| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/ |
| H A D | MysqlAssemblyDbi.cpp | 77 MysqlAssemblyAdapter *MysqlAssemblyDbi::getAdapter(const U2DataId &assemblyId, U2OpStatus &os) { in getAdapter()
108 U2Assembly MysqlAssemblyDbi::getAssemblyObject(const U2DataId &assemblyId, U2OpStatus &os) { in getAssemblyObject()
129 qint64 MysqlAssemblyDbi::countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os) { in countReads()
174 qint64 MysqlAssemblyDbi::getMaxPackedRow(const U2DataId &assemblyId, const U2Region &r, U2OpStatus … in getMaxPackedRow()
188 qint64 MysqlAssemblyDbi::getMaxEndPos(const U2DataId &assemblyId, U2OpStatus &os) { in getMaxEndPos()
264 void MysqlAssemblyDbi::removeAssemblyData(const U2DataId &assemblyId, U2OpStatus &os) { in removeAssemblyData()
290 void MysqlAssemblyDbi::removeReads(const U2DataId &assemblyId, const QList<U2DataId> &rowIds, U2OpS… in removeReads()
311 void MysqlAssemblyDbi::removeTables(const U2DataId &assemblyId, U2OpStatus &os) { in removeTables()
320 void MysqlAssemblyDbi::removeAssemblyEntry(const U2DataId &assemblyId, U2OpStatus &os) { in removeAssemblyEntry()
335 void MysqlAssemblyDbi::addReads(const U2DataId &assemblyId, U2DbiIterator<U2AssemblyRead> *it, U2Op… in addReads()
[all …]
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_assembly/ |
| H A D | CalculateCoveragePerBaseTask.h | 46 GetAssemblyLengthTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId) in GetAssemblyLengthTask()
58 const U2DataId assemblyId; variable
78 const U2DataId assemblyId; variable
103 const U2DataId assemblyId; variable
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| H A D | ExportCoverageTask.h | 70 GetAssemblyVisibleNameTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId) in GetAssemblyVisibleNameTask()
82 const U2DataId assemblyId; variable
107 const U2DataId assemblyId; variable
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| H A D | ExportCoverageTask.cpp | 61 ExportCoverageTask::ExportCoverageTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const Ex… in ExportCoverageTask()
155 …ogramTask::ExportCoverageHistogramTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const E… in ExportCoverageHistogramTask()
196 …PerBaseTask::ExportCoveragePerBaseTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const E… in ExportCoveragePerBaseTask()
258 …dgraphTask::ExportCoverageBedgraphTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const E… in ExportCoverageBedgraphTask()
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| H A D | CalculateCoveragePerBaseTask.cpp | 34 …::CalculateCoveragePerBaseOnRegionTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const U… in CalculateCoveragePerBaseOnRegionTask()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/ |
| H A D | SQLiteAssemblyDbi.cpp | 71 AssemblyAdapter *SQLiteAssemblyDbi::getAdapter(const U2DataId &assemblyId, U2OpStatus &os) { in getAdapter()
103 U2Assembly SQLiteAssemblyDbi::getAssemblyObject(const U2DataId &assemblyId, U2OpStatus &os) { in getAssemblyObject()
125 qint64 SQLiteAssemblyDbi::countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os)… in countReads()
170 qint64 SQLiteAssemblyDbi::getMaxPackedRow(const U2DataId &assemblyId, const U2Region &r, U2OpStatus… in getMaxPackedRow()
184 qint64 SQLiteAssemblyDbi::getMaxEndPos(const U2DataId &assemblyId, U2OpStatus &os) { in getMaxEndPos()
237 void SQLiteAssemblyDbi::removeAssemblyData(const U2DataId &assemblyId, U2OpStatus &os) { in removeAssemblyData()
262 void SQLiteAssemblyDbi::removeReads(const U2DataId &assemblyId, const QList<U2DataId> &rowIds, U2Op… in removeReads()
291 void SQLiteAssemblyDbi::removeTables(const U2DataId &assemblyId, U2OpStatus &os) { in removeTables()
297 void SQLiteAssemblyDbi::removeAssemblyEntry(const U2DataId &assemblyId, U2OpStatus &os) { in removeAssemblyEntry()
305 void SQLiteAssemblyDbi::addReads(const U2DataId &assemblyId, U2DbiIterator<U2AssemblyRead> *it, U2O… in addReads()
[all …]
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| H A D | SQLiteAssemblyDbi.h | 144 …SQLiteAssemblyAdapter(const U2DataId &assemblyId, const AssemblyCompressor *compressor, DbRef *ref) in SQLiteAssemblyAdapter()
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| /dports/biology/jalview/jalview/src/jalview/datamodel/ |
| H A D | GeneLocus.java | 51 public GeneLocus(String speciesId, String assemblyId, String chromosomeId, in GeneLocus()
64 public GeneLocus(String speciesId, String assemblyId, String chromosomeId) in GeneLocus()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/ |
| H A D | AlignedAssembly.java | 18 public final int assemblyId; field in AlignedAssembly
22 public AlignedAssembly(final int assemblyId, final List<AlignedContig> alignedContigs) { in AlignedAssembly()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/ |
| H A D | cn3d_cache.cpp | 148 const string& uid, int mmdbID, EModel_type modelType, int assemblyId = 0) in GetStructureViaHTTPAndAddToCache()
243 …LoadStructureViaCache(const std::string& uid, ncbi::objects::EModel_type modelType, int assemblyId) in LoadStructureViaCache()
