Package ome.model.roi

Class Roi

  • All Implemented Interfaces:
    java.io.Serializable, IAnnotated, IMutable, IObject, Filterable
    @Entity
@Indexed(index="FullText")
@ClassBridge(name="details",
             impl=DetailsFieldBridge.class,
             index=UN_TOKENIZED,
             store=NO)
public class Roi
extends java.lang.Object
implements java.io.Serializable, IObject, IMutable, IAnnotated
    These filter definitions are used by the security system to eliminate non-readable objects from queries. The regular user does not need to worry about them, as they will be injected directly into the SQL (not HQL)
    See Also:
    Serialized Form

    • Field Detail

      • id

        protected java.lang.Long id

      • version

        protected java.lang.Integer version

      • name

        protected java.lang.String name

      • shapes

        protected java.util.List<Shape> shapes

      • OWNER_FILTER_SHAPES

        public static final java.lang.String OWNER_FILTER_SHAPES
        See Also:
        Constant Field Values

      • GROUP_FILTER_SHAPES

        public static final java.lang.String GROUP_FILTER_SHAPES
        See Also:
        Constant Field Values

      • EVENT_FILTER_SHAPES

        public static final java.lang.String EVENT_FILTER_SHAPES
        See Also:
        Constant Field Values

      • PERMS_FILTER_SHAPES

        public static final java.lang.String PERMS_FILTER_SHAPES
        See Also:
        Constant Field Values

      • image

        protected Image image

      • folderLinks

        protected java.util.Set<FolderRoiLink> folderLinks

      • OWNER_FILTER_FOLDERLINKS

        public static final java.lang.String OWNER_FILTER_FOLDERLINKS
        See Also:
        Constant Field Values

      • GROUP_FILTER_FOLDERLINKS

        public static final java.lang.String GROUP_FILTER_FOLDERLINKS
        See Also:
        Constant Field Values

      • EVENT_FILTER_FOLDERLINKS

        public static final java.lang.String EVENT_FILTER_FOLDERLINKS
        See Also:
        Constant Field Values

      • PERMS_FILTER_FOLDERLINKS

        public static final java.lang.String PERMS_FILTER_FOLDERLINKS
        See Also:
        Constant Field Values

      • OWNER_FILTER_ANNOTATIONLINKS

        public static final java.lang.String OWNER_FILTER_ANNOTATIONLINKS
        See Also:
        Constant Field Values

      • GROUP_FILTER_ANNOTATIONLINKS

        public static final java.lang.String GROUP_FILTER_ANNOTATIONLINKS
        See Also:
        Constant Field Values

      • EVENT_FILTER_ANNOTATIONLINKS

        public static final java.lang.String EVENT_FILTER_ANNOTATIONLINKS
        See Also:
        Constant Field Values

      • PERMS_FILTER_ANNOTATIONLINKS

        public static final java.lang.String PERMS_FILTER_ANNOTATIONLINKS
        See Also:
        Constant Field Values

      • description

        protected java.lang.String description

      • details

        protected Details details

      • FOLDERLINKSCOUNTPEROWNER

        public static final java.lang.String FOLDERLINKSCOUNTPEROWNER
        See Also:
        Constant Field Values

      • ANNOTATIONLINKSCOUNTPEROWNER

        public static final java.lang.String ANNOTATIONLINKSCOUNTPEROWNER
        See Also:
        Constant Field Values

      • FIELDS

        public static final java.util.Set<java.lang.String> FIELDS

      • _dynamicFields

        protected java.util.Map<java.lang.String,​java.lang.Object> _dynamicFields

      • _loaded

        protected boolean _loaded

    • Constructor Detail

      • Roi

        public Roi()

      • Roi

        protected Roi​(java.lang.Long id)

      • Roi

        public Roi​(java.lang.Long id,
           boolean loaded)
        Main constructor.

    • Method Detail

      • getId

        @DocumentId
public java.lang.Long getId()
        The DB unique identifier for this object. You are not responsible for setting the id; however, it can be useful for creating "unloaded" versions of your objects. Each top-level entity contains an id field of type long. For all objects returned from the server, this value will be non-null, which doesn't necessarily hold for the other fields.
        Specified by:
        getId in interface IObject
        Returns:
        Long primary key. May be null.

