return *m_Atlas; in Get() 354 m_Atlas.Unlock(*this); in ~CSeqDBLockHold() 359 CSeqDBAtlas * CSeqDBAtlasHolder::m_Atlas = NULL; member in CSeqDBAtlasHolder 364 : m_Atlas(atlas), m_Ptr(ptr) in CSeqDB_AtlasRegionHolder() 371 CSeqDBLockHold locked(m_Atlas); in ~CSeqDB_AtlasRegionHolder() 372 m_Atlas.Lock(locked); in ~CSeqDB_AtlasRegionHolder()
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H A D | seqdbgimask.cpp | 46 : m_Atlas (atlas), in CSeqDBGiMask() 51 m_IndexFile (m_Atlas), in CSeqDBGiMask() 52 m_OffsetFile (m_Atlas) in CSeqDBGiMask() 155 m_DataFile.push_back(new CSeqDBRawFile(m_Atlas)); in x_Open() 156 m_DataLease.push_back(new CSeqDBFileMemMap(m_Atlas)); in x_Open() 166 m_DataFile.push_back(new CSeqDBRawFile(m_Atlas)); in x_Open() 167 m_DataLease.push_back(new CSeqDBFileMemMap(m_Atlas)); in x_Open()
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H A D | seqdbalias.cpp | 103 : m_Atlas (atlas), in CSeqDBAliasNode() 162 : m_Atlas (atlas), in CSeqDBAliasNode() 193 m_Atlas); in x_FindBlastDBPath() 308 m_Atlas); in x_ResolveNames() 550 CSeqDBFileMemMap lease(m_Atlas,aset_path.GetPathS()); in x_ReadAliasSetFile() 553 m_Atlas.GetFileSizeL(aset_path.GetPathS(), length); in x_ReadAliasSetFile() 609 if (! m_Atlas.DoesFileExist(aset_path)) { in ReadAliasFile() 673 CSeqDBFileMemMap lease(m_Atlas,path.GetPathS()); in x_ReadValues() 719 subnode( new CSeqDBAliasNode(m_Atlas, in x_AppendSubNode() 842 if (m_Atlas.DoesFileExist(new_vol_path)) { in x_ExpandAliases() [all …]
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H A D | seqdbalias.hpp | 233 : m_Atlas(atlas) in CSeqDBAliasSets() 382 CSeqDBAtlas & m_Atlas; member in CSeqDBAliasSets 921 CSeqDBAtlas & m_Atlas; member in CSeqDBAliasNode
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H A D | seqdbgilistset.hpp | 172 CSeqDBAtlas & m_Atlas; member in CSeqDBGiListSet
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H A D | seqdbvol.cpp | 79 : m_Atlas (atlas), in CSeqDBVol() 117 m_Seq.Reset(new CSeqDBSeqFile(m_Atlas, m_VolName, (m_IsAA?'p':'n'))); in x_OpenSeqFile() 126 m_Hdr.Reset(new CSeqDBHdrFile(m_Atlas, m_VolName, (m_IsAA?'p':'n'))); in x_OpenHdrFile() 139 m_IsamPig = new CSeqDBIsam(m_Atlas, m_VolName, (m_IsAA?'p':'n'), 'p', ePigId); in x_OpenPigFile() 164 m_IsamGi = new CSeqDBIsam(m_Atlas, m_VolName, (m_IsAA?'p':'n'), 'n', eGiId); in x_OpenGiFile() 214 m_IsamTi = new CSeqDBIsam(m_Atlas, m_VolName, (m_IsAA?'p':'n'), 't', eTiId); in x_OpenTiFile() 239 new CSeqDBIsam(m_Atlas, in x_OpenHashFile() 256 new CSeqDBGiIndex(m_Atlas, in x_OpenOidFile() 3296 if (CSeqDBColumn::ColumnExists(m_VolName, ei, m_Atlas)) { in x_OpenAllColumns() 3298 bool big = CSeqDBColumn::ColumnExists(m_VolName, ed, m_Atlas); in x_OpenAllColumns() [all …]
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H A D | seqdboidlist.cpp | 50 : m_Atlas (atlas), in CSeqDBOIDList() 84 CSeqDBGiListSet gi_list_set(m_Atlas, in x_Setup() 455 CSeqDBRawFile volmask(m_Atlas); in x_GetOidMask() 456 CSeqDBFileMemMap lease(m_Atlas); in x_GetOidMask()
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