Package org.intermine.xml.full

Class Item

  • All Implemented Interfaces:
    java.lang.Comparable<Item>
    public class Item
extends java.lang.Object
implements java.lang.Comparable<Item>
    Representation of an object
    Author:
    Andrew Varley, Kim Rutherford

    • Constructor Summary

      Constructors 
      Modifier Constructor Description
      protected Item()
      Construct an item.
      protected Item​(java.lang.String identifier, java.lang.String className, java.lang.String implementations)
      Construct an item with no Model.
      protected Item​(Model model, java.lang.String identifier, java.lang.String className, java.lang.String implementations)
      Construct an item.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addAttribute​(Attribute attribute)
      Add an attribute.
      void addCollection​(ReferenceList collection)
      Add a collection.
      void addReference​(Reference reference)
      Add a reference.
      void addToCollection​(java.lang.String name, java.lang.String refId)
      Add a reference to a collection of this item.
      void addToCollection​(java.lang.String name, Item item)
      Add the identifier of the given Item to a collection.
      boolean canHaveCollection​(java.lang.String name)
      Return true if and only if the argument names a possible collection for this Item.
      boolean canHaveReference​(java.lang.String name)
      Return true if and only if the argument names a possible reference for this Item.
      boolean checkAttribute​(java.lang.String name)
      Return true if the name parameter is an attribute of the class for this Item or if the Model or the className of this Item haven't been set.
      protected void checkCollection​(java.lang.String name)
      Throw a RuntimeException if the name parameter isn't an collection in the class set by setClassName() in the Model set by setModel().
      protected void checkImplementations​(java.lang.String implementations)
      Throw RuntimeException if the given implementations don't match the model.
      protected void checkReference​(java.lang.String name)
      Throw a RuntimeException if the name parameter isn't an reference in the class set by setClassName() in the Model set by setModel().
      int compareTo​(Item i)
      Compare items first by class, then by identifier, intended for creating ordered output files.
      boolean equals​(java.lang.Object o)
      protected java.util.List<ClassDescriptor> getAllClassDescriptors()
      Return the ClassDescriptors of the class of this Item (as given by className) and all the implementations.
      Attribute getAttribute​(java.lang.String attributeName)
      Get a named attribute.
      java.util.Collection<Attribute> getAttributes()
      Get all the attributes.
      protected ClassDescriptor getClassDescriptorByName​(java.lang.String className)
      Throw a RuntimeException if any of the named class isn't in the Model set by setModel().
      java.lang.String getClassName()
      Get the class name of this item.
      ReferenceList getCollection​(java.lang.String collectionName)
      Get a named collection.
      java.util.Collection<ReferenceList> getCollections()
      Get all the collections.
      java.lang.String getIdentifier()
      Get the identifier of this item.
      java.lang.String getImplementations()
      Get the interfaces implemented by this item.
      protected java.util.List<ClassDescriptor> getImplementClassDescriptors​(java.lang.String implementations)
      Returns the ClassDescriptors for the given implementations.
      Model getModel()
      Return the model that was passed to the constructor or set with setModel().
      Reference getReference​(java.lang.String referenceName)
      Get a named reference.
      java.util.Collection<Reference> getReferences()
      Get all the references.
      boolean hasAttribute​(java.lang.String attributeName)
      Return true if named attribute exists.
      boolean hasCollection​(java.lang.String collectionName)
      Return true if named collection exists.
      int hashCode()
      boolean hasReference​(java.lang.String referenceName)
      Return true if named reference exists.
      void removeAttribute​(java.lang.String attributeName)
      Remove a attribute of the specified name if it exists.
      void removeCollection​(java.lang.String collectionName)
      Remove a collection of the specified name if it exists.
      void removeReference​(java.lang.String referenceName)
      Remove a reference of the specified name if it exists.
      void setAttribute​(java.lang.String name, java.lang.String value)
      Add an attribute to this item.
      void setAttributeIfNotNull​(java.lang.String name, java.lang.String value)
      Add an attribute to this item only if value is not empty or NULL
      void setAttributeToEmptyString​(java.lang.String name)
      Add an attribute to this item and set it to the empty string.
      protected void setClassDescriptor​(java.lang.String className)
      Set the classDescriptor attribute to be the ClassDescriptor for the given className in the Model set by setModel().
      void setClassName​(java.lang.String className)
      Set the class of this item.
      void setCollection​(java.lang.String collectionName, java.util.List<java.lang.String> refIds)
      Set a collection.
      void setIdentifier​(java.lang.String identifier)
      Set the identifier of this item.
      void setImplementations​(java.lang.String implementations)
      Set the "implements" of this item.
      void setModel​(Model model)
      Set the Model to use when checking calls to the other set methods
      void setReference​(java.lang.String name, java.lang.String refId)
      Add a reference to this item.
      void setReference​(java.lang.String name, Item item)
      Add a reference that points to a particular item.
      java.lang.String toString()

      • Methods inherited from class java.lang.Object

        clone, finalize, getClass, notify, notifyAll, wait, wait, wait

    • Constructor Detail

      • Item

        protected Item()
        Construct an item.