      • setId

        public void setId​(java.lang.Long id)
        Description copied from interface: IObject
        usually unneeded. Ids are managed by the backend.
        Specified by:
        setId in interface IObject
        Parameters:
        id - Long value for this id.

      • getVersion

        public java.lang.Integer getVersion()
        This version number is controlled by the database for optimisitic locking.
        Specified by:
        getVersion in interface IMutable

      • setVersion

        public void setVersion​(java.lang.Integer version)
        Description copied from interface: IMutable
        use with caution. In general, the version should only be altered by the backend. In the best case, an exception will be thrown for a version not equal to the current DB value. In the worst (though rare) case, the new version could match the database, and override optimistic lock checks that are supposed to prevent data loss.
        Specified by:
        setVersion in interface IMutable
        Parameters:
        version - Value for this objects version.

      • getName

        @Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields")
public java.lang.String getName()
        Simple field ome.model.roi.Roi.name (java.lang.String)

      • setName

        public void setName​(java.lang.String name)

      • getShapes

        protected java.util.List<Shape> getShapes()
        returns shapes . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many List ome.model.roi.Roi.shapes (ome.model.roi.Shape) Values are indexed by the column "index" on ome.model.roi.Shape

      • setShapes

        protected void setShapes​(java.util.List<Shape> shapes)
        setter for shapes should be avoided. Does not fulfill normal semantics.

      • sizeOfShapes

        public int sizeOfShapes()
        returns the size of shapes. If less than zero, the Set was null.

      • iterateShapes

        public java.util.Iterator<Shape> iterateShapes()
        should be used rather than accessing the shapes set directly. This method will never return null, but rather will return an instance of EmptyIterator. To test for a null collection, see of sizeOfShapes() is less than zero.

      • unmodifiableShapes

        public java.util.Collection<Shape> unmodifiableShapes()
        Returns an unmodifiable collection-view

      • collectShapes

        public <E> java.util.List<E> collectShapes​(CBlock<E> block)
        takes a CBlock and calls the block once for each ome.model.roi.Shape while collecting the results. If block == null, then the iterator values themselves are collected. This method uses iterateShapes() internally and so will return a value even if the underlying collection is null.

      • addShape

        public void addShape​(Shape target)
        use instead of setShapes . Makes the necessary call on ome.model.roi.Shape as well.

      • addShapeSet

        public void addShapeSet​(java.util.Collection<Shape> targets)
        use like addShape.

      • removeShape

        public void removeShape​(Shape target)
        removes a single element from this set and makes the inverse call on ome.model.roi.Shape

      • removeShapeSet

        public void removeShapeSet​(java.util.Collection<Shape> targets)
        use like removeShape

      • clearShapes

        public void clearShapes()
        clears the set.

      • getShape

        public Shape getShape​(int index)
               throws java.lang.IndexOutOfBoundsException
        Gets the ome.model.roi.Shape at the given index.
        Throws:
        java.lang.IndexOutOfBoundsException

      • setShape

        public Shape setShape​(int index,
                      Shape element)
               throws java.lang.IndexOutOfBoundsException
        Sets the ome.model.roi.Shape at the given index. Adheres to the List.set(int, Object) contract. To extend the list, use addShape(Shape).
        Throws:
        java.lang.IndexOutOfBoundsException
        See Also:
        List.set(int, Object)

      • getPrimaryShape

        public Shape getPrimaryShape()
                      throws java.lang.IndexOutOfBoundsException
        Gets the first element of shapes which can be interpreted as the primary or default element in some situations. If there is not first element, an IndexOutOfBoundsException is throws. This method will also throw an ApiUsageException if the collection is unloaded. See sizeOfShapes() for more information.
        Throws:
        java.lang.IndexOutOfBoundsException

      • setPrimaryShape

        public Shape setPrimaryShape​(Shape element)
                      throws java.lang.IndexOutOfBoundsException
        Swaps the first element of shapes with the first instance of the given element. If the given element is not in the list, an IndexOutOfBoundsException will be thrown. Returns the swapped element. This method will also throw an ApiUsageException if the collection is unloaded. See sizeOfShapes() for more information.
        Throws:
        java.lang.IndexOutOfBoundsException

      • getImage

        public Image getImage()
        Many-to-one field ome.model.roi.Roi.image (ome.model.core.Image)

      • setImage

        public void setImage​(Image image)

      • getSource

        public OriginalFile getSource()
        Many-to-one field ome.model.roi.Roi.source (ome.model.core.OriginalFile)

      • setSource

        public void setSource​(OriginalFile source)

      • getFolderLinks

        protected java.util.Set<FolderRoiLink> getFolderLinks()
        returns folderLinks . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many Set ome.model.roi.Roi.folderLinks (ome.model.containers.FolderRoiLink)

      • setFolderLinks

        protected void setFolderLinks​(java.util.Set<FolderRoiLink> folderLinks)
        setter for folderLinks should be avoided. Does not fulfill normal semantics.

