/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/blast/seqdb_reader/impl/ |
H A D | seqdbfile.hpp | 123 const char * GetFileDataPtr(CSeqDBFileMemMap & lease, // commented in GetFileDataPtr() function in CSeqDBRawFile 131 const char *p = (const char *)lease.GetFileDataPtr(m_FileName,start); in GetFileDataPtr() 650 return (Uint4*) m_HdrLease.GetFileDataPtr(m_FileName, m_OffHdr); in x_GetHdr() 657 return (Uint4*) m_SeqLease.GetFileDataPtr(m_FileName, m_OffSeq); in x_GetSeq() 665 return (Uint4*) m_AmbLease.GetFileDataPtr(m_FileName, m_OffAmb); in x_GetAmb() 822 … const char * GetFileDataPtr(TIndx start) const // commented in GetFileDataPtr() function in CSeqDBSeqFile 824 const char *p = (const char *)m_Lease.GetFileDataPtr(start); in GetFileDataPtr() 907 … const char * GetFileDataPtr(TIndx start) const // commented in GetFileDataPtr() function in CSeqDBHdrFile 912 const char *p = (const char *)m_Lease.GetFileDataPtr(start); in GetFileDataPtr() 927 memcpy(buf, lease.GetFileDataPtr(m_FileName,start), end-start); in ReadBytes()
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H A D | seqdbisam.hpp | 504 const char * keydatap = lease.GetFileDataPtr(m_KeySampleOffset); in x_LoadIndex() 526 const char * keydatap = lease.GetFileDataPtr(begin); in x_LoadData() 1296 keydatap = index_lease.GetFileDataPtr(offset_begin); in x_TestNumericSample() 1325 keydatap = index_lease.GetFileDataPtr(offset_begin); in x_GetNumericSample() 1340 const char * keydatap = lease.GetFileDataPtr(m_KeySampleOffset); in x_LoadIndex() 1362 const char * keydatap = lease.GetFileDataPtr(begin); in x_LoadData() 1380 const Uint4 * offset = (const Uint4 *) lease.GetFileDataPtr(offset_begin); in x_LoadIndex() 1387 offset = (const Uint4 *) lease.GetFileDataPtr(sample_begin); in x_LoadIndex() 1393 const char * keydatap = (const char *) lease.GetFileDataPtr(offset_begin) - 1; in x_LoadIndex() 1413 const char * keydatap = (const char *) lease.GetFileDataPtr(begin) - 1; in x_LoadData() [all …]
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H A D | seqdbatlas.hpp | 754 const char *GetFileDataPtr(const string & fname,TIndx offset) in GetFileDataPtr() function in CSeqDBFileMemMap 763 const char *GetFileDataPtr(TIndx offset) in GetFileDataPtr() function in CSeqDBFileMemMap
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/blast/seqdb_reader/impl/ |
H A D | seqdbfile.hpp | 123 const char * GetFileDataPtr(CSeqDBFileMemMap & lease, // commented in GetFileDataPtr() function in CSeqDBRawFile 131 const char *p = (const char *)lease.GetFileDataPtr(m_FileName,start); in GetFileDataPtr() 650 return (Uint4*) m_HdrLease.GetFileDataPtr(m_FileName, m_OffHdr); in x_GetHdr() 657 return (Uint4*) m_SeqLease.GetFileDataPtr(m_FileName, m_OffSeq); in x_GetSeq() 665 return (Uint4*) m_AmbLease.GetFileDataPtr(m_FileName, m_OffAmb); in x_GetAmb() 822 … const char * GetFileDataPtr(TIndx start) const // commented in GetFileDataPtr() function in CSeqDBSeqFile 824 const char *p = (const char *)m_Lease.GetFileDataPtr(start); in GetFileDataPtr() 907 … const char * GetFileDataPtr(TIndx start) const // commented in GetFileDataPtr() function in CSeqDBHdrFile 912 const char *p = (const char *)m_Lease.GetFileDataPtr(start); in GetFileDataPtr() 927 memcpy(buf, lease.GetFileDataPtr(m_FileName,start), end-start); in ReadBytes()
