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Searched refs:m_Atlas (Results 1 – 25 of 42) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/blast/seqdb_reader/impl/
H A Dseqdbatlas.hpp179 : 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 …]
H A Dseqdbfile.hpp78 : 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
H A Dseqdbcol.hpp202 CSeqDBAtlas & m_Atlas; member in CSeqDBColumn
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/blast/seqdb_reader/impl/
H A Dseqdbatlas.hpp179 : 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 …]
H A Dseqdbfile.hpp78 : 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
H A Dseqdbcol.hpp202 CSeqDBAtlas & m_Atlas; member in CSeqDBColumn
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_reader/
H A Dseqdbimpl.cpp185 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 …]
H A Dseqdbcol.cpp109 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 …]
H A Dseqdbatlas.cpp296 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()
H A Dseqdbgimask.cpp46 : 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()
H A Dseqdbalias.cpp103 : 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 …]
H A Dseqdbalias.hpp233 : m_Atlas(atlas) in CSeqDBAliasSets()
382 CSeqDBAtlas & m_Atlas; member in CSeqDBAliasSets
921 CSeqDBAtlas & m_Atlas; member in CSeqDBAliasNode
H A Dseqdbgilistset.hpp172 CSeqDBAtlas & m_Atlas; member in CSeqDBGiListSet
H A Dseqdbvol.cpp79 : 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 …]
H A Dseqdboidlist.cpp50 : 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()
H A Dseqdboidlist.hpp285 CSeqDBAtlas & m_Atlas; member in CSeqDBOIDList
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_reader/
H A Dseqdbimpl.cpp185 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 …]
H A Dseqdbcol.cpp109 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 …]
H A Dseqdbatlas.cpp309 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()
H A Dseqdbgimask.cpp46 : 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()
H A Dseqdbalias.cpp103 : 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 …]
H A Dseqdbalias.hpp233 : m_Atlas(atlas) in CSeqDBAliasSets()
382 CSeqDBAtlas & m_Atlas; member in CSeqDBAliasSets
921 CSeqDBAtlas & m_Atlas; member in CSeqDBAliasNode
H A Dseqdbgilistset.hpp172 CSeqDBAtlas & m_Atlas; member in CSeqDBGiListSet
H A Dseqdbvol.cpp79 : 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 …]
H A Dseqdboidlist.cpp50 : 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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