      • sizeOfFolderLinks

        public int sizeOfFolderLinks()
        returns the size of folderLinks. If less than zero, the Set was null.

      • iterateFolderLinks

        public java.util.Iterator<FolderRoiLink> iterateFolderLinks()
        should be used rather than accessing the folderLinks set directly. This method will never return null, but rather will return an instance of EmptyIterator. To test for a null collection, see of sizeOfFolderLinks() is less than zero.

      • unmodifiableFolderLinks

        public java.util.Collection<FolderRoiLink> unmodifiableFolderLinks()
        Returns an unmodifiable collection-view

      • collectFolderLinks

        public <E> java.util.List<E> collectFolderLinks​(CBlock<E> block)
        takes a CBlock and calls the block once for each ome.model.containers.FolderRoiLink while collecting the results. If block == null, then the iterator values themselves are collected. This method uses iterateFolderLinks() internally and so will return a value even if the underlying collection is null.

      • addFolderRoiLink

        public void addFolderRoiLink​(FolderRoiLink target)
        use instead of setFolderLinks . Makes the necessary call on ome.model.containers.FolderRoiLink as well.

      • addFolderRoiLinkSet

        public void addFolderRoiLinkSet​(java.util.Collection<FolderRoiLink> targets)
        use like addFolderRoiLink.

      • removeFolderRoiLink

        public void removeFolderRoiLink​(FolderRoiLink target)
        removes a single element from this set and makes the inverse call on ome.model.containers.FolderRoiLink

      • removeFolderRoiLinkSet

        public void removeFolderRoiLinkSet​(java.util.Collection<FolderRoiLink> targets)
        use like removeFolderRoiLink

      • linkFolder

        public FolderRoiLink linkFolder​(Folder addition)
        Adds a ome.model.containers.FolderRoiLink to folderLinks . This entails changing our folderLinks Set, creating a new ome.model.containers.FolderRoiLink and calling linkFolder on the ome.model.containers.Folder.

      • addFolderRoiLink

        public void addFolderRoiLink​(FolderRoiLink link,
                             boolean bothSides)
        Adds a ome.model.containers.FolderRoiLink to folderLinks, allowing for recursion -- whether or not addFolderRoiLink will be called on the addition if it is loaded

      • linkedFolderIterator

        public java.util.Iterator<Folder> linkedFolderIterator()
        provides an iterator over the child values of the folderLinks. Like with most Collection iterators, modifications to the underlying collection while iterating will result in an ConcurrentModificationException. Use linkedFolderList() instead.

      • findFolderRoiLink

        public java.util.Set<FolderRoiLink> findFolderRoiLink​(Folder target)
        find all ome.model.containers.FolderRoiLink which have the argument as their parent.

      • linkedFolderList

        public java.util.List<Folder> linkedFolderList()
        produces a List-copy of the underlying collection. Unlike, linkedFolderIterator(), while using the returned List, modifications can be made to the underlying collection without throwing ConcurrentModificationException.

      • eachLinkedFolder

        public <E> java.util.List<E> eachLinkedFolder​(CBlock<E> block)
        takes a CBlock and calls the block once for each ome.model.containers.Folder while collecting the results. If block == null, then the iterator values themselves are collected.

      • unlinkFolder

        public void unlinkFolder​(Folder removal)
        unlinks all ome.model.containers.Folder instances from this instance.

      • removeFolderRoiLink

        public void removeFolderRoiLink​(FolderRoiLink link,
                                boolean bothSides)
        removes the given FolderRoiLink from folderLinks, allowing for recursion -- whether or not the removal will call unlinkRoi again if loaded.

      • clearFolderLinks

        public void clearFolderLinks()
        clears the set.

