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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/
H A DMysqlAssemblyDbi.cpp78 qint64 dbiId = U2DbiUtils::toDbiId(assemblyId); in getAdapter()
86 q.bindDataId(":object", assemblyId); in getAdapter()
111 DBI_TYPE_CHECK(assemblyId, U2Type::Assembly, os, res); in getAssemblyObject()
120 q.bindDataId(":object", assemblyId); in getAssemblyObject()
131 MysqlAssemblyAdapter *a = getAdapter(assemblyId, os); in countReads()
140 MysqlAssemblyAdapter *a = getAdapter(assemblyId, os); in getReads()
151 MysqlAssemblyAdapter *a = getAdapter(assemblyId, os); in getReadsByRow()
167 MysqlAssemblyAdapter *a = getAdapter(assemblyId, os); in getReadsByName()
268 removeTables(assemblyId, os); in removeAssemblyData()
270 removeAssemblyEntry(assemblyId, os); in removeAssemblyData()
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H A DMysqlAssemblyDbi.h44 virtual U2Assembly getAssemblyObject(const U2DataId &assemblyId, U2OpStatus &os);
50 virtual qint64 countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
74 virtual qint64 getMaxPackedRow(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
77 virtual qint64 getMaxEndPos(const U2DataId &assemblyId, U2OpStatus &os);
97 virtual void removeAssemblyData(const U2DataId &assemblyId, U2OpStatus &os);
109 …virtual void removeReads(const U2DataId &assemblyId, const QList<U2DataId> &rowIds, U2OpStatus &os…
115 …virtual void addReads(const U2DataId &assemblyId, U2DbiIterator<U2AssemblyRead> *it, U2OpStatus &o…
118 virtual void pack(const U2DataId &assemblyId, U2AssemblyPackStat &stat, U2OpStatus &os);
129 void removeTables(const U2DataId &assemblyId, U2OpStatus &os);
130 void removeAssemblyEntry(const U2DataId &assemblyId, U2OpStatus &os);
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/
H A DSQLiteAssemblyDbi.h42 virtual U2Assembly getAssemblyObject(const U2DataId &assemblyId, U2OpStatus &os);
48 virtual qint64 countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
72 virtual qint64 getMaxPackedRow(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
75 virtual qint64 getMaxEndPos(const U2DataId &assemblyId, U2OpStatus &os);
95 virtual void removeAssemblyData(const U2DataId &assemblyId, U2OpStatus &os);
116 virtual void pack(const U2DataId &assemblyId, U2AssemblyPackStat &stat, U2OpStatus &os);
132 void removeTables(const U2DataId &assemblyId, U2OpStatus &os);
133 void removeAssemblyEntry(const U2DataId &assemblyId, U2OpStatus &os);
136 AssemblyAdapter *getAdapter(const U2DataId &assemblyId, U2OpStatus &os);
144 …SQLiteAssemblyAdapter(const U2DataId &assemblyId, const AssemblyCompressor *compressor, DbRef *ref) in SQLiteAssemblyAdapter() argument
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H A DSQLiteAssemblyDbi.cpp72 qint64 sqliteId = U2DbiUtils::toDbiId(assemblyId); in getAdapter()
79 q.bindDataId(1, assemblyId); in getAdapter()
116 q.bindDataId(1, assemblyId); in getAssemblyObject()
127 AssemblyAdapter *a = getAdapter(assemblyId, os); in countReads()
136 AssemblyAdapter *a = getAdapter(assemblyId, os); in getReads()
147 AssemblyAdapter *a = getAdapter(assemblyId, os); in getReadsByRow()
163 AssemblyAdapter *a = getAdapter(assemblyId, os); in getReadsByName()
173 AssemblyAdapter *a = getAdapter(assemblyId, os); in getMaxPackedRow()
241 removeTables(assemblyId, os); in removeAssemblyData()
243 removeAssemblyEntry(assemblyId, os); in removeAssemblyData()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/dbi/
H A DU2AssemblyDbi.h115 virtual qint64 countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os) = 0;
