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Searched refs:getEntityRef (Results 1 – 25 of 157) sorted by relevance

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/dports/biology/ugene/ugene-40.1/src/plugins/workflow_designer/src/tasks/
H A DSequenceQualityTrimTask.cpp84 const U2DbiRef dbiRef = settings.sequenceObject->getEntityRef().dbiRef; in cloneSequence()
89 const U2DbiRef dbiRef = settings.sequenceObject->getEntityRef().dbiRef; in cloneChromatogram()
90 …ramUtils::getChromatogramIdByRelatedSequenceId(stateInfo, settings.sequenceObject->getEntityRef()); in cloneChromatogram()
107 dbRelation.id = trimmedChromatogramObject->getEntityRef().entityId; in restoreRelation()
109 dbRelation.referencedObject = trimmedSequenceObject->getEntityRef().entityId; in restoreRelation()
113 DbiConnection connection(settings.sequenceObject->getEntityRef().dbiRef, stateInfo); in restoreRelation()
H A DRenameChromosomeInVariationTask.cpp53 DbiConnection connection(objects.first()->getEntityRef().dbiRef, stateInfo); in run()
61 …U2VariantTrack variantTrack = variantDbi->getVariantTrack(object->getEntityRef().entityId, stateIn… in run()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/mca_reads/
H A DMcaAlternativeMutationsWidget.cpp72 U2UseCommonUserModStep userModStep(mcaObject->getEntityRef(), os); in sl_updateAlternativeMutations()
97 …QScopedPointer<DbiConnection> con(MaDbiUtils::getCheckedConnection(mcaObject->getEntityRef().dbiRe… in updateValuesFromDb()
104 …auto objectAttributes = attributeDbi->getObjectAttributes(mcaObject->getEntityRef().entityId, name… in updateValuesFromDb()
112 mcaDbiObj.dbiId = mcaObject->getEntityRef().dbiRef.dbiId; in updateValuesFromDb()
113 mcaDbiObj.id = mcaObject->getEntityRef().entityId; in updateValuesFromDb()
141 …QScopedPointer<DbiConnection> con(MaDbiUtils::getCheckedConnection(mcaObject->getEntityRef().dbiRe… in updateDb()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/
H A DUndoRedoFramework.cpp83 DbiConnection con(maObj->getEntityRef().dbiRef, os); in checkUndoRedoEnabled()
89 bool enableUndo = objDbi->canUndo(maObj->getEntityRef().entityId, os); in checkUndoRedoEnabled()
91 bool enableRedo = objDbi->canRedo(maObj->getEntityRef().entityId, os); in checkUndoRedoEnabled()
105 U2EntityRef msaRef = maObj->getEntityRef(); in sl_undo()
128 U2EntityRef msaRef = maObj->getEntityRef(); in sl_redo()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/gobjects/
H A DMultipleChromatogramAlignmentObject.cpp71 DbiConnection srcCon(getEntityRef().dbiRef, os); in clone()
77 …U2Sequence referenceCopy = U2SequenceUtils::copySequence(getReferenceObj()->getEntityRef(), dstDbi… in clone()
83 obj.id = clonedObject->getEntityRef().entityId; in clone()
98 DbiConnection con(getEntityRef().dbiRef, status); in getReferenceObj()
101 … U2AttributeUtils::findByteArrayAttribute(con.dbi->getAttributeDbi(), getEntityRef().entityId, MCA… in getReferenceObj()
166 … getReferenceObj()->replaceRegion(getEntityRef().entityId, regionsToDelete[i], DNASequence(), os); in deleteColumnsWithGaps()
183 U2EntityRef entityRef = getEntityRef(); in trimRow()
243 McaDbiUtils::replaceCharactersInRow(getEntityRef(), modifiedRowId, newCharList, os); in updateAlternativeMutations()
H A DUnloadedObject.cpp45 …UnloadedObject *cln = new UnloadedObject(getGObjectName(), getLoadedObjectType(), getEntityRef(), … in clone()
60 entityRef = obj->getEntityRef(); in UnloadedObjectInfo()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/datatype/
H A DAnnotation.cpp71 U2FeatureUtils::updateFeatureName(id, name, parentObject->getEntityRef().dbiRef, os); in setName()
85 U2FeatureUtils::updateFeatureType(id, type, parentObject->getEntityRef().dbiRef, os); in setType()
118 …cation(id, parentObject->getRootFeatureId(), newLocation, parentObject->getEntityRef().dbiRef, os); in setStrand()
139 …cation(id, parentObject->getRootFeatureId(), newLocation, parentObject->getEntityRef().dbiRef, os); in setLocationOperator()
157 …eLocation(id, parentObject->getRootFeatureId(), location, parentObject->getEntityRef().dbiRef, os); in setLocation()
