org.cybertory.MSS
Class X_GridFeaturesIntensities

java.lang.Object
  extended byorg.cybertory.MSS.XMLHandler
      extended byorg.cybertory.MSS.XMLHandlerStd
          extended byorg.cybertory.MSS.X_GridFeaturesIntensities
All Implemented Interfaces:
java.lang.Comparable

public class X_GridFeaturesIntensities
extends XMLHandlerStd

XML wrapper for GridFeaturesIntensities. For microarrays where all zones are the same size, located on a regular grid (evenly spaced metarows and metacols). Also, the spacing between rows and columns (within zones) is consistent amongst all the zones.


Field Summary
 
Fields inherited from class org.cybertory.MSS.XMLHandler
handledClass
 
Constructor Summary
X_GridFeaturesIntensities()
           
 
Method Summary
 java.lang.Object parseElement(org.jdom.Element elem, XMLAltData altData)
          Given that the element already extracted from it's context, parse the data (whose type should match that of the handler).
 org.jdom.Element schemaTypedef()
          From somewhere, we have to get the number of metarows,metarows as well as the number of rows,cols.
 java.lang.String typeDescription()
           
 
Methods inherited from class org.cybertory.MSS.XMLHandlerStd
allowBackwardRef, allowMultiple, needsTypedef, xmlTypeName
 
Methods inherited from class org.cybertory.MSS.XMLHandler
alternateElement, compareTo, extractChildren, getAllHandlers, getHandledClasses, getHandler, getHandlersDefs, getXMLChildFilter, getXMLChildFilter, handledClass, handlersReport, parseChildren, parseRequest, parseXMLDocument, schemaDocument, schemaInContext, schemaInContext, schemaInContext, schemaInContext
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

X_GridFeaturesIntensities

public X_GridFeaturesIntensities()
                          throws XMLUnhandledTypeException
Method Detail

typeDescription

public java.lang.String typeDescription()
Overrides:
typeDescription in class XMLHandler

schemaTypedef

public org.jdom.Element schemaTypedef()
                               throws XMLUnhandledTypeException
From somewhere, we have to get the number of metarows,metarows as well as the number of rows,cols. This information could be explicit or it could be inferred from the raw data.

Specified by:
schemaTypedef in class XMLHandlerStd
Returns:
a JDOM Element with schema for type
Throws:
XMLUnhandledTypeException

parseElement

public java.lang.Object parseElement(org.jdom.Element elem,
                                     XMLAltData altData)
                              throws XMLParseException,
                                     XMLUnhandledTypeException
Description copied from class: XMLHandlerStd
Given that the element already extracted from it's context, parse the data (whose type should match that of the handler).

Specified by:
parseElement in class XMLHandlerStd
Parameters:
elem - the JDOM element containing the data
altData - the background data context for parsing
Returns:
an object of the appropriate type
Throws:
XMLParseException
XMLUnhandledTypeException