123 …virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2DataId &assemblyId, const U2Region &r, U2O…
131 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByRow(const U2DataId &assemblyId, const U2Region &r…
139 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByName(const U2DataId &assemblyId, const QByteArray…
146 … virtual qint64 getMaxPackedRow(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os) = 0;
152 virtual qint64 getMaxEndPos(const U2DataId &assemblyId, U2OpStatus &os) = 0;
179 virtual void removeAssemblyData(const U2DataId &assemblyId, U2OpStatus &os) = 0;
194 …virtual void removeReads(const U2DataId &assemblyId, const QList<U2DataId> &readIds, U2OpStatus &o…
202 …virtual void addReads(const U2DataId &assemblyId, U2DbiIterator<U2AssemblyRead> *it, U2OpStatus &o…
210 virtual void pack(const U2DataId &assemblyId, U2AssemblyPackStat &stats, U2OpStatus &os) = 0;
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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 DAlignedAssembly.java18 public final int assemblyId; field in AlignedAssembly
22 public AlignedAssembly(final int assemblyId, final List<AlignedContig> alignedContigs) { in AlignedAssembly() argument
23 this.assemblyId = assemblyId; in AlignedAssembly()
29 this.assemblyId = input.readInt(); in AlignedAssembly()
40 output.writeInt(assemblyId); in serialize()
65 if (assemblyId != that.assemblyId) return false; in equals()
71 int result = assemblyId; in hashCode()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_assembly/
H A DCalculateCoveragePerBaseTask.h46 GetAssemblyLengthTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId) in GetAssemblyLengthTask() argument
47 … : Task(tr("Get length of Assembly"), TaskFlag_None), dbiRef(dbiRef), assemblyId(assemblyId) { in GetAssemblyLengthTask()
58 const U2DataId assemblyId; variable
65 …CalculateCoveragePerBaseOnRegionTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const U2R…
78 const U2DataId assemblyId; variable
86 CalculateCoveragePerBaseTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId);
103 const U2DataId assemblyId; variable
H A DExportCoverageTask.h70 GetAssemblyVisibleNameTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId) in GetAssemblyVisibleNameTask() argument
71 …: Task(tr("Get visible name of Assembly"), TaskFlag_None), dbiRef(dbiRef), assemblyId(assemblyId) { in GetAssemblyVisibleNameTask()
82 const U2DataId assemblyId; variable
89 …ExportCoverageTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const ExportCoverageSetting…
107 const U2DataId assemblyId; variable
124 …ExportCoverageHistogramTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const ExportCovera…
139 …ExportCoveragePerBaseTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const ExportCoverage…
154 …ExportCoverageBedgraphTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const ExportCoverag…
H A DCalculateCoveragePerBaseTask.cpp34 …ateCoveragePerBaseOnRegionTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const U2Region … in CalculateCoveragePerBaseOnRegionTask() argument
37 assemblyId(assemblyId), in CalculateCoveragePerBaseOnRegionTask()
41 SAFE_POINT_EXT(!assemblyId.isEmpty(), setError(tr("Invalid assembly ID")), ); in CalculateCoveragePerBaseOnRegionTask()
56 …QScopedPointer<U2DbiIterator<U2AssemblyRead>> readsIterator(assemblyDbi->getReads(assemblyId, regi… in run()
137 assemblyId(_assemblyId), in CalculateCoveragePerBaseTask()
140 SAFE_POINT_EXT(!assemblyId.isEmpty(), setError(tr("Invalid assembly ID")), ); in CalculateCoveragePerBaseTask()
