ome.xml

Class OMEXMLNode

java.lang.Object

ome.xml.OMEXMLNode

Direct Known Subclasses:

ArcNode, ChannelComponentNode, ChannelInfoNode, ChannelSpecTypeNode, CustomNode, DatasetNode, DatasetRefNode, DescriptionNode, DisplayOptionsNode, ExperimenterTypeNode, ExperimentNode, FeatureNode, FilamentNode, FilterNode, FilterSpecNode, GroupNode, ImageNode, ImagingEnvironmentNode, InstrumentNode, LaserNode, ManufactSpecNode, OMENode, OTFNode, PixelsNode, PlateNode, ProjectionNode, ProjectNode, ReferenceNode, ROINode, ScreenNode, StageLabelNode, ThumbnailNode, TiffDataNode, TimeNode

Deprecated.

The r2003fc classes are replaced by the ome.xml.model classes

@Deprecated
public abstract class OMEXMLNode
extends Object

OMEXMLNode is the superclass of all OME-XML nodes. These nodes are similar to, but more sophisticated than, the nodes obtained from a direct DOM parse of an OME-XML file. Every OME-XML node is backed by a corresponding DOM element from the directly parsed XML, but not all DOM elements have a corresponding OME-XML node; some (such as FirstName within Experimenter) are implicit within more significant OME-XML nodes (e.g., ExperimenterNode). In general, it is not guaranteed that all DOM elements and attributes be exposed through subclasses of OMEXMLNode, though the intent is for the OMEXMLNode infrastructure to be as complete as possible. Subclasses of OMEXMLNode provide OME-specific functionality such as more intuitive traversal of OME structures.

Source code:

Trac, Gitweb

Field Summary

Fields

Modifier and Type	Field and Description
protected String	basePackage Deprecated. Base package of this node.
protected static Hashtable	classHash Deprecated. Table of existing classes for known node types.
protected static Hashtable	constructorHash Deprecated. Table of existing constructor signatures corresponding to known OMEXMLNode subclasses.
protected Element	element Deprecated. Associated DOM element for this node.
protected static String	idPrefix Deprecated. Prefix used for generated internal ID values.
protected static String	LEGACY_VERSION Deprecated.
protected static Hashtable	nextIds Deprecated. Next free ID numbers for generating internal ID attribute values.
protected static String[]	NODE_PACKAGES Deprecated.
protected static Hashtable	nodeHash Deprecated. Table of existing nodes corresponding to known elements.

Constructor Summary

Constructors

Constructor and Description
OMEXMLNode(Element element) Deprecated. Constructs an OME-XML node with the given associated DOM element.

