DataSetBase

#include <pbbam/DataSetTypes.h>

class PacBio::BAM::DataSetBase

The DataSetBase class provides the attributes & child elements shared by all dataset types.

Client code should not need to use this class directly. It should be considered as more of an implementation detail and may in fact be removed from public API in the future. The top-level DataSet is the recommended entry point.

Inherits from StrictEntityType

Subclassed by PacBio::BAM::AlignmentSet, PacBio::BAM::BarcodeSet, PacBio::BAM::ConsensusAlignmentSet, PacBio::BAM::ConsensusReadSet, PacBio::BAM::ContigSet, PacBio::BAM::HdfSubreadSet, PacBio::BAM::ReferenceSet, PacBio::BAM::SubreadSet

Public Functions

DataSetBase()

Creates an empty, generic DataSetBase.

DataSetBase &operator+=(const DataSetBase &other)

Merges dataset contents.

Adds contents of other to this dataset object

Return

reference to this dataset object

Parameters

• other: some other dataset to add to this one

const PacBio::BAM::ExternalResources &ExternalResources() const

Fetches the dataset’s ExternalResources element.

Return

const reference to child element

Exceptions

• std::runtime_error: if element does not exist

const PacBio::BAM::Filters &Filters() const

Fetches the dataset’s Filters element.

Return

const reference to child element

const PacBio::BAM::DataSetMetadata &Metadata() const

Fetches the dataset’s DataSetMetadata element.

Return

const reference to child element

const PacBio::BAM::SubDataSets &SubDataSets() const

Fetches the dataset’s DataSets element.

Return

const reference to child element

const NamespaceRegistry &Namespaces() const

Access this dataset’s namespace info.

Return

const reference to dataset’s NamespaceRegistry

PacBio::BAM::ExternalResources &ExternalResources()

Fetches the dataset’s ExternalResources element.

This element will be created if it does not yet exist.

Return

non-const reference to child element

PacBio::BAM::Filters &Filters()

Fetches the dataset’s Filters element.

This element will be created if it does not yet exist.

Return

non-const reference to child element

PacBio::BAM::DataSetMetadata &Metadata()

Fetches the dataset’s DataSetMetadata element.

This element will be created if it does not yet exist.

Return

non-const reference to child element

PacBio::BAM::SubDataSets &SubDataSets()

Fetches the dataset’s DataSets element.

This element will be created if it does not yet exist.

Return

non-const reference to child element

DataSetBase &ExternalResources(const PacBio::BAM::ExternalResources &resources)

Sets this dataset’s ExternalResources element.

This element will be created if it does not yet exist.

Return

reference to this dataset object

Parameters

• resources: new value for the element

DataSetBase &Filters(const PacBio::BAM::Filters &filters)

Sets this dataset’s Filters element.

This element will be created if it does not yet exist.

Return

reference to this dataset object

Parameters

• filters: new value for the element

DataSetBase &Metadata(const PacBio::BAM::DataSetMetadata &metadata)

Sets this dataset’s DataSetMetadata element.

This element will be created if it does not yet exist.

Return

reference to this dataset object

Parameters

• metadata: new value for the element

DataSetBase &SubDataSets(const PacBio::BAM::SubDataSets &subdatasets)

Sets this dataset’s DataSets element.

This element will be created if it does not yet exist.

Return

reference to this dataset object

Parameters

• subdatasets: new value for the element

NamespaceRegistry &Namespaces()

Access this dataset’s namespace info.

Return

non-const reference to dataset’s NamespaceRegistry

Public Static Functions

static std::shared_ptr<DataSetBase> Create(const std::string &typeName)

Creates a DataSetBase object, or one of its subclasses, from an XML element name (e.g. SubreadSet)

Protected Functions

DataSetBase(const std::string &metatype, const std::string &label, const XsdType &xsd)

Creates a DataSetBase with key values initialized.

DataSetBase *DeepCopy() const

Returns a new DataSetBase containing a deep copy of contents.