Package com.biomatters.geneious.publicapi.utilities.xml

Class PluginDocumentXmlCollection

java.lang.Object

com.biomatters.geneious.publicapi.utilities.xml.PluginDocumentXmlCollection

public class PluginDocumentXmlCollection
extends java.lang.Object

Provides a system for serializing and deserializing a PluginDocument that contains a large number of sub-elements so that all the elements do not need to be in memory simultaneously.

This is used for example when serializing DefaultSequenceListDocument and DefaultAlignmentDocument, each of which may contain millions of sequences which would take up too much memory if all the contained sequences were simultaneously in memory in their XML form.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PluginDocumentXmlCollection.ElementHandler

Constructor Summary

Constructors

Constructor	Description
PluginDocumentXmlCollection()

Method Summary

Modifier and Type	Method	Description
static void	fromXml(org.jdom.Element rootElement, PluginDocumentXmlCollection.ElementHandler childElementHandler, jebl.util.ProgressListener progressListener)	deserializes some XML elements, calling PluginDocumentXmlCollection.ElementHandler.handleElement(org.jdom.Element) for each child element.
static org.jdom.Element	toXml(org.jdom.Element rootElement, java.lang.Iterable<org.jdom.Element> childElements, int childElementsSize, jebl.util.ProgressListener progressListener, boolean serializeToFileInsteadOfMemory)	Serializes these elements into a single parent element, potentially storing them in a file (using PluginDocument.FILE_DATA_ATTRIBUTE_NAME)

Methods inherited from class java.lang.Object

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

Constructor Detail

PluginDocumentXmlCollection

public PluginDocumentXmlCollection()

Method Detail

toXml

public static org.jdom.Element toXml(org.jdom.Element rootElement,
                                     java.lang.Iterable<org.jdom.Element> childElements,
                                     int childElementsSize,
                                     jebl.util.ProgressListener progressListener,
                                     boolean serializeToFileInsteadOfMemory)
                              throws XMLSerializationException

Serializes these elements into a single parent element, potentially storing them in a file (using PluginDocument.FILE_DATA_ATTRIBUTE_NAME)

Parameters:

rootElement - the root element under which to store the child elements (or the element on which to attach the file data attribute if there are too many child elements)

childElements - the child elements to serialize. These may be added directly to a parent element, so they must not already be a child element of some other element.

childElementsSize - the number of elements that are in childElements.

progressListener - for reporting progress and handling cancelling.

serializeToFileInsteadOfMemory - true to serialized to a file instead of in memory.

Returns:

rootElement

Throws:

XMLSerializationException

fromXml

public static void fromXml(org.jdom.Element rootElement,
                           PluginDocumentXmlCollection.ElementHandler childElementHandler,
                           jebl.util.ProgressListener progressListener)
                    throws XMLSerializationException

deserializes some XML elements, calling PluginDocumentXmlCollection.ElementHandler.handleElement(org.jdom.Element) for each child element. There could potentially be a lot of child elements (more than can be held simultaneously in memory as jdom elements).

Parameters:

rootElement - a root element returned from a previous call to toXml(org.jdom.Element, Iterable, int, jebl.util.ProgressListener, boolean)

childElementHandler - a callback to pass each child element of rootElement to.

progressListener - for reporting progress and handling canceling.

Throws:

XMLSerializationException