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Searched refs:U2Assembly (Results 1 – 25 of 35) sorted by relevance

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/dports/biology/ugene/ugene-40.1/src/plugins/dbi_bam/src/
H A DConvertToSQLiteTask.h52 QList<U2Assembly> getAssemblies() const;
70 …void updateReferenceLengthAttribute(int length, const U2Assembly &assembly, U2AttributeDbi *attrib…
71 …void updateReferenceMd5Attribute(const QByteArray &md5, const U2Assembly &assembly, U2AttributeDbi…
72 …void updateReferenceSpeciesAttribute(const QByteArray &species, const U2Assembly &assembly, U2Attr…
73 …void updateReferenceUriAttribute(const QString &uri, const U2Assembly &assembly, U2AttributeDbi *a…
75 …nfoMaxProwAttribute(const U2AssemblyReadsImportInfo &importInfo, const U2Assembly &assembly, U2Att…
76 …ReadsCountAttribute(const U2AssemblyReadsImportInfo &importInfo, const U2Assembly &assembly, U2Att…
77 …verageStatAttribute(const U2AssemblyReadsImportInfo &importInfo, const U2Assembly &assembly, U2Att…
90 QList<U2Assembly> importedAssemblies;
H A DConvertToSQLiteTask.cpp488 QList<U2Assembly> ConvertToSQLiteTask::getAssemblies() const { in getAssemblies()
560 const U2Assembly &assembly = importers[referenceId]->getAssembly(); in updateAttributes()
605 U2Assembly assembly; in importMappedSortedReads()
679 U2Assembly assembly; in importUnmappedSortedReads()
725 U2Assembly assembly; in createAssemblyObjectForUnsortedReads()
779 void ConvertToSQLiteTask::updateReferenceLengthAttribute(int length, const U2Assembly &assembly, U2… in updateReferenceLengthAttribute()
793 void ConvertToSQLiteTask::updateReferenceMd5Attribute(const QByteArray &md5, const U2Assembly &asse… in updateReferenceMd5Attribute()
809 …Task::updateReferenceSpeciesAttribute(const QByteArray &species, const U2Assembly &assembly, U2Att… in updateReferenceSpeciesAttribute()
825 void ConvertToSQLiteTask::updateReferenceUriAttribute(const QString &uri, const U2Assembly &assembl… in updateReferenceUriAttribute()
841 …nfoMaxProwAttribute(const U2AssemblyReadsImportInfo &importInfo, const U2Assembly &assembly, U2Att… in updateImportInfoMaxProwAttribute()
[all …]
H A DSamtoolsBasedDbi.cpp561 U2Assembly SamtoolsBasedAssemblyDbi::getAssemblyObject(const U2DataId &id, U2OpStatus &os) { in getAssemblyObject()
564 U2Assembly()); in getAssemblyObject()
567 SAFE_POINT(nullptr != header, "NULL BAM header", U2Assembly()); in getAssemblyObject()
571 U2Assembly()); in getAssemblyObject()
574 CHECK_OP(os, U2Assembly()); in getAssemblyObject()
575 CHECK(dbId < header->n_targets, U2Assembly()); in getAssemblyObject()
577 U2Assembly result; in getAssemblyObject()
H A DBAMDbiPlugin.cpp293 QList<U2Assembly> assemblies = convertTask->getAssemblies(); in initCloneObjectTasks()
294 foreach (const U2Assembly &assembly, assemblies) { in initCloneObjectTasks()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/util/
H A DAssemblyImporter.h36 AssemblyImporter(const U2DbiRef &dbiRef, U2Assembly &assembly, U2OpStatus &os);
39 void createAssembly(const U2DbiRef &dbiRef, const QString &folder, U2Assembly &assembly);
40 …rator<U2AssemblyRead> *readsIterator, U2AssemblyReadsImportInfo &importInfo, U2Assembly &assembly);
46 const U2Assembly &getAssembly() const;
52 U2Assembly assembly;