Method Summary

Methods

Modifier and Type	Method and Description
static void	clearCaches() Deprecated. Clears the cached nodes and resets node indices.
protected void	createReference(OMEXMLNode node) Deprecated. Creates a reference element beneath this node.
boolean	equals(Object obj) Deprecated. Tests whether two OME-XML nodes are equal.
protected Element	getAncestorElement(String name) Deprecated. Gets the first ancestor DOM element with the specified name.
protected OMEXMLNode	getAncestorNode(String name) Deprecated. Gets an OME-XML node representing the first ancestor element with the given name.
String	getAttribute(String name) Deprecated. Gets the value of the DOM element's attribute with the given name.
protected String[]	getAttributeNames() Deprecated. Gets a list of all DOM element attribute names.
protected String[]	getAttributeValues() Deprecated. Gets a list of all DOM element attribute values.
protected OMEXMLNode	getAttrReferencedNode(String nodeType, String attrName) Deprecated. Gets an OME-XML node of the given type representing the first element referenced by an attribute with the given name.
protected int	getAttrReferringCount(String name, String attrName) Deprecated. Gets the number of elements of a certain type (with the given name) that reference this OME-XML node using an attribute.
protected Vector	getAttrReferringNodes(String name, String attrName) Deprecated. Gets a list of nodes of a certain type (with the given name) that refer to this OME-XML node using an attribute.
protected Boolean	getBooleanAttribute(String name) Deprecated. Gets the value of the DOM element's attribute with the given name as a Boolean, or null if the value is not a boolean.
protected Boolean	getBooleanCData(String name) Deprecated. Gets the given child node's character data as a Boolean, or null if the value is not a boolean.
String	getCData() Deprecated. Gets the node's character data.
protected String	getCData(String name) Deprecated. Gets the given child node's character data.
protected int	getChildCount(String name) Deprecated. Gets the number of child elements with the given name.
OMEXMLNode	getChildNode(String name) Deprecated. Gets an OME-XML node representing the first child with the given name.
protected OMEXMLNode	getChildNode(String name, int index) Deprecated. Gets the index-th OME-XML node child with the given name.
protected OMEXMLNode	getChildNode(String nodeType, String name) Deprecated. Gets an OME-XML node of the specified type representing the first child with the given name.
Vector	getChildNodes() Deprecated. NB: This method exists only for legacy reasons, and usage is discouraged.
Vector	getChildNodes(String name) Deprecated. Gets a list of OME-XML node children with the given name.
Element	getDOMElement() Deprecated. Gets the DOM element backing this OME-XML node.
protected Double	getDoubleAttribute(String name) Deprecated. Gets the value of the DOM element's attribute with the given name as a Double, or null if the value is not a double.
protected Double	getDoubleCData(String name) Deprecated. Gets the given child node's character data as a Double, or null if the value is not a double.
String	getElementName() Deprecated. Gets the name of the DOM element.
protected Float	getFloatAttribute(String name) Deprecated. Gets the value of the DOM element's attribute with the given name as a Float, or null if the value is not a float.
protected Float	getFloatCData(String name) Deprecated. Gets the given child node's character data as a Float, or null if the value is not a float.
static String	getIDPrefix() Deprecated. Gets the prefix used when generating internal ID values.
protected Integer	getIntegerAttribute(String name) Deprecated. Gets the value of the DOM element's attribute with the given name as an Integer, or null if the value is not an integer.
protected Integer	getIntegerCData(String name) Deprecated. Gets the given child node's character data as a Integer, or null if the value is not an integer.
protected Long	getLongAttribute(String name) Deprecated. Gets the value of the DOM element's attribute with the given name as a Long, or null if the value is not a long.
protected Long	getLongCData(String name) Deprecated. Gets the given child node's character data as a Long, or null if the value is not a long.
protected OMEXMLNode	getNode(Element el) Deprecated. Gets the OME-XML node corresponding to the specified DOM element.
String	getNodeID() Deprecated. Gets the ID for this node, or null if none.
protected OMEXMLNode	getReferencedNode(String nodeType, String refName) Deprecated. Gets an OME-XML node of the given type representing the first element referenced by a child element with the given name.
protected Vector	getReferencedNodes(String nodeType, String refName) Deprecated. Gets a list of all OME-XML nodes of the given type representing the elements referenced by the child elements with the given name.
protected int	getReferringCount(String name) Deprecated. Gets the number of elements of a certain type (with the given name) that reference this OME-XML node using a *Ref child element.
protected int	getReferringCount(String name, String refName) Deprecated. Gets the number of elements of a certain type (with the given name) that reference this OME-XML node using a child element with name refName.
protected Vector	getReferringNodes(String name) Deprecated. Gets a list of nodes of a certain type (with the given name) that reference this OME-XML node using a *Ref child element.
protected Vector	getReferringNodes(String name, String refName) Deprecated. Gets a list of nodes of a certain type (with the given name) that refer to this OME-XML node using a child element with name refName.
protected String	getStringAttribute(String name) Deprecated. Gets the value of the DOM element's attribute with the given name.
protected String	getStringCData(String name) Deprecated. Gets the given child node's character data.
String	getVersion() Deprecated. Gets the OME-XML schema version ("2003-FC", "2007-06", etc.) for the current OME-XML hierarchy.
abstract boolean	hasID() Deprecated. Gets whether this type of node should have an ID.
boolean	isLegacy() Deprecated. Gets whether the current OME-XML hierarchy is a legacy version.
String	makeID(String nodeType) Deprecated. Gets the next available internal ID for use within this OME-XML node's tree structure.
protected void	setAttribute(String name, Object value) Deprecated. Sets the value of the DOM element's attribute with the given name to the specified Object's string representation.
void	setAttribute(String name, String value) Deprecated. Sets the value of the DOM element's attribute with the given name to the specified value.
protected void	setAttrReferencedNode(OMEXMLNode node, String attrName) Deprecated. Sets the OME-XML referenced by the attribute with the given name.
void	setCData(String value) Deprecated. Sets the node's character data.
protected void	setCData(String name, Object value) Deprecated. Sets the given child node's character data to the specified Object's string representation, creating the child node if necessary.
protected void	setCData(String name, String value) Deprecated. Sets the given child node's character data to the specified value, creating the child node if necessary.
static void	setIDPrefix(String prefix) Deprecated. Sets the prefix used when generating internal ID values.
void	setNodeID(String id) Deprecated. Sets the ID for this node.
String	toString() Deprecated. Gets a string representation of this node.