187 …cation(id, parentObject->getRootFeatureId(), newLocation, parentObject->getEntityRef().dbiRef, os); in updateRegions()
223 …U2FeatureUtils::addFeatureKey(id, U2FeatureKey(q.name, q.value), parentObject->getEntityRef().dbiR… in addQualifier()
237 …U2FeatureUtils::removeFeatureKey(id, U2FeatureKey(q.name, q.value), parentObject->getEntityRef().d… in removeQualifier()
261 …FeatureKey(id, U2FeatureKey(U2FeatureKeyCase, QString()), parentObject->getEntityRef().dbiRef, os); in setCaseAnnotation()
263 …FeatureKey(id, U2FeatureKey(U2FeatureKeyCase, QString()), parentObject->getEntityRef().dbiRef, os); in setCaseAnnotation()
[all …]
H A DAnnotationGroup.cpp113 DbiOperationsBlock opBlock(parentObject->getEntityRef().dbiRef, os); in addAnnotations()
117 …onDataToFeatures(d, parentObject->getRootFeatureId(), id, parentObject->getEntityRef().dbiRef, os); in addAnnotations()
160 U2FeatureUtils::removeFeatures(annotationsIds, parentObject->getEntityRef().dbiRef, os); in removeAnnotations()
184 U2FeatureUtils::removeFeature(g->id, parentObject->getEntityRef().dbiRef, os); in removeSubgroup()
202 U2FeatureUtils::updateFeatureName(id, newName, parentObject->getEntityRef().dbiRef, os); in setName()
246 const U2DbiRef dbiRef = parentObject->getEntityRef().dbiRef; in getSubgroup()
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/blast_plus/align_worker_subtasks/
H A DComposeResultSubTask.cpp100 …con.dbi->getObjectDbi()->setObjectRank(referenceSequenceObject->getEntityRef().entityId, U2DbiObje… in run()
208 …on.dbi->getObjectDbi()->setParent(mcaObject->getEntityRef().entityId, referenceSequenceObject->get… in createAlignmentAndAnnotations()
214 obj.id = mcaObject->getEntityRef().entityId; in createAlignmentAndAnnotations()
217 attribute.value = referenceSequenceObject->getEntityRef().entityId; in createAlignmentAndAnnotations()
224 annotations = storage->getDataHandler(annsObject->getEntityRef()); in createAlignmentAndAnnotations()
232 U2DataId id = mcaObject->getEntityRef().entityId; in enlargeReferenceByGaps()
309 …f = ChromatogramUtils::getChromatogramIdByRelatedSequenceId(stateInfo, readObject->getEntityRef()); in getReadChromatogram()
H A DBlastReadsSubTask.cpp365 msa = storage->getDataHandler(msaObj->getEntityRef()); in createAlignment()
395 settings->msaRef = msaObject->getEntityRef(); in createSettings()
396 settings->firstSequenceRef = U2EntityRef(msaObject->getEntityRef().dbiRef, referenceId); in createSettings()
397 settings->secondSequenceRef = U2EntityRef(msaObject->getEntityRef().dbiRef, readId); in createSettings()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/realign_to_alignment/
H A DRealignSequencesInAlignmentTask.cpp50 msaObject = msaObjectToClone->clone(msaObjectToClone->getEntityRef().dbiRef, stateInfo); in RealignSequencesInAlignmentTask()
89 U2UseCommonUserModStep modStep(originalMsaObject->getEntityRef(), stateInfo); in report()
98 DbiConnection con(msaObject->getEntityRef().dbiRef, stateInfo); in report()
101 con.dbi->getObjectDbi()->removeObject(msaObject->getEntityRef().entityId, true, stateInfo); in report()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Lang/src/model/
H A DDbiDataStorage.cpp159 U2EntityRef entityRef = sequenceObject->getEntityRef(); in putSequence()
160 if (sequenceObject->getEntityRef().dbiRef != dbiHandle->getDbiRef()) { in putSequence()
163 entityRef = clonedSequenceObject->getEntityRef(); in putSequence()
183 …SharedDbiDataHandler handler(new DbiDataHandler(obj->getEntityRef(), connection->dbi->getObjectDbi… in putAlignment()
196 U2EntityRef ent = obj.getEntityRef(); in putAnnotationTable()
212 U2EntityRef entityRef = annTable->getEntityRef(); in putAnnotationTable()
213 if (annTable->getEntityRef().dbiRef != dbiHandle->getDbiRef()) { in putAnnotationTable()
216 entityRef = clonedTable->getEntityRef(); in putAnnotationTable()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/tasks/
H A DAddSequencesToAlignmentTask.cpp75 U2UseCommonUserModStep modStep(maObj->getEntityRef(), stateInfo); in run()
119 U2EntityRef entityRef = maObj->getEntityRef(); in createMsaRowsFromResultSequenceList()