148 getLengthTask = new GetAssemblyLengthTask(dbiRef, assemblyId); in prepare()
161 res.append(new CalculateCoveragePerBaseOnRegionTask(dbiRef, assemblyId, region)); in onSubTaskFinished()
194 …lengthAttribute = U2AttributeUtils::findIntegerAttribute(attributeDbi, assemblyId, U2BaseAttribute… in run()
H A DExportCoverageTask.cpp56 const U2Assembly assembly = assemblyDbi->getAssemblyObject(assemblyId, stateInfo); in run()
61 ExportCoverageTask::ExportCoverageTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const Ex… in ExportCoverageTask() argument
64 assemblyId(assemblyId), in ExportCoverageTask()
70 SAFE_POINT_EXT(!assemblyId.isEmpty(), setError(tr("Invalid assembly ID")), ); in ExportCoverageTask()
77 getAssemblyNameTask = new GetAssemblyVisibleNameTask(dbiRef, assemblyId); in prepare()
96 calculateTask = new CalculateCoveragePerBaseTask(dbiRef, assemblyId); in prepare()
156 : ExportCoverageTask(dbiRef, assemblyId, settings, TaskFlags_FOSE_COSC) { in ExportCoverageHistogramTask()
196 …ask::ExportCoveragePerBaseTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const ExportCov… in ExportCoveragePerBaseTask() argument
197 : ExportCoverageTask(dbiRef, assemblyId, settings) { in ExportCoveragePerBaseTask()
258 …sk::ExportCoverageBedgraphTask(const U2DbiRef &dbiRef, const U2DataId &assemblyId, const ExportCov… in ExportCoverageBedgraphTask() argument
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/
H A DAlignedAssemblyOrExcuse.java36 private final int assemblyId; field in AlignedAssemblyOrExcuse
45 return assemblyId; in getAssemblyId()
70 public AlignedAssemblyOrExcuse( final int assemblyId, final String errorMessage ) { in AlignedAssemblyOrExcuse() argument
71 this.assemblyId = assemblyId; in AlignedAssemblyOrExcuse()
84 this.assemblyId = assemblyId; in AlignedAssemblyOrExcuse()
92 this.assemblyId = input.readInt(); in AlignedAssemblyOrExcuse()
209 output.writeInt(assemblyId); in serialize()
261 public static String formatContigName( final int assemblyId, final int contigIdx ) { in formatContigName() argument
262 return formatAssemblyID(assemblyId) + ":" + formatContigID(contigIdx); in formatContigName()
265 public static String formatAssemblyID( final int assemblyId ) { in formatAssemblyID() argument
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/dports/biology/ugene/ugene-40.1/src/plugins/dbi_bam/src/
H A DSamtoolsBasedDbi.h74 …SamtoolsBasedReadsIterator(int assemblyId, const U2Region &r, SamtoolsBasedDbi &dbi, const QByteAr…
83 int assemblyId;
107 virtual qint64 countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
108 …virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2DataId &assemblyId, const U2Region &r, U2O…
109 virtual qint64 getMaxEndPos(const U2DataId &assemblyId, U2OpStatus &os);
110 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByName(const U2DataId &assemblyId, const QByteArray…
112 static int toSamtoolsId(const U2DataId &assemblyId, U2OpStatus &os);
117 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByRow(const U2DataId &assemblyId, const U2Region &r…
118 virtual qint64 getMaxPackedRow(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
123 U2Region getCorrectRegion(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
H A DSamtoolsBasedDbi.cpp385 int assemblyId, in SamtoolsBasedReadsIterator() argument
389 : U2DbiIterator<U2AssemblyRead>(), assemblyId(assemblyId), dbi(_dbi), nameFilter(_nameFilter) { in SamtoolsBasedReadsIterator()
540 bam_fetch(bam, idx, assemblyId, startPos, endPos, data, bamFetchFunction); in fetchNextChunk()
