Class AnnotationTypeData

    • Field Detail

      • entryDate

        private Date entryDate
      • defaultUnit

        private UnitData defaultUnit
      • MAX_EXTERNAL_ID_LENGTH

        public static final int MAX_EXTERNAL_ID_LENGTH
        The maximum length of the external id that can be stored in the database.
        Since:
        2.2
        See Also:
        setExternalId(String), Constant Field Values
      • externalId

        private String externalId
      • multiplicity

        private int multiplicity
      • requiredForMiame

        private boolean requiredForMiame
      • isEnumeration

        private boolean isEnumeration
      • height

        private int height
      • width

        private int width
      • defaultValue

        private String defaultValue
      • MAX_DEFAULT_VALUE_LENGTH

        public static final int MAX_DEFAULT_VALUE_LENGTH
        See Also:
        Constant Field Values
      • valueType

        private int valueType
      • disableLogOfValues

        private boolean disableLogOfValues
      • disableInheritance

        private boolean disableInheritance
      • projectAnnotations

        private boolean projectAnnotations
      • isIdentifier

        private boolean isIdentifier
      • isProtocolParameter

        private boolean isProtocolParameter
    • Constructor Detail

      • AnnotationTypeData

        public AnnotationTypeData()
    • Method Detail

      • getEntryDate

        public Date getEntryDate()
        Description copied from interface: RegisteredData
        Get the date this item was added to the database. The value is generated at creation time and can't be modified later.
        Specified by:
        getEntryDate in interface RegisteredData
      • setEntryDate

        public void setEntryDate​(Date entryDate)
      • getQuantity

        public QuantityData getQuantity()
        Get the quantity this annotation type uses. Can't be changed after creation.
        Since:
        2.9
        Hibernate: many-to-one
        column="`quantity_id`" not-null="false" outer-join="false"
      • setQuantity

        public void setQuantity​(QuantityData quantity)
        Since:
        2.9
      • getDefaultUnit

        public UnitData getDefaultUnit()
        Get the unit used to store annotation values for this type. NOTE! If the unit changes to another unit with a different reference factor all annotation values must be recalculated. NOTE! This value is always null if the quantity is null.
        Since:
        2.9
        Hibernate: many-to-one
        column="`default_unit_id`" not-null="false" outer-join="false"
      • setDefaultUnit

        public void setDefaultUnit​(UnitData defaultUnit)
        Since:
        2.9
      • getUsableUnits

        public Set<UnitData> getUsableUnits()
        The units that it makes sense to use with this annotation type. If empty, any unit for the given quantity can be used.
        Since:
        2.9
        Hibernate: set
        table="`AnnotationTypeUnits`" lazy="true"
        Hibernate: collection-key
        column="`annotationtype_id`"
        Hibernate: collection-many-to-many
        column="`unit_id`" class="net.sf.basedb.core.data.UnitData"
      • setUsableUnits

        void setUsableUnits​(Set<UnitData> usableUnits)
        Since:
        2.9
      • getExternalId

        public String getExternalId()
        Get the external id for the biomaterial
        Since:
        2.2
        Hibernate: property
        column="`external_id`" type="string" length="255" not-null="false"
      • setExternalId

        public void setExternalId​(String externalId)
      • getMultiplicity

        public int getMultiplicity()
        How many values are allowed for this annotations of this type. 0 = no limit
        Hibernate: property
        column="`multiplicity`" type="int" not-null="true"
      • setMultiplicity

        public void setMultiplicity​(int multiplicity)
      • isRequiredForMiame

        public boolean isRequiredForMiame()
        If an annotation of this type must be present for an annotatable item to be compliant with MIAME.
        Hibernate: property
        column="`required_for_miame`" type="boolean" not-null="true"
      • setRequiredForMiame

        public void setRequiredForMiame​(boolean requiredForMiame)
      • isEnumeration

        public boolean isEnumeration()
        If this annotation type defines a list of allowed values or not.
        Hibernate: property
        column="`is_enumeration`" type="boolean" not-null="true"
      • setEnumeration

        public void setEnumeration​(boolean isEnumeration)
      • getHeight

        public int getHeight()
        The recommended height (lines) to display input fields for this annotation in client applications.
        Hibernate: property
        column="`height`" type="int" not-null="true"
      • setHeight

        public void setHeight​(int height)
      • getWidth

        public int getWidth()
        The recommended width (characters) to display input fields for this annotation in client applications.
        Hibernate: property
        column="`width`" type="int" not-null="true"
      • setWidth

        public void setWidth​(int width)
      • getDefaultValue

        public String getDefaultValue()
        The default value of new annotations.
        Hibernate: property
        column="`default_value`" type="string" length="255" not-null="false"
      • setDefaultValue