146 const U2EntityRef &entityRef = maObj->getEntityRef(); in addRowsToAlignment()
161 const U2EntityRef &entityRef = maObj->getEntityRef(); in updateAlphabet()
H A DCreateAnnotationTask.cpp72 DbiOperationsBlock opBlock(annotationTableObject->getEntityRef().dbiRef, stateInfo); in run()
76 const U2DbiRef dbiRef = annotationTableObject->getEntityRef().dbiRef; in run()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_assembly/
H A DAddReadsToDocumentTask.cpp55 seqNameById[seqObj->getEntityRef().entityId] = seqObj->getGObjectName(); in run()
57 objectsGuard.objects.append(seqObj->getEntityRef().entityId); in run()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Lang/src/library/script/
H A DSequencePrototype.cpp148 …equence clonedSeq = U2SequenceUtils::copySequence(seqObj->getEntityRef(), seqObj->getEntityRef().d… in copySequence()
151 U2EntityRef newEnt(seqObj->getEntityRef().dbiRef, clonedSeq.id); in copySequence()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/ace/
H A DCloneAssemblyWithReferenceToDbiTask.cpp86 … = con.dbi->getAssemblyDbi()->getAssemblyObject(clonedAssemblyObject->getEntityRef().entityId, sta… in run()
88 … = con.dbi->getSequenceDbi()->getSequenceObject(clonedSequenceObject->getEntityRef().entityId, sta… in run()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Gui/src/util/project/
H A DDocumentFolders.cpp77 U2DataId id = obj->getEntityRef().entityId; in init()
365 objectsIds[obj->getEntityRef().entityId] = obj; in addObject()
368 lastUpdate.objectIdFolders[obj->getEntityRef().entityId] = path; in addObject()
372 int count1 = objectsIds.remove(obj->getEntityRef().entityId); in removeObject()
375 int count4 = lastUpdate.objectIdFolders.remove(obj->getEntityRef().entityId); in removeObject()
383 const U2DataId objId = obj->getEntityRef().entityId; in moveObject()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/
H A DMcaEditorSequenceArea.cpp145 U2DataId id = mcaEditor->getMaObject()->getEntityRef().entityId; in adjustReferenceLength()
306 U2UseCommonUserModStep userModStep(editor->getMaObject()->getEntityRef(), os); in sl_removeColumnsOfGaps()
352 U2UseCommonUserModStep userModStep(mcaObj->getEntityRef(), os); in trimRowEnd()
426 U2UseCommonUserModStep userModStep(maObj->getEntityRef(), os); in insertChar()
439 …ref->replaceRegion(maObj->getEntityRef().entityId, region, DNASequence(QByteArray(1, U2Msa::GAP_CH… in insertChar()
H A DMcaEditorStatusBar.cpp128 …QScopedPointer<DbiConnection> con(MaDbiUtils::getCheckedConnection(maObject->getEntityRef().dbiRef… in updateMutationsLabel()
135 …auto objectAttributes = attributeDbi->getObjectAttributes(maObject->getEntityRef().entityId, attri… in updateMutationsLabel()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/dbi/
H A DDbiDocumentFormat.cpp134 …, relatedObject->getGObjectName(), relatedObject->getGObjectType(), relatedObject->getEntityRef()); in prepareObjects()
179 U2DbiRef srcDbiRef = object->getEntityRef().dbiRef; in storeDocument()
189 …url, resultObject->getGObjectName(), resultObject->getGObjectType(), resultObject->getEntityRef()); in storeDocument()
/dports/net-im/matterhorn/matterhorn-50200.13.0/_cabal_deps/hxt-9.3.1.18/src/Text/XML/HXT/DOM/
H A DXmlNode.hs80 getEntityRef :: a -> Maybe String
230 getEntityRef (XEntityRef e) = Just e function
231 getEntityRef _ = Nothing function
380 getEntityRef = getEntityRef . getNode function
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/align_to_alignment/
H A DAlignSequencesToAlignmentTask.cpp85 U2EntityRef seqRef(curObj->getEntityRef().dbiRef, row->getRowDbInfo().sequenceId); in extractSequencesFromObjects()
93 sequenceRefs << dnaObj->getEntityRef(); in extractSequencesFromObjects()
220 settings.msaRef = maObjPointer->getEntityRef(); in AlignSequencesToAlignmentTask()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Gui/src/util/
H A DImportSequenceFromRawDataTask.h37 const U2EntityRef &getEntityRef() const;
H A DImportSequenceFromRawDataTask.cpp42 const U2EntityRef &ImportSequenceFromRawDataTask::getEntityRef() const { in getEntityRef() function in U2::ImportSequenceFromRawDataTask

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