/dports/biology/ugene/ugene-40.1/src/plugins/workflow_designer/src/tasks/ |
H A D | SequenceQualityTrimTask.cpp | 84 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 D | RenameChromosomeInVariationTask.cpp | 53 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 D | McaAlternativeMutationsWidget.cpp | 72 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 D | UndoRedoFramework.cpp | 83 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 D | MultipleChromatogramAlignmentObject.cpp | 71 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 D | UnloadedObject.cpp | 45 …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 D | Annotation.cpp | 71 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 D | AnnotationGroup.cpp | 113 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 D | ComposeResultSubTask.cpp | 100 …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 D | BlastReadsSubTask.cpp | 365 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 D | RealignSequencesInAlignmentTask.cpp | 50 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 D | DbiDataStorage.cpp | 159 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 D | AddSequencesToAlignmentTask.cpp | 75 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 D | CreateAnnotationTask.cpp | 72 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 D | AddReadsToDocumentTask.cpp | 55 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 D | SequencePrototype.cpp | 148 …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 D | CloneAssemblyWithReferenceToDbiTask.cpp | 86 … = 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 D | DocumentFolders.cpp | 77 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 D | McaEditorSequenceArea.cpp | 145 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 D | McaEditorStatusBar.cpp | 128 …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 D | DbiDocumentFormat.cpp | 134 …, 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 D | XmlNode.hs | 80 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 D | AlignSequencesToAlignmentTask.cpp | 85 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 D | ImportSequenceFromRawDataTask.h | 37 const U2EntityRef &getEntityRef() const;
|
H A D | ImportSequenceFromRawDataTask.cpp | 42 const U2EntityRef &ImportSequenceFromRawDataTask::getEntityRef() const { in getEntityRef() function in U2::ImportSequenceFromRawDataTask
|