/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/ |
H A D | MysqlAssemblyDbi.cpp | 78 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() [all …]
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H A D | MysqlAssemblyDbi.h | 44 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); [all …]
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/ |
H A D | SQLiteAssemblyDbi.h | 42 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 [all …]
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H A D | SQLiteAssemblyDbi.cpp | 72 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() [all …]
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/dbi/ |
H A D | U2AssemblyDbi.h | 115 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; [all …]
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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() 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()
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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() 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
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H A D | ExportCoverageTask.h | 70 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…
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H A D | CalculateCoveragePerBaseTask.cpp | 34 …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()
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H A D | ExportCoverageTask.cpp | 56 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 [all …]
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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 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 [all …]
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/dports/biology/ugene/ugene-40.1/src/plugins/dbi_bam/src/ |
H A D | SamtoolsBasedDbi.h | 74 …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);
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H A D | SamtoolsBasedDbi.cpp | 385 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() [all …]
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H A D | Dbi.h | 142 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);
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H A D | Dbi.cpp | 595 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() [all …]
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H A D | Header.cpp | 45 return assemblyId; in getAssemblyId() 68 void Header::Reference::setAssemblyId(const QByteArray &assemblyId) { in setAssemblyId() argument 69 this->assemblyId = assemblyId; in setAssemblyId()
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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() 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()
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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() argument 39 : assemblyId(assemblyId), compressor(compressor) { in AssemblyAdapter() 70 U2DataId assemblyId;
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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() 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()
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H A D | cn3d_cache.hpp | 69 …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);
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/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() 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()
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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 59 const qint64 assemblyLength = dbi->getMaxEndPos(assemblyId, os) + 1; in getTranslation() 63 const qint64 countOfReads = dbi->countReads(assemblyId, wholeAssembly, os); in getTranslation()
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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() 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()
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H A D | RTreeAssemblyAdapter.cpp | 40 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()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/util/ |
H A D | MysqlSingleTableAssemblyAdapter.cpp | 44 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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