Methods inherited from class java.lang.Object

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

Field Detail

NODE_PACKAGES

protected static final String[] NODE_PACKAGES

Deprecated.

LEGACY_VERSION

protected static final String LEGACY_VERSION

Deprecated.

See Also:

Constant Field Values

nextIds

protected static Hashtable nextIds

Deprecated.

Next free ID numbers for generating internal ID attribute values.

idPrefix

protected static String idPrefix

Deprecated.

Prefix used for generated internal ID values.

nodeHash

protected static Hashtable nodeHash

Deprecated.

Table of existing nodes corresponding to known elements. This table allows us to have one node instance per element object, and reuse this node on demand, rather than creating a new one every time.

classHash

protected static Hashtable classHash

Deprecated.

Table of existing classes for known node types. This table allows us to avoid searching for a Class object corresponding to a particular node type string within each schema version's package.

constructorHash

protected static Hashtable constructorHash

Deprecated.

Table of existing constructor signatures corresponding to known OMEXMLNode subclasses. This table allows us to avoid searching the Class object for the appropriate constructor every time we need it.

element

protected Element element

Deprecated.

Associated DOM element for this node.

basePackage

protected String basePackage

Deprecated.

Base package of this node.

Constructor Detail

OMEXMLNode

public OMEXMLNode(Element element)

Deprecated.

Constructs an OME-XML node with the given associated DOM element.

Method Detail

getIDPrefix

public static String getIDPrefix()

Deprecated.

Gets the prefix used when generating internal ID values.

setIDPrefix

public static void setIDPrefix(String prefix)

Deprecated.

Sets the prefix used when generating internal ID values.

clearCaches

public static void clearCaches()

Deprecated.

Clears the cached nodes and resets node indices.

getDOMElement

public Element getDOMElement()

Deprecated.

Gets the DOM element backing this OME-XML node.

getElementName

public String getElementName()

Deprecated.

Gets the name of the DOM element.

hasID

public abstract boolean hasID()

Deprecated.

Gets whether this type of node should have an ID.

getNodeID

public String getNodeID()

Deprecated.

Gets the ID for this node, or null if none.

setNodeID

public void setNodeID(String id)

Deprecated.

Sets the ID for this node.

makeID

public String makeID(String nodeType)

Deprecated.

Gets the next available internal ID for use within this OME-XML node's tree structure.

getCData

public String getCData()

Deprecated.

Gets the node's character data.

setCData

public void setCData(String value)

Deprecated.

Sets the node's character data.

isLegacy

public boolean isLegacy()

Deprecated.

Gets whether the current OME-XML hierarchy is a legacy version.

getVersion

public String getVersion()

Deprecated.

Gets the OME-XML schema version ("2003-FC", "2007-06", etc.) for the current OME-XML hierarchy.

getChildCount

protected int getChildCount(String name)

Deprecated.

Gets the number of child elements with the given name.

getChildNode

public OMEXMLNode getChildNode(String name)

Deprecated.