      • setFolderLinksCountPerOwner

        protected void setFolderLinksCountPerOwner​(java.util.Map<java.lang.Long,​java.lang.Long> map)

      • getFolderLinksCountPerOwner

        public java.util.Map<java.lang.Long,​java.lang.Long> getFolderLinksCountPerOwner()
        If fetched, returns the count(*) of ome.model.containers.FolderRoiLink that a user has. If unfetched, returns null. No entries in the collection should be null.

      • getAnnotationLinks

        protected java.util.Set<RoiAnnotationLink> getAnnotationLinks()
        returns annotationLinks . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many Set ome.model.roi.Roi.annotationLinks (ome.model.annotations.RoiAnnotationLink)

      • setAnnotationLinks

        protected void setAnnotationLinks​(java.util.Set<RoiAnnotationLink> annotationLinks)
        setter for annotationLinks should be avoided. Does not fulfill normal semantics.

      • sizeOfAnnotationLinks

        public int sizeOfAnnotationLinks()
        returns the size of annotationLinks. If less than zero, the Set was null.
        Specified by:
        sizeOfAnnotationLinks in interface IAnnotated

      • collectAnnotationLinks

        public <E> java.util.List<E> collectAnnotationLinks​(CBlock<E> block)
        takes a CBlock and calls the block once for each ome.model.annotations.RoiAnnotationLink while collecting the results. If block == null, then the iterator values themselves are collected. This method uses iterateAnnotationLinks() internally and so will return a value even if the underlying collection is null.
        Specified by:
        collectAnnotationLinks in interface IAnnotated

      • addRoiAnnotationLink

        public void addRoiAnnotationLink​(RoiAnnotationLink target)
        use instead of setAnnotationLinks . Makes the necessary call on ome.model.annotations.RoiAnnotationLink as well.

      • addRoiAnnotationLinkSet

        public void addRoiAnnotationLinkSet​(java.util.Collection<RoiAnnotationLink> targets)
        use like addRoiAnnotationLink.

      • removeRoiAnnotationLink

        public void removeRoiAnnotationLink​(RoiAnnotationLink target)
        removes a single element from this set and makes the inverse call on ome.model.annotations.RoiAnnotationLink

      • removeRoiAnnotationLinkSet

        public void removeRoiAnnotationLinkSet​(java.util.Collection<RoiAnnotationLink> targets)
        use like removeRoiAnnotationLink

      • linkAnnotation

        public RoiAnnotationLink linkAnnotation​(Annotation addition)
        Adds a ome.model.annotations.RoiAnnotationLink to annotationLinks . This entails changing our annotationLinks Set, creating a new ome.model.annotations.RoiAnnotationLink and calling linkAnnotation on the ome.model.annotations.Annotation.
        Specified by:
        linkAnnotation in interface IAnnotated

      • addRoiAnnotationLink

        public void addRoiAnnotationLink​(RoiAnnotationLink link,
                                 boolean bothSides)
        Adds a ome.model.annotations.RoiAnnotationLink to annotationLinks, allowing for recursion -- whether or not addRoiAnnotationLink will be called on the addition if it is loaded

      • linkedAnnotationIterator

        public java.util.Iterator<Annotation> linkedAnnotationIterator()
        provides an iterator over the parent values of the annotationLinks. Like with most Collection iterators, modifications to the underlying collection while iterating will result in an ConcurrentModificationException. Use linkedAnnotationList() instead.
        Specified by:
        linkedAnnotationIterator in interface IAnnotated

      • findRoiAnnotationLink

        public java.util.Set<RoiAnnotationLink> findRoiAnnotationLink​(Annotation target)
        find all ome.model.annotations.RoiAnnotationLink which have the argument as their child.

      • linkedAnnotationList

        public java.util.List<Annotation> linkedAnnotationList()
        produces a List-copy of the underlying collection. Unlike, linkedAnnotationIterator(), while using the returned List, modifications can be made to the underlying collection without throwing ConcurrentModificationException.
        Specified by:
        linkedAnnotationList in interface IAnnotated

      • eachLinkedAnnotation

        public <E> java.util.List<E> eachLinkedAnnotation​(CBlock<E> block)
        takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results. If block == null, then the iterator values themselves are collected.
        Specified by:
        eachLinkedAnnotation in interface IAnnotated

      • unlinkAnnotation

        public void unlinkAnnotation​(Annotation removal)
        unlinks all ome.model.annotations.Annotation instances from this instance.
        Specified by:
        unlinkAnnotation in interface IAnnotated

      • removeRoiAnnotationLink

        public void removeRoiAnnotationLink​(RoiAnnotationLink link,
                                    boolean bothSides)
        removes the given RoiAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkRoi again if loaded.