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H A D | seqdbisam.hpp | 504 const char * keydatap = lease.GetFileDataPtr(m_KeySampleOffset); in x_LoadIndex() 526 const char * keydatap = lease.GetFileDataPtr(begin); in x_LoadData() 1296 keydatap = index_lease.GetFileDataPtr(offset_begin); in x_TestNumericSample() 1325 keydatap = index_lease.GetFileDataPtr(offset_begin); in x_GetNumericSample() 1340 const char * keydatap = lease.GetFileDataPtr(m_KeySampleOffset); in x_LoadIndex() 1362 const char * keydatap = lease.GetFileDataPtr(begin); in x_LoadData() 1380 const Uint4 * offset = (const Uint4 *) lease.GetFileDataPtr(offset_begin); in x_LoadIndex() 1387 offset = (const Uint4 *) lease.GetFileDataPtr(sample_begin); in x_LoadIndex() 1393 const char * keydatap = (const char *) lease.GetFileDataPtr(offset_begin) - 1; in x_LoadIndex() 1413 const char * keydatap = (const char *) lease.GetFileDataPtr(begin) - 1; in x_LoadData() [all …]
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H A D | seqdbatlas.hpp | 754 const char *GetFileDataPtr(const string & fname,TIndx offset) in GetFileDataPtr() function in CSeqDBFileMemMap 763 const char *GetFileDataPtr(TIndx offset) in GetFileDataPtr() function in CSeqDBFileMemMap
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_reader/ |
H A D | seqdbgimask.cpp | 91 m_OffsetFile.GetFileDataPtr(m_OffsetLease, begin, end); in GetMaskData() 104 m_DataFile[vol]->GetFileDataPtr(*m_DataLease[vol], off, off+4); in GetMaskData() 109 m_DataFile[vol]->GetFileDataPtr(*m_DataLease[vol], off+4, off + 8*n + 4); in GetMaskData() 195 const char * ptr = file.GetFileDataPtr(lease, begin, end); in s_GetFileRange() 250 m_IndexFile.GetFileDataPtr(m_IndexLease, begin, end); in x_ReadFields()
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H A D | seqdbfile.cpp | 76 *value = SeqDB_GetStdOrd((Uint4 *) lease.GetFileDataPtr(m_FileName,offset)); in ReadSwapped() 86 *value = SeqDB_GetBroken((Int8 *) lease.GetFileDataPtr(m_FileName,offset)); in ReadSwapped() 97 len = SeqDB_GetStdOrd((Int4 *) lease.GetFileDataPtr(m_FileName,offset)); in ReadSwapped() 101 value->assign(lease.GetFileDataPtr(offset), (int) len); in ReadSwapped()
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H A D | seqdbisam.cpp | 74 Int4 * FileInfo = (Int4*)m_IndexLease.GetFileDataPtr(m_IndexFname,0); in x_InitSearch() 175 keydatap = m_IndexLease.GetFileDataPtr(m_IndexFname,offset_begin); in x_SearchIndexNumeric() 442 KeyDataPageStart = m_DataLease.GetFileDataPtr(m_DataFname,offset_begin); in x_SearchDataNumeric() 545 const char * file_data = (const char *)lease.GetFileDataPtr(file_name,offset_begin); in x_DiffCharLease() 831 Int4 * key_offset_addr = (Int4 *)m_IndexLease.GetFileDataPtr(offset_begin); in x_GetIndexKeyOffset() 845 (const char *)m_IndexLease.GetFileDataPtr(key_offset); in x_GetIndexString() 885 KeyOffset = SeqDB_GetStdOrd((Int4*)m_IndexLease.GetFileDataPtr(offset_begin)); in x_DiffSample() 912 Uint4 * key_offsets((Uint4*)m_IndexLease.GetFileDataPtr(begin_offset)); in x_LoadPage() 918 *beginp = (const char *) m_DataLease.GetFileDataPtr(m_DataFname,key_off1); in x_LoadPage() 919 *endp = (const char *) m_DataLease.GetFileDataPtr(key_off2); in x_LoadPage() [all …]
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H A D | seqdbvol.cpp | 58 data = m_Lease.GetFileDataPtr(0); in GetSeqGI() 68 data = m_Lease.GetFileDataPtr(offset); in GetSeqGI() 1777 *buffer = m_Seq->GetFileDataPtr(start_offset-1) + 1; in x_GetSequence() 1792 *buffer = m_Seq->GetFileDataPtr(start_offset); in x_GetSequence() 2266 const char * asn_region = m_Hdr->GetFileDataPtr(hdr_start); in x_GetHdrAsn1Binary() 2326 (Int4*) m_Seq->GetFileDataPtr(start_offset); in x_GetAmbChar() 3011 *buffer = m_Seq->GetFileDataPtr(map_begin); in GetRawSeqAndAmbig()
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H A D | seqdbcol.cpp | 194 const char * ptr = file.GetFileDataPtr(lease, begin, end); in x_GetFileRange()
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H A D | seqdboidlist.cpp | 472 volmask.GetFileDataPtr(lease, sizeof(Int4), file_length); in x_GetOidMask() 474 bitmap = (TCUC*) lease.GetFileDataPtr(sizeof(Int4)); in x_GetOidMask()