Gets an OME-XML node representing the first child with the given name. NB: This method has public access only for legacy reasons, and direct usage is discouraged.

getChildNode

protected OMEXMLNode getChildNode(String nodeType,
                      String name)

Deprecated.

Gets an OME-XML node of the specified type representing the first child with the given name.

getChildNodes

public Vector getChildNodes(String name)

Deprecated.

Gets a list of OME-XML node children with the given name. NB: This method has public access only for legacy reasons, and direct usage is discouraged.

getChildNode

protected OMEXMLNode getChildNode(String name,
                      int index)

Deprecated.

Gets the index-th OME-XML node child with the given name.

getAncestorNode

protected OMEXMLNode getAncestorNode(String name)

Deprecated.

Gets an OME-XML node representing the first ancestor element with the given name.

getReferencedNode

protected OMEXMLNode getReferencedNode(String nodeType,
                           String refName)

Deprecated.

Gets an OME-XML node of the given type representing the first element referenced by a child element with the given name. For example, if this node is an ImageNode, getReferencedNode("Pixels", "AcquiredPixelsRef") will return a PixelsNode for the Pixels element whose ID matches the one given by the AcquiredPixelsRef child element.

getReferencedNodes

protected Vector getReferencedNodes(String nodeType,
                        String refName)

Deprecated.

Gets a list of all OME-XML nodes of the given type representing the elements referenced by the child elements with the given name. For example, if this node is an ImageNode, getReferencedNodes("Dataset", "DatasetRef") will return a list of DatasetNode objects for the Dataset elements whose IDs match the ones given by the DatasetRef child elements.

getAttrReferencedNode

protected OMEXMLNode getAttrReferencedNode(String nodeType,
                               String attrName)

Deprecated.

Gets an OME-XML node of the given type representing the first element referenced by an attribute with the given name. For example, if this node is an ImageNode, getAttrReferencedNode("Pixels", "DefaultPixels") will return a PixelsNode for the Pixels element whose ID matches the one given by the DefaultPixels attribute.

setAttrReferencedNode

protected void setAttrReferencedNode(OMEXMLNode node,
                         String attrName)

Deprecated.

Sets the OME-XML referenced by the attribute with the given name. For example, if this node is an ImageNode, setAttrReferencedNode(pixelsNode, "DefaultPixels") will set the DefaultPixels attribute value to match the given PixelsNode's ID.

getReferringCount

protected int getReferringCount(String name)

Deprecated.

Gets the number of elements of a certain type (with the given name) that reference this OME-XML node using a *Ref child element.

getReferringCount

protected int getReferringCount(String name,
                    String refName)

Deprecated.

Gets the number of elements of a certain type (with the given name) that reference this OME-XML node using a child element with name refName.

getReferringNodes

protected Vector getReferringNodes(String name)

Deprecated.

Gets a list of nodes of a certain type (with the given name) that reference this OME-XML node using a *Ref child element. For example, if this node is a Project node and getReferringNodes("Dataset") is called, it will search the DOM structure for Datasets with child ProjectRefs element whose IDs match this Project node's ID value.

getReferringNodes

protected Vector getReferringNodes(String name,
                       String refName)

Deprecated.

Gets a list of nodes of a certain type (with the given name) that refer to this OME-XML node using a child element with name refName. For example, if this node is an Experimenter node and getReferringNodes("ExperimenterGroup", "Contact") is called, it will search the DOM structure for ExperimenterGroups with child Contact elements whose IDs match this Experimenter node's ID value.

getAttrReferringCount

protected int getAttrReferringCount(String name,
                        String attrName)

Deprecated.

Gets the number of elements of a certain type (with the given name) that reference this OME-XML node using an attribute.

getAttrReferringNodes

protected Vector getAttrReferringNodes(String name,
                           String attrName)

Deprecated.

Gets a list of nodes of a certain type (with the given name) that refer to this OME-XML node using an attribute. For example, if this node is a PixelsNode and getAttrReferringNodes("ChannelComponent", "Pixels") is called, it will search the DOM structure for ChannelComponents with Pixels attributes whose values match this Pixels node's ID value.

createReference

protected void createReference(OMEXMLNode node)

Deprecated.