      • setAnnotationLinksCountPerOwner

        protected void setAnnotationLinksCountPerOwner​(java.util.Map<java.lang.Long,​java.lang.Long> map)

      • getAnnotationLinksCountPerOwner

        public java.util.Map<java.lang.Long,​java.lang.Long> getAnnotationLinksCountPerOwner()
        If fetched, returns the count(*) of ome.model.annotations.RoiAnnotationLink that a user has. If unfetched, returns null. No entries in the collection should be null.

      • getDescription

        @Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields")
public java.lang.String getDescription()
        Simple field ome.model.roi.Roi.description (java.lang.String)

      • setDescription

        public void setDescription​(java.lang.String description)

      • getDetails

        public Details getDetails()
        The details of this object correspond to low-level system information. Owner, permissions, Details is always guaranteed to be non-null, unless the user actively nulls it. Every entity also contains a Detail reference, which doesn't refer to a separate table but rather to a collection of fields collected into a Hibernate "component" which is embedded in the object. HQL queries which refer to the Details component cannot directly fetch the entity like this: select o from Object join fetch o.details but rather each field of the Details instance must be explicitly joined: select o from Object join fetch o.details.owner It should also be noted that not all types have all the fields which are present on Details. For example, select e from Experimenter e join fetch e.details.owner will fail. Experimenter has no owner, for obvious reasons. Note: subclasses of this class will return a subclass of the Details type.
        Specified by:
        getDetails in interface IObject

      • setDetails

        protected void setDetails​(Details details)

      • isValid

        public boolean isValid()
        Description copied from interface: IObject
        calls the class-specific validator for this instance and returns the value from Validation.isValid()
        Specified by:
        isValid in interface IObject

      • validate

        public Validation validate()
        Description copied from interface: IObject
        calls the class-specific validator for this instance and returns the Validation object.
        Specified by:
        validate in interface IObject
        Returns:
        Validation collecting parameter.

      • newInstance

        public Roi newInstance()

      • proxy

        public Roi proxy()

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • fields

        public java.util.Set<java.lang.String> fields()
        Description copied from interface: IObject
        returns a Set of field names that belong to this class
        Specified by:
        fields in interface IObject

      • retrieve

        public java.lang.Object retrieve​(java.lang.String field)
        Description copied from interface: IObject
        retrieves a value from this instance. Values for field which match a field of this instance will be delegated to the accessors. Otherwise, values will be retrieved from a lazy-loaded map filled by calls to IObject.putAt(String, Object)
        Specified by:
        retrieve in interface IObject

      • putAt

        public void putAt​(java.lang.String field,
                  java.lang.Object value)
        Description copied from interface: IObject
        stores a value in this instance. Values for field which match a field of this instance will be delegated to the accessors. Otherwise, values will be stored in a lazy-loaded map.
        Specified by:
        putAt in interface IObject
        Parameters:
        field - Field name
        value - Any object to be stored.

      • isLoaded

        public boolean isLoaded()
        Description copied from interface: IObject
        transient field (not stored in the DB) which specifies whether this object has been loaded from the DB or is only a wrapper around the ID.
        Specified by:
        isLoaded in interface IObject

      • errorIfUnloaded

        protected void errorIfUnloaded()

      • unload

        public void unload()
        Description copied from interface: IObject
        set the loaded field to false, and set all non-ID fields to null. Subsequent calls to all accessors other than getId/setId will throw an ApiUsageException
        Specified by:
        unload in interface IObject

      • getGraphHolder

        public final GraphHolder getGraphHolder()
        Description copied from interface: IObject
        retrieves the GraphHolder for this entity. If the GraphHolder has not been actively set, a new one will be instatiated.
        Specified by:
        getGraphHolder in interface IObject
        Returns:
        Non-null GraphHolder

      • throwNullCollectionException

        protected void throwNullCollectionException​(java.lang.String propertyName)