      • Item

        protected Item​(Model model,
               java.lang.String identifier,
               java.lang.String className,
               java.lang.String implementations)
        Construct an item.
        Parameters:
        model - the Model used to type-check set methods; if null no type checking is done
        identifier - item identifier
        className - name of described class
        implementations - names of implemented classes
        See Also:
        ItemFactory

      • Item

        protected Item​(java.lang.String identifier,
               java.lang.String className,
               java.lang.String implementations)
        Construct an item with no Model. The calls to the set methods won't be type checked unless setModel() is called.
        Parameters:
        identifier - item identifier
        className - name of described class
        implementations - names of implemented classes
        See Also:
        ItemFactory

    • Method Detail

      • setModel

        public void setModel​(Model model)
        Set the Model to use when checking calls to the other set methods
        Parameters:
        model - the Model

      • getModel

        public Model getModel()
        Return the model that was passed to the constructor or set with setModel().
        Returns:
        the Model

      • setIdentifier

        public void setIdentifier​(java.lang.String identifier)
        Set the identifier of this item.
        Parameters:
        identifier - the identifier

      • getIdentifier

        public java.lang.String getIdentifier()
        Get the identifier of this item.
        Returns:
        the identifier

      • setClassName

        public void setClassName​(java.lang.String className)
        Set the class of this item.
        Parameters:
        className - the class

      • getClassName

        public java.lang.String getClassName()
        Get the class name of this item.
        Returns:
        the class name

      • setImplementations

        public void setImplementations​(java.lang.String implementations)
        Set the "implements" of this item.
        Parameters:
        implementations - the interfaces that this item implements

      • getImplementations

        public java.lang.String getImplementations()
        Get the interfaces implemented by this item.
        Returns:
        the implemented interfaces

      • addAttribute

        public void addAttribute​(Attribute attribute)
        Add an attribute.
        Parameters:
        attribute - the Attribute to add

      • removeAttribute

        public void removeAttribute​(java.lang.String attributeName)
        Remove a attribute of the specified name if it exists.
        Parameters:
        attributeName - name of the attribute to remove

      • getAttributes

        public java.util.Collection<Attribute> getAttributes()
        Get all the attributes.
        Returns:
        all the attributes

      • getAttribute

        public Attribute getAttribute​(java.lang.String attributeName)
        Get a named attribute.
        Parameters:
        attributeName - the attribute name
        Returns:
        the Attribute with the given name

      • hasAttribute

        public boolean hasAttribute​(java.lang.String attributeName)
        Return true if named attribute exists.
        Parameters:
        attributeName - the attribute name
        Returns:
        true if the attribute exists

      • addReference

        public void addReference​(Reference reference)
        Add a reference.
        Parameters:
        reference - the reference to add

      • removeReference

        public void removeReference​(java.lang.String referenceName)
        Remove a reference of the specified name if it exists.
        Parameters:
        referenceName - name of the reference to remove

      • getReferences

        public java.util.Collection<Reference> getReferences()
        Get all the references.
        Returns:
        all the references

      • getReference

        public Reference getReference​(java.lang.String referenceName)
        Get a named reference.
        Parameters:
        referenceName - the reference name
        Returns:
        the Reference with the given name

      • hasReference

        public boolean hasReference​(java.lang.String referenceName)
        Return true if named reference exists.
        Parameters:
        referenceName - the reference name
        Returns:
        true if the reference exists

      • addCollection

        public void addCollection​(ReferenceList collection)
        Add a collection.
        Parameters:
        collection - the collection to add

      • removeCollection

        public void removeCollection​(java.lang.String collectionName)
        Remove a collection of the specified name if it exists.
        Parameters:
        collectionName - name of the collection to remove

      • getCollections

        public java.util.Collection<ReferenceList> getCollections()
        Get all the collections.
        Returns:
        all the collections

      • hasCollection

        public boolean hasCollection​(java.lang.String collectionName)
        Return true if named collection exists.
        Parameters:
        collectionName - the collection name
        Returns:
        true if the collection exists

      • getCollection

        public ReferenceList getCollection​(java.lang.String collectionName)
        Get a named collection.
        Parameters:
        collectionName - the collection name
        Returns:
        the Collection with the given name

      • setCollection

        public void setCollection​(java.lang.String collectionName,
                          java.util.List<java.lang.String> refIds)
        Set a collection.
        Parameters:
        collectionName - collection name
        refIds - ids to reference