H A DAssemblyImporter.cpp37 AssemblyImporter::AssemblyImporter(const U2DbiRef &dbiRef, U2Assembly &assembly, U2OpStatus &os) in AssemblyImporter()
48 void AssemblyImporter::createAssembly(const U2DbiRef &dbiRef, const QString &folder, U2Assembly &as… in createAssembly()
53 …ator<U2AssemblyRead> *readsIterator, U2AssemblyReadsImportInfo &importInfo, U2Assembly &assembly) { in createAssembly()
111 const U2Assembly &AssemblyImporter::getAssembly() const { in getAssembly()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/
H A DMysqlAssemblyDbi.h44 virtual U2Assembly getAssemblyObject(const U2DataId &assemblyId, U2OpStatus &os);
84 …virtual void createAssemblyObject(U2Assembly &assembly, const QString &folder, U2DbiIterator<U2Ass…
90 virtual void finalizeAssemblyObject(U2Assembly &assembly, U2OpStatus &os);
103 virtual void updateAssemblyObject(U2Assembly &, U2OpStatus &os);
131 void correctAssemblyType(U2Assembly &assembly, U2OpStatus &os);
H A DMysqlAssemblyDbi.cpp108 U2Assembly MysqlAssemblyDbi::getAssemblyObject(const U2DataId &assemblyId, U2OpStatus &os) { in getAssemblyObject()
109 U2Assembly res; in getAssemblyObject()
201 void MysqlAssemblyDbi::createAssemblyObject(U2Assembly &assembly, in createAssemblyObject()
247 void MysqlAssemblyDbi::finalizeAssemblyObject(U2Assembly &assembly, U2OpStatus &os) { in finalizeAssemblyObject()
273 void MysqlAssemblyDbi::updateAssemblyObject(U2Assembly &assembly, U2OpStatus &os) { in updateAssemblyObject()
330 void MysqlAssemblyDbi::correctAssemblyType(U2Assembly &assembly, U2OpStatus &os) { in correctAssemblyType()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/dbi/
H A DU2AssemblyDbi.h101 virtual U2Assembly getAssemblyObject(const U2DataId &id, U2OpStatus &os) = 0;
163 …virtual void createAssemblyObject(U2Assembly &assembly, const QString &folder, U2DbiIterator<U2Ass…
172 virtual void finalizeAssemblyObject(U2Assembly &assembly, U2OpStatus &os) = 0;
186 virtual void updateAssemblyObject(U2Assembly &assembly, U2OpStatus &os) = 0;
H A DU2AbstractDbi.h273 …virtual void createAssemblyObject(U2Assembly &, const QString &, U2DbiIterator<U2AssemblyRead> *, … in createAssemblyObject() argument
277 virtual void finalizeAssemblyObject(U2Assembly & /*assembly*/, U2OpStatus &os) { in finalizeAssemblyObject() argument
285 virtual void updateAssemblyObject(U2Assembly &, U2OpStatus &os) { in updateAssemblyObject() argument
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/
H A DSQLiteAssemblyDbi.h42 virtual U2Assembly getAssemblyObject(const U2DataId &assemblyId, U2OpStatus &os);
81 …virtual void createAssemblyObject(U2Assembly &assembly, const QString &folder, U2DbiIterator<U2Ass…
88 virtual void finalizeAssemblyObject(U2Assembly &assembly, U2OpStatus &os);
101 virtual void updateAssemblyObject(U2Assembly &, U2OpStatus &os);
H A DSQLiteAssemblyDbi.cpp103 U2Assembly SQLiteAssemblyDbi::getAssemblyObject(const U2DataId &assemblyId, U2OpStatus &os) { in getAssemblyObject()
104 U2Assembly res; in getAssemblyObject()
197 void SQLiteAssemblyDbi::createAssemblyObject(U2Assembly &assembly, const QString &folder, U2DbiIter… in createAssemblyObject()
225 void SQLiteAssemblyDbi::finalizeAssemblyObject(U2Assembly &assembly, U2OpStatus &os) { in finalizeAssemblyObject()