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H A D | seqdbgilistset.cpp | 97 const char * fbeginp = memlease.GetFileDataPtr(0); in CSeqDBNodeFileIdList()
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H A D | seqdbalias.cpp | 555 const char * bp = lease.GetFileDataPtr(0); in x_ReadAliasSetFile() 663 *bp = lease.GetFileDataPtr(0); in x_ReadAliasFile()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_reader/ |
H A D | seqdbgimask.cpp | 91 m_OffsetFile.GetFileDataPtr(m_OffsetLease, begin, end); in GetMaskData() 104 m_DataFile[vol]->GetFileDataPtr(*m_DataLease[vol], off, off+4); in GetMaskData() 109 m_DataFile[vol]->GetFileDataPtr(*m_DataLease[vol], off+4, off + 8*n + 4); in GetMaskData() 195 const char * ptr = file.GetFileDataPtr(lease, begin, end); in s_GetFileRange() 250 m_IndexFile.GetFileDataPtr(m_IndexLease, begin, end); in x_ReadFields()
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H A D | seqdbfile.cpp | 76 *value = SeqDB_GetStdOrd((Uint4 *) lease.GetFileDataPtr(m_FileName,offset)); in ReadSwapped() 86 *value = SeqDB_GetBroken((Int8 *) lease.GetFileDataPtr(m_FileName,offset)); in ReadSwapped() 97 len = SeqDB_GetStdOrd((Int4 *) lease.GetFileDataPtr(m_FileName,offset)); in ReadSwapped() 101 value->assign(lease.GetFileDataPtr(offset), (int) len); in ReadSwapped()
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H A D | seqdbisam.cpp | 74 Int4 * FileInfo = (Int4*)m_IndexLease.GetFileDataPtr(m_IndexFname,0); in x_InitSearch() 175 keydatap = m_IndexLease.GetFileDataPtr(m_IndexFname,offset_begin); in x_SearchIndexNumeric() 442 KeyDataPageStart = m_DataLease.GetFileDataPtr(m_DataFname,offset_begin); in x_SearchDataNumeric() 545 const char * file_data = (const char *)lease.GetFileDataPtr(file_name,offset_begin); in x_DiffCharLease() 831 Int4 * key_offset_addr = (Int4 *)m_IndexLease.GetFileDataPtr(offset_begin); in x_GetIndexKeyOffset() 845 (const char *)m_IndexLease.GetFileDataPtr(key_offset); in x_GetIndexString() 885 KeyOffset = SeqDB_GetStdOrd((Int4*)m_IndexLease.GetFileDataPtr(offset_begin)); in x_DiffSample() 912 Uint4 * key_offsets((Uint4*)m_IndexLease.GetFileDataPtr(begin_offset)); in x_LoadPage() 918 *beginp = (const char *) m_DataLease.GetFileDataPtr(m_DataFname,key_off1); in x_LoadPage() 919 *endp = (const char *) m_DataLease.GetFileDataPtr(key_off2); in x_LoadPage() [all …]
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H A D | seqdbvol.cpp | 58 data = m_Lease.GetFileDataPtr(0); in GetSeqGI() 68 data = m_Lease.GetFileDataPtr(offset); in GetSeqGI() 1777 *buffer = m_Seq->GetFileDataPtr(start_offset-1) + 1; in x_GetSequence() 1792 *buffer = m_Seq->GetFileDataPtr(start_offset); in x_GetSequence() 2266 const char * asn_region = m_Hdr->GetFileDataPtr(hdr_start); in x_GetHdrAsn1Binary() 2326 (Int4*) m_Seq->GetFileDataPtr(start_offset); in x_GetAmbChar() 3011 *buffer = m_Seq->GetFileDataPtr(map_begin); in GetRawSeqAndAmbig()
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H A D | seqdbcol.cpp | 194 const char * ptr = file.GetFileDataPtr(lease, begin, end); in x_GetFileRange()
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H A D | seqdboidlist.cpp | 472 volmask.GetFileDataPtr(lease, sizeof(Int4), file_length); in x_GetOidMask() 474 bitmap = (TCUC*) lease.GetFileDataPtr(sizeof(Int4)); in x_GetOidMask()
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H A D | seqdbgilistset.cpp | 97 const char * fbeginp = memlease.GetFileDataPtr(0); in CSeqDBNodeFileIdList()
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H A D | seqdbalias.cpp | 555 const char * bp = lease.GetFileDataPtr(0); in x_ReadAliasSetFile() 663 *bp = lease.GetFileDataPtr(0); in x_ReadAliasFile()
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