#include <ncbi_pch.hpp>#include <gui/widgets/seq_graphic/bed_coverage_graph.hpp>#include <gui/widgets/seq_graphic/graph_cache.hpp>#include <gui/utils/rmtfilestatus.hpp>#include <gui/utils/url_utils.hpp>#include <objmgr/scope.hpp>#include <objects/seq/seq_id_handle.hpp>#include <util/bitset/bmserial.h>#include <util/bitset/bmsparsevec_serial.h>#include <util/checksum.hpp>#include <corelib/rwstream.hpp>#include <connect/ncbi_conn_stream.hpp>#include <corelib/ncbiexec.hpp>
Include dependency graph for bed_coverage_graph.cpp:
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Functions | |
| USING_SCOPE (objects) | |
| static bool | s_ReadData (ICache &icache, const string &data_key, int &bin_count, bm::sparse_vector< unsigned, bm::bvector<> > &sv, bm::word_t *tb) |
| void | s_GetBigBedSummary (const string &data_url, const string &chrom, const string &from, const string &to, int bin_count, vector< unsigned int > &data_points) |
| void | s_GetBigBedFeats (const string &data_url, const string &chrom, const string &from, const string &to, vector< TSeqRange > &ranges) |
Function Documentation
◆ s_GetBigBedFeats()
| void s_GetBigBedFeats | ( | const string & | data_url, |
| const string & | chrom, | ||
| const string & | from, | ||
| const string & | to, | ||
| vector< TSeqRange > & | ranges | ||
| ) |
Definition at line 233 of file bed_coverage_graph.cpp.
References CRmtFileStatus::Check(), CDirEntry::CreateTmpFile(), CProcess::eHandle, CExec::eNoWait, CRmtFileStatus::ESuggestedAction_Access, CRmtFileStatus::ESuggestedAction_Skip, CDirEntry::eTmpFileCreate, eUnknown, NStr::fAllowLeadingSpaces, NStr::fAllowTrailingSpaces, NStr::fConvErr_NoThrow, CRmtScriptTimeout::Get(), CProcess::CExitInfo::GetExitCode(), CExec::CResult::GetProcessHandle(), CDirEntry::GetTmpName(), NCBI_THROW, NcbiGetline(), NULL, NStr::NumericToString(), CRmtFileStatus::Set(), CExec::SpawnL(), NStr::SplitInTwo(), NStr::StringToInt(), val, and CProcess::Wait().
◆ s_GetBigBedSummary()
| void s_GetBigBedSummary | ( | const string & | data_url, |
| const string & | chrom, | ||
| const string & | from, | ||
| const string & | to, | ||
| int | bin_count, | ||
| vector< unsigned int > & | data_points | ||
| ) |
Definition at line 190 of file bed_coverage_graph.cpp.
References CRmtFileStatus::Check(), CDirEntry::CreateTmpFile(), CProcess::eHandle, CExec::eNoWait, CRmtFileStatus::ESuggestedAction_Access, CRmtFileStatus::ESuggestedAction_Skip, CDirEntry::eTmpFileCreate, eUnknown, NStr::fAllowLeadingSpaces, NStr::fAllowTrailingSpaces, NStr::fConvErr_NoThrow, CRmtScriptTimeout::Get(), CProcess::CExitInfo::GetExitCode(), CExec::CResult::GetProcessHandle(), CDirEntry::GetTmpName(), NCBI_THROW, NcbiGetline(), NULL, NStr::NumericToString(), round(), CRmtFileStatus::Set(), CExec::SpawnL(), NStr::StringToDouble(), val, and CProcess::Wait().
Referenced by CBedCoverageGraph::x_InitData().
◆ s_ReadData()
|
static |
Definition at line 132 of file bed_coverage_graph.cpp.
References buffer, ERR_POST, Error(), eUnknown, CRWStreambuf::fOwnReader, ICache::GetReadStream(), ICache::GetSize(), int, NCBI_THROW, NcbiEmptyString, ncbi::grid::netcache::search::fields::size, and bm::sparse_vector_deserialize().
Referenced by CBedCoverageGraph::Init().
◆ USING_SCOPE()
| USING_SCOPE | ( | objects | ) |