Creates a reference element beneath this node. For example, if this node is a DatasetNode and "project" is a ProjectNode, createReference(project) references the Project from this Dataset by adding a child XML element called ProjectRef with an ID attribute matching the ID of the referenced Project.

getCData

protected String getCData(String name)

Deprecated.

Gets the given child node's character data.

getStringCData

protected String getStringCData(String name)

Deprecated.

Gets the given child node's character data.

See Also:

getCData(String)

setCData

protected void setCData(String name,
            String value)

Deprecated.

Sets the given child node's character data to the specified value, creating the child node if necessary.

setCData

protected void setCData(String name,
            Object value)

Deprecated.

Sets the given child node's character data to the specified Object's string representation, creating the child node if necessary.

getBooleanCData

protected Boolean getBooleanCData(String name)

Deprecated.

Gets the given child node's character data as a Boolean, or null if the value is not a boolean.

getDoubleCData

protected Double getDoubleCData(String name)

Deprecated.

Gets the given child node's character data as a Double, or null if the value is not a double.

getFloatCData

protected Float getFloatCData(String name)

Deprecated.

Gets the given child node's character data as a Float, or null if the value is not a float.

getIntegerCData

protected Integer getIntegerCData(String name)

Deprecated.

Gets the given child node's character data as a Integer, or null if the value is not an integer.

getLongCData

protected Long getLongCData(String name)

Deprecated.

Gets the given child node's character data as a Long, or null if the value is not a long.

getAttributeNames

protected String[] getAttributeNames()

Deprecated.

Gets a list of all DOM element attribute names.

getAttributeValues

protected String[] getAttributeValues()

Deprecated.

Gets a list of all DOM element attribute values.

setAttribute

public void setAttribute(String name,
                String value)

Deprecated.

Sets the value of the DOM element's attribute with the given name to the specified value. NB: This method has public access only for legacy reasons, and direct usage is discouraged.

setAttribute

protected void setAttribute(String name,
                Object value)

Deprecated.

Sets the value of the DOM element's attribute with the given name to the specified Object's string representation.

getAttribute

public String getAttribute(String name)

Deprecated.

Gets the value of the DOM element's attribute with the given name. NB: This method has public access only for legacy reasons, and direct usage is discouraged.

getBooleanAttribute

protected Boolean getBooleanAttribute(String name)

Deprecated.

Gets the value of the DOM element's attribute with the given name as a Boolean, or null if the value is not a boolean.

getDoubleAttribute

protected Double getDoubleAttribute(String name)

Deprecated.

Gets the value of the DOM element's attribute with the given name as a Double, or null if the value is not a double.

getFloatAttribute

protected Float getFloatAttribute(String name)

Deprecated.

Gets the value of the DOM element's attribute with the given name as a Float, or null if the value is not a float.

getIntegerAttribute

protected Integer getIntegerAttribute(String name)

Deprecated.

Gets the value of the DOM element's attribute with the given name as an Integer, or null if the value is not an integer.

getLongAttribute

protected Long getLongAttribute(String name)

Deprecated.

Gets the value of the DOM element's attribute with the given name as a Long, or null if the value is not a long.

getStringAttribute

protected String getStringAttribute(String name)

Deprecated.

Gets the value of the DOM element's attribute with the given name.

getNode

protected OMEXMLNode getNode(Element el)

Deprecated.

Gets the OME-XML node corresponding to the specified DOM element.

getAncestorElement

protected Element getAncestorElement(String name)

Deprecated.

Gets the first ancestor DOM element with the specified name.

equals

public boolean equals(Object obj)

Deprecated.

Tests whether two OME-XML nodes are equal. Nodes are considered equal if they are instances of the same class with the same backing DOM element.

Overrides:

equals in class Object

toString

public String toString()

Deprecated.

Gets a string representation of this node.

Overrides:

toString in class Object

getChildNodes

public Vector getChildNodes()

Deprecated. NB: This method exists only for legacy reasons, and usage is discouraged.