275 …LoadStructureViaCache(const std::string& uid, ncbi::objects::EModel_type modelType, int assemblyId, in LoadStructureViaCache()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ |
| H A D | AlignedAssemblyOrExcuse.java | 36 private final int assemblyId; field in AlignedAssemblyOrExcuse
70 public AlignedAssemblyOrExcuse( final int assemblyId, final String errorMessage ) { in AlignedAssemblyOrExcuse()
78 …public AlignedAssemblyOrExcuse( final int assemblyId, final FermiLiteAssembly assembly, final int … in AlignedAssemblyOrExcuse()
261 public static String formatContigName( final int assemblyId, final int contigIdx ) { in formatContigName()
265 public static String formatAssemblyID( final int assemblyId ) { in formatAssemblyID()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/util/ |
| H A D | AssemblyAdapter.h | 38 AssemblyAdapter(const U2DataId &assemblyId, const AssemblyCompressor *compressor) in AssemblyAdapter()
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| /dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/cufflinks/ |
| H A D | CufflinksSettings.h | 53 Workflow::SharedDbiDataHandler assemblyId; variable
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| /dports/biology/ugene/ugene-40.1/src/plugins/dbi_bam/src/ |
| H A D | SamtoolsBasedDbi.cpp | 385 int assemblyId, in SamtoolsBasedReadsIterator()
552 int SamtoolsBasedAssemblyDbi::toSamtoolsId(const U2DataId &assemblyId, U2OpStatus &os) { in toSamtoolsId()
591 qint64 SamtoolsBasedAssemblyDbi::countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStat… in countReads()
605 U2DbiIterator<U2AssemblyRead> *SamtoolsBasedAssemblyDbi::getReads(const U2DataId &assemblyId, const… in getReads()
622 U2DbiIterator<U2AssemblyRead> *SamtoolsBasedAssemblyDbi::getReadsByName(const U2DataId &assemblyId,… in getReadsByName()
629 qint64 SamtoolsBasedAssemblyDbi::getMaxEndPos(const U2DataId &assemblyId, U2OpStatus &os) { in getMaxEndPos()
642 U2Region SamtoolsBasedAssemblyDbi::getCorrectRegion(const U2DataId &assemblyId, const U2Region &r, … in getCorrectRegion()
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| H A D | Dbi.cpp | 590 qint64 AssemblyDbi::countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os) { in countReads()
618 U2DbiIterator<U2AssemblyRead> *AssemblyDbi::getReads(const U2DataId &assemblyId, const U2Region &r,… in getReads()
692 qint64 AssemblyDbi::getMaxPackedRow(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os) { in getMaxPackedRow()
720 U2DbiIterator<U2AssemblyRead> *AssemblyDbi::getReadsByRow(const U2DataId &assemblyId, const U2Regio… in getReadsByRow()
767 qint64 AssemblyDbi::getMaxEndPos(const U2DataId &assemblyId, U2OpStatus &os) { in getMaxEndPos()
842 qint64 AssemblyDbi::getMaxReadLength(const U2DataId &assemblyId, const U2Region & /*r*/) { in getMaxReadLength()
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| H A D | Header.h | 65 QByteArray assemblyId; variable
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| H A D | Header.cpp | 68 void Header::Reference::setAssemblyId(const QByteArray &assemblyId) { in setAssemblyId()
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| /dports/biology/ugene/ugene-40.1/src/plugins/workflow_designer/src/debug_messages_translation/ |
| H A D | AssemblyMessageTranslator.cpp | 58 const U2DataId assemblyId = assemblyRef.entityId; in getTranslation() local
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/util/ |
| H A D | MysqlAssemblyAdapter.cpp | 30 MysqlAssemblyAdapter::MysqlAssemblyAdapter(const U2DataId &assemblyId, in MysqlAssemblyAdapter()
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| H A D | MysqlSingleTableAssemblyAdapter.cpp | 44 const U2DataId &assemblyId, in MysqlSingleTableAssemblyAdapter()
279 QString MysqlSingleTableAssemblyAdapter::getReadsTableName(const U2DataId &assemblyId, char prefix,… in getReadsTableName()
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| /dports/games/ufoai/ufoai-2.5-source/src/client/cgame/campaign/ |
| H A D | cp_parse.h | 37 char assemblyId[MAX_VAR]; /**< The name of the assembly (i.e. the UFO) */ member
|
| /dports/lang/mono/mono-5.10.1.57/mcs/class/referencesource/System.ServiceModel/System/ServiceModel/ComIntegration/ |
| H A D | ServiceInfo.cs | 322 internal Type[] GetTypes(Guid assemblyId) in GetTypes()
333 internal void AddUdt(Type udt, Guid assemblyId) in AddUdt()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/assembly/ |
| H A D | SingleTableAssemblyAdapter.cpp | 42 SingleTableAssemblyAdapter::SingleTableAssemblyAdapter(SQLiteDbi *_dbi, const U2DataId &assemblyId,… in SingleTableAssemblyAdapter()
53 QString SingleTableAssemblyAdapter::getReadsTableName(const U2DataId &assemblyId, char prefix, cons… in getReadsTableName()
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| /dports/biology/ugene/ugene-40.1/src/plugins/workflow_designer/src/library/ |
| H A D | AssemblyToSequenceWorker.cpp | 106 U2DataId assemblyId = assemblyObj->getEntityRef().entityId; in run() local
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| H A D | WriteAssemblyWorkers.cpp | 61 …SharedDbiDataHandler assemblyId = data[BaseSlots::ASSEMBLY_SLOT().getId()].value<SharedDbiDataHand… in data2doc() local
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