      • setAttribute

        public void setAttribute​(java.lang.String name,
                         java.lang.String value)
        Add an attribute to this item.
        Parameters:
        name - the name of the attribute
        value - the value of the attribute - cannot be null or empty

      • setAttributeIfNotNull

        public void setAttributeIfNotNull​(java.lang.String name,
                                  java.lang.String value)
        Add an attribute to this item only if value is not empty or NULL
        Parameters:
        name - the name of the attribute
        value - the value of the attribute - ignored if empty or NULL

      • setAttributeToEmptyString

        public void setAttributeToEmptyString​(java.lang.String name)
        Add an attribute to this item and set it to the empty string.
        Parameters:
        name - the name of the attribute

      • setReference

        public void setReference​(java.lang.String name,
                         java.lang.String refId)
        Add a reference to this item.
        Parameters:
        name - the name of the attribute
        refId - the value of the attribute

      • setReference

        public void setReference​(java.lang.String name,
                         Item item)
        Add a reference that points to a particular item.
        Parameters:
        name - the name of the attribute
        item - the item to refer to

      • addToCollection

        public void addToCollection​(java.lang.String name,
                            Item item)
        Add the identifier of the given Item to a collection.
        Parameters:
        name - the name of the collection
        item - the item whose identifier is to be added to the collection

      • addToCollection

        public void addToCollection​(java.lang.String name,
                            java.lang.String refId)
        Add a reference to a collection of this item.
        Parameters:
        name - the name of the collection
        refId - the item to add to the collection

      • checkAttribute

        public boolean checkAttribute​(java.lang.String name)
        Return true if the name parameter is an attribute of the class for this Item or if the Model or the className of this Item haven't been set.
        Parameters:
        name - the attribute name
        Returns:
        true if the name is a valid attribute name

      • checkReference

        protected void checkReference​(java.lang.String name)
        Throw a RuntimeException if the name parameter isn't an reference in the class set by setClassName() in the Model set by setModel(). Returns immediately if the Model or the className of this Item haven't been set.
        Parameters:
        name - the reference name

      • canHaveReference

        public boolean canHaveReference​(java.lang.String name)
        Return true if and only if the argument names a possible reference for this Item. ie. the ClassDescriptor for this Item contains a ReferenceDescriptor for this name.
        Parameters:
        name - the field name
        Returns:
        Return true if and only if this Item has a reference of the given name in the model

      • canHaveCollection

        public boolean canHaveCollection​(java.lang.String name)
        Return true if and only if the argument names a possible collection for this Item. ie. the ClassDescriptor for this Item contains a CollectionDescriptor for this name.
        Parameters:
        name - the field name
        Returns:
        Return true if and only if this Item has a collection of the given name in the model

      • checkCollection

        protected void checkCollection​(java.lang.String name)
        Throw a RuntimeException if the name parameter isn't an collection in the class set by setClassName() in the Model set by setModel(). Returns immediately if the Model or the className of this Item haven't been set.
        Parameters:
        name - the collection name

      • checkImplementations

        protected void checkImplementations​(java.lang.String implementations)
        Throw RuntimeException if the given implementations don't match the model.
        Parameters:
        implementations - the interfaces that this item implements

      • getClassDescriptorByName

        protected ClassDescriptor getClassDescriptorByName​(java.lang.String className)
        Throw a RuntimeException if any of the named class isn't in the Model set by setModel(). Returns null if the model isn't set or className is "".
        Parameters:
        className - the class name
        Returns:
        the ClassDescriptor for the given class

      • setClassDescriptor

        protected void setClassDescriptor​(java.lang.String className)
        Set the classDescriptor attribute to be the ClassDescriptor for the given className in the Model set by setModel(). Returns immediately if the Model hasn't been set or the className parameter is "".
        Parameters:
        className - the class name

      • getAllClassDescriptors

        protected java.util.List<ClassDescriptor> getAllClassDescriptors()
        Return the ClassDescriptors of the class of this Item (as given by className) and all the implementations. Call only if model, className and implementations are set.
        Returns:
        all the ClassDescriptors for this Item

      • getImplementClassDescriptors

        protected java.util.List<ClassDescriptor> getImplementClassDescriptors​(java.lang.String implementations)
        Returns the ClassDescriptors for the given implementations. Returns null if the Model hasn't been set. Throw a RuntimeException if any of the classes named in the implementations parameter aren't in the Model.
        Parameters:
        implementations - the interfaces that this item implements
        Returns:
        the ClassDescriptors for the given implementations. Returns null if the Model hasn't been set

      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object

      • compareTo

        public int compareTo​(Item i)
        Compare items first by class, then by identifier, intended for creating ordered output files.
        Specified by:
        compareTo in interface java.lang.Comparable<Item>

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object

      • toString

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