554 int dbId = assemblyId.toInt(&ok); in toSamtoolsId()
592 int id = SamtoolsBasedAssemblyDbi::toSamtoolsId(assemblyId, os); in countReads()
597 U2Region targetReg = this->getCorrectRegion(assemblyId, r, os); in countReads()
606 int id = SamtoolsBasedAssemblyDbi::toSamtoolsId(assemblyId, os); in getReads()
608 U2Region targetReg = this->getCorrectRegion(assemblyId, r, os); in getReads()
623 int id = SamtoolsBasedAssemblyDbi::toSamtoolsId(assemblyId, os); in getReadsByName()
630 int id = SamtoolsBasedAssemblyDbi::toSamtoolsId(assemblyId, os); in getMaxEndPos()
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H A DDbi.h142 virtual qint64 countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
144 …virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2DataId &assemblyId, const U2Region &r, U2O…
146 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByRow(const U2DataId &assemblyId, const U2Region &r…
148 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByName(const U2DataId &assemblyId, const QByteArray…
150 virtual qint64 getMaxPackedRow(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
152 virtual qint64 getMaxEndPos(const U2DataId &assemblyId, U2OpStatus &os);
159 qint64 getMaxReadLength(const U2DataId &assemblyId, const U2Region &r);
H A DDbi.cpp595 if (dbi.getEntityTypeById(assemblyId) != U2Type::Assembly) { in countReads()
602 q.bindDataId(1, assemblyId); in countReads()
623 if (dbi.getEntityTypeById(assemblyId) != U2Type::Assembly) { in getReads()
631 q.bindDataId(1, assemblyId); in getReads()
697 if (dbi.getEntityTypeById(assemblyId) != U2Type::Assembly) { in getMaxPackedRow()
704 q.bindDataId(1, assemblyId); in getMaxPackedRow()
725 if (dbi.getEntityTypeById(assemblyId) != U2Type::Assembly) { in getReadsByRow()
733 q.bindDataId(1, assemblyId); in getReadsByRow()
772 if (dbi.getEntityTypeById(assemblyId) != U2Type::Assembly) { in getMaxEndPos()
779 q.bindDataId(1, assemblyId); in getMaxEndPos()
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H A DHeader.cpp45 return assemblyId; in getAssemblyId()
68 void Header::Reference::setAssemblyId(const QByteArray &assemblyId) { in setAssemblyId() argument
69 this->assemblyId = assemblyId; in setAssemblyId()
/dports/biology/jalview/jalview/src/jalview/datamodel/
H A DGeneLocus.java51 public GeneLocus(String speciesId, String assemblyId, String chromosomeId, in GeneLocus() argument
54 super(speciesId, assemblyId, chromosomeId, mapping); in GeneLocus()
64 public GeneLocus(String speciesId, String assemblyId, String chromosomeId) in GeneLocus() argument
66 this(speciesId, assemblyId, chromosomeId, null); in GeneLocus()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/util/
H A DAssemblyAdapter.h38 AssemblyAdapter(const U2DataId &assemblyId, const AssemblyCompressor *compressor) in AssemblyAdapter() argument
39 : assemblyId(assemblyId), compressor(compressor) { in AssemblyAdapter()
70 U2DataId assemblyId;
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/
H A Dcn3d_cache.cpp148 const string& uid, int mmdbID, EModel_type modelType, int assemblyId = 0) in GetStructureViaHTTPAndAddToCache() argument
152 if (assemblyId == 0) { in GetStructureViaHTTPAndAddToCache()
199 args += "&buidx=" + NStr::IntToString(assemblyId); in GetStructureViaHTTPAndAddToCache()
243 …LoadStructureViaCache(const std::string& uid, ncbi::objects::EModel_type modelType, int assemblyId) in LoadStructureViaCache() argument
270 mime = GetStructureViaHTTPAndAddToCache(uid, mmdbID, modelType, assemblyId); in LoadStructureViaCache()