246 void SQLiteAssemblyDbi::updateAssemblyObject(U2Assembly &assembly, U2OpStatus &os) { in updateAssemblyObject()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/datatype/
H A DU2Assembly.h227 class U2CORE_EXPORT U2Assembly : public U2Object {
229 U2Assembly() { in U2Assembly() function
231 U2Assembly(U2DataId id, QString dbId, qint64 version) in U2Assembly() function
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/ace/
H A DCloneAssemblyWithReferenceToDbiTask.h36 CloneAssemblyWithReferenceToDbiTask(const U2Assembly &assembly,
46 U2Assembly assembly;
H A DConvertAceToSqliteTask.h44 QMap<U2Sequence, U2Assembly> getImportedObjects() const;
59 QMap<int, U2Assembly> assemblies;
H A DConvertAceToSqliteTask.cpp124 QMap<U2Sequence, U2Assembly> ConvertAceToSqliteTask::getImportedObjects() const { in getImportedObjects()
125 QMap<U2Sequence, U2Assembly> importedObjects; in getImportedObjects()
151 U2Assembly assembly; in importAssemblies()
248 const U2Assembly &assembly = assemblies[assemblyNum]; in updateAttributeDbi()
H A DCloneAssemblyWithReferenceToDbiTask.cpp38 CloneAssemblyWithReferenceToDbiTask::CloneAssemblyWithReferenceToDbiTask(const U2Assembly &assembly, in CloneAssemblyWithReferenceToDbiTask()
86 …U2Assembly clonedAssembly = con.dbi->getAssemblyDbi()->getAssemblyObject(clonedAssemblyObject->get… in run()
H A DAceImporter.cpp125 const QMap<U2Sequence, U2Assembly> importedObjects = convertTask->getImportedObjects(); in initCloneObjectTasks()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_assembly/
H A DAssemblyModel.h71 void setAssembly(U2AssemblyDbi *dbi, const U2Assembly &assm);
72 U2Assembly getAssembly() { in getAssembly()
143 U2Assembly assembly;
/dports/biology/ugene/ugene-40.1/src/plugins/genome_aligner/src/
H A DGenomeAlignerIO.h171 GenomeAlignerDbiReader(U2AssemblyDbi *rDbi, U2Assembly assembly);
179 U2Assembly assembly;
206 U2Assembly assembly;
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Lang/src/model/
H A DDbiDataStorage.cpp117 U2Assembly assembly = dbi->getAssemblyObject(objectId, os); in getObject()
120 return new U2Assembly(assembly); in getObject()
319 QScopedPointer<U2Assembly> assembly(dynamic_cast<U2Assembly *>(storage->getObject(handler, 4))); in getAssemblyObject()
/dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/dbi/assembly/
H A DAssemblyDbiUnitTests.cpp130 U2Assembly assembly = assemblyDbi->getAssemblyObject(id, os); in Test()
143 const U2Assembly &assembly = assemblyDbi->getAssemblyObject(invalidId, os); in Test()
432 U2Assembly assembly; in Test()
439 U2Assembly res = assemblyDbi->getAssemblyObject(assembly.id, os); in Test()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/util/
H A DSqliteUpgraderFrom_1_13_To_1_25.cpp70 U2Assembly assembly = assemblyDbi->getAssemblyObject(id, os); in upgradeCoverageAttribute()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/util/upgraders/
H A DMysqlUpgraderFrom_1_24_To_1_25.cpp78 U2Assembly assembly = assemblyDbi->getAssemblyObject(id, os); in upgradeCoverageAttribute()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/tasks/
H A DConvertAssemblyToSamTask.cpp111 U2Assembly assembly = handle->dbi->getAssemblyDbi()->getAssemblyObject(id, stateInfo); in run()

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