        public void setDefaultValue​(String defaultValue)
      • getValueType

        public int getValueType()
        The code for the value type.
        Hibernate: property
        column="`value_type`" type="int" not-null="true" update="false"
      • setValueType

        public void setValueType​(int valueType)
      • getDisableLogOfValues

        public boolean getDisableLogOfValues()
        If this flag is set, logging of actual annotation values should not be done in the change history.
        Since:
        3.3
        Hibernate: property
        column="`disable_log`" type="boolean" not-null="true"
      • setDisableLogOfValues

        public void setDisableLogOfValues​(boolean disableLogOfValues)
      • getDisableInheritance

        public boolean getDisableInheritance()
        If this flag is set, annotation of this type can't be inherited.
        Since:
        3.5
        Hibernate: property
        column="`disable_inherit`" type="boolean" not-null="true"
      • setDisableInheritance

        public void setDisableInheritance​(boolean disableInheritance)
      • getProjectAnnotations

        public boolean getProjectAnnotations()
        If this flag is set, annotation values can be set per project.
        Since:
        3.10
        Hibernate: property
        column="`project_annotations`" type="boolean" not-null="true"
      • setProjectAnnotations

        public void setProjectAnnotations​(boolean projectAnnotations)
      • isIdentifier

        public boolean isIdentifier()
        If this flag is set, annotation values can be used as identifiers to items.
        Since:
        3.15
        Hibernate: property
        column="`is_identifier`" type="boolean" not-null="true"
      • setIdentifier

        public void setIdentifier​(boolean isIdentifier)
      • getItemTypes

        public Set<Integer> getItemTypes()
        The item code for all items this annotation type can be applied to.
        Hibernate: set
        table="`AnnotationTypeItems`" lazy="true"
        Hibernate: collection-key
        column="`annotationtype_id`"
        Hibernate: collection-element
        column="`item_type`" type="int"
      • setItemTypes

        void setItemTypes​(Set<Integer> itemTypes)
      • getOptions

        public Map<String,​String> getOptions()
        Additional options depending on the value type.
        Hibernate: map
        table="`AnnotationTypeOptions`" lazy="true"
        Hibernate: collection-key
        column="`annotationtype_id`"
        Hibernate: collection-index
        column="`name`" type="string" length="255" not-null="true"
        Hibernate: collection-element
        column="`value`" type="string" length="255" not-null="true"
      • getEnumerationValues

        public ParameterValueData<?> getEnumerationValues()
        The allowed values if this is an enumeration.
        Hibernate: many-to-one
        column="`enumerationvalues_id`" not-null="false" cascade="all" unique="true"
      • setEnumerationValues

        public void setEnumerationValues​(ParameterValueData<?> enumerationValues)
      • getExperiments

        Set<ExperimentData> getExperiments()
        This is the inverse end.
        See Also:
        ExperimentData.getExperimentalFactors()
        Hibernate: set
        table="`ExperimentalFactors`" lazy="true" inverse="true"
        Hibernate: collection-key
        column="`annotationtype_id`"
        Hibernate: collection-many-to-many
        column="`experiment_id`" class="net.sf.basedb.core.data.ExperimentData"
      • getAnnotations

        Set<AnnotationData> getAnnotations()
        This is the inverse end.
        Since:
        2.15
        See Also:
        AnnotationData.getAnnotationType()
        Hibernate: set
        lazy="true" inverse="true"
        Hibernate: collection-key
        column="`annotationtype_id`"
        Hibernate: collection-one-to-many
        column="`annotation_id`" class="net.sf.basedb.core.data.AnnotationData"
      • isProtocolParameter

        public boolean isProtocolParameter()
        If this annotation type is intended to be used as a protocol parameter or as a regular annotation.
        Since:
        2.2
        Hibernate: property
        column="`is_parameter`" type="boolean" not-null="true"
      • setProtocolParameter

        public void setProtocolParameter​(boolean isProtocolParameter)
      • getProtocols

        Set<ProtocolData> getProtocols()
        This is the inverse end.
        Since:
        2.2
        See Also:
        ProtocolData.getParameters()
        Hibernate: set
        table="`ProtocolParameters`" lazy="true" inverse="true"
        Hibernate: collection-key
        column="`annotationtype_id`"
        Hibernate: collection-many-to-many
        column="`protocol_id`" class="net.sf.basedb.core.data.ProtocolData"
      • getCategories

        public Set<AnnotationTypeCategoryData> getCategories()
        Get the set that manages the categories of this annotation type.
        Hibernate: set
        table="`CategorisedAnnotationTypes`" lazy="true"
        Hibernate: collection-key
        column="`annotationtype_id`"
        Hibernate: collection-many-to-many
        column="`category_id`" class="net.sf.basedb.core.data.AnnotationTypeCategoryData"