275 …LoadStructureViaCache(const std::string& uid, ncbi::objects::EModel_type modelType, int assemblyId, in LoadStructureViaCache() argument
278 CRef < CNcbi_mime_asn1 > mime(LoadStructureViaCache(uid, modelType, assemblyId)); in LoadStructureViaCache()
H A Dcn3d_cache.hpp69 …oadStructureViaCache(const std::string& uid, ncbi::objects::EModel_type modelType, int assemblyId,
72 …oadStructureViaCache(const std::string& uid, ncbi::objects::EModel_type modelType, int assemblyId);
/dports/lang/mono/mono-5.10.1.57/mcs/class/referencesource/System.ServiceModel/System/ServiceModel/ComIntegration/
H A DServiceInfo.cs322 internal Type[] GetTypes(Guid assemblyId) in GetTypes() argument
325 udts.TryGetValue(assemblyId, out ret); in GetTypes()
333 internal void AddUdt(Type udt, Guid assemblyId) in AddUdt() argument
335 if (!udts.ContainsKey(assemblyId)) in AddUdt()
336 udts[assemblyId] = new List<Type>(); in AddUdt()
338 if (!udts[assemblyId].Contains(udt)) in AddUdt()
339 udts[assemblyId].Add(udt); in AddUdt()
/dports/biology/ugene/ugene-40.1/src/plugins/workflow_designer/src/debug_messages_translation/
H A DAssemblyMessageTranslator.cpp58 const U2DataId assemblyId = assemblyRef.entityId; in getTranslation() local
59 const qint64 assemblyLength = dbi->getMaxEndPos(assemblyId, os) + 1; in getTranslation()
63 const qint64 countOfReads = dbi->countReads(assemblyId, wholeAssembly, os); in getTranslation()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/assembly/
H A DSingleTableAssemblyAdapter.cpp42 SingleTableAssemblyAdapter::SingleTableAssemblyAdapter(SQLiteDbi *_dbi, const U2DataId &assemblyId,… in SingleTableAssemblyAdapter() argument
43 : SQLiteAssemblyAdapter(assemblyId, compressor, db) { in SingleTableAssemblyAdapter()
47 readsTable = getReadsTableName(assemblyId, tablePrefix, tableSuffix); in SingleTableAssemblyAdapter()
53 QString SingleTableAssemblyAdapter::getReadsTableName(const U2DataId &assemblyId, char prefix, cons… in getReadsTableName() argument
54 …return QString("AssemblyRead_%1%2_%3").arg(prefix).arg(U2DbiUtils::toDbiId(assemblyId)).arg(suffix… in getReadsTableName()
216 SQLiteObjectDbi::incrementVersion(assemblyId, db, os); in removeReads()
223 SQLiteObjectDbi::incrementVersion(assemblyId, db, os); in dropReadsTables()
H A DRTreeAssemblyAdapter.cpp40 RTreeAssemblyAdapter::RTreeAssemblyAdapter(SQLiteDbi *_dbi, const U2DataId &assemblyId, const Assem… in RTreeAssemblyAdapter() argument
41 : SQLiteAssemblyAdapter(assemblyId, compressor, db) { in RTreeAssemblyAdapter()
43 readsTable = QString("AssemblyRead_R%1").arg(U2DbiUtils::toDbiId(assemblyId)); in RTreeAssemblyAdapter()
194 SQLiteObjectDbi::incrementVersion(assemblyId, db, os); in removeReads()
201 SQLiteObjectDbi::incrementVersion(assemblyId, db, os); in dropReadsTables()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/util/
H A DMysqlSingleTableAssemblyAdapter.cpp44 const U2DataId &assemblyId, in MysqlSingleTableAssemblyAdapter() argument
50 : MysqlAssemblyAdapter(assemblyId, compressor, db), in MysqlSingleTableAssemblyAdapter()
52 readsTable(getReadsTableName(assemblyId, tablePrefix, tableSuffix)), in MysqlSingleTableAssemblyAdapter()
234 MysqlObjectDbi::incrementVersion(assemblyId, db, os); in removeReads()
241 MysqlObjectDbi::incrementVersion(assemblyId, db, os); in dropReadsTables()
279 QString MysqlSingleTableAssemblyAdapter::getReadsTableName(const U2DataId &assemblyId, char prefix,… in getReadsTableName() argument
280 …return QString("AssemblyRead_%1%2_%3").arg(prefix).arg(U2DbiUtils::toDbiId(assemblyId)).arg(suffix… in getReadsTableName()

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