uk.ac.ebi.arrayexpress2.magetab.datamodel.layout

Class SDRFLayout

java.lang.Object

uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout

All Implemented Interfaces:

Layout<SDRF>

public class SDRFLayout
extends Object
implements Layout<SDRF>

An object that describes the relationship between an SDRF datamodel object and the serialized version of it.

The SDRF datamodel is considerably more complex than IDF, as the parsed version of the SDRF is a graph. This graph has a mapping to the spreadsheet view where each node can occupy several locations in the spreadsheet. Furthermore, the set of attributes attached to the node in each of these locations need not actually be identical (although they should be, and usually are, the same). To this end, each node in the SDRF graph must be assigned one or more locations, and each attribute for each node must also be assigned one or more locations.

Tracking this location information on parsing ensures that SDRF objects can be roundtripped from spreadsheet to graph view and back whilst preserving row and column order, so that a 'diff' of the two files should be identical.

Author:

Tony Burdett

Constructor Summary

Constructors

Constructor and Description
SDRFLayout()

Method Summary

Methods

Modifier and Type	Method and Description
void	addAttributeLocation(SDRFAttribute attribute, Location location)
void	addNodeLocation(SDRFNode node, Location location)
void	addPrimitiveLocation(String primitiveValue, String columnName, Location location)
void	calculateLocations(SDRF sdrf) A factory method for fully calculates the layout of the given datamodel object, using Limpopo's own MAGE-TAB printing algorithms.
void	calculateUnassignedLocations(SDRF sdrf) A factory method for calculating the locations of any data items not already assigned.
boolean	containsUnassignedElements(SDRF sdrf) Returns true if the supplied datamodel has elements with no assigned location in this layout.
SDRFAttribute	getAttribute(Location location)
String[]	getHeaders()
int	getLineCount()
Collection<Location>	getLocationsForAttribute(SDRFAttribute attribute)
Collection<Location>	getLocationsForNode(SDRFNode node)
Collection<Location>	getLocationsForPrimitive(String primitive)
protected org.slf4j.Logger	getLog()
SDRFNode	getNode(Location location)
String	getPrimitive(Location location)
boolean	isCompletelyUnassigned() Returns true if there is no layout information contained within this layout
void	storeHeaders(String[] originalHeaders)

Methods inherited from class java.lang.Object

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

Constructor Detail

SDRFLayout

public SDRFLayout()

Method Detail

getLog

protected org.slf4j.Logger getLog()

storeHeaders

public void storeHeaders(String[] originalHeaders)

addNodeLocation

public void addNodeLocation(SDRFNode node,
                   Location location)

addAttributeLocation

public void addAttributeLocation(SDRFAttribute attribute,
                        Location location)

addPrimitiveLocation

public void addPrimitiveLocation(String primitiveValue,
                        String columnName,
                        Location location)

getHeaders

public String[] getHeaders()

getNode

public SDRFNode getNode(Location location)

getAttribute

public SDRFAttribute getAttribute(Location location)

getPrimitive

public String getPrimitive(Location location)

getLocationsForNode

public Collection<Location> getLocationsForNode(SDRFNode node)

getLocationsForAttribute

public Collection<Location> getLocationsForAttribute(SDRFAttribute attribute)

getLocationsForPrimitive

public Collection<Location> getLocationsForPrimitive(String primitive)

getLineCount

public int getLineCount()

containsUnassignedElements

public boolean containsUnassignedElements(SDRF sdrf)

Description copied from interface: Layout

Returns true if the supplied datamodel has elements with no assigned location in this layout.

Specified by:

containsUnassignedElements in interface Layout<SDRF>

Returns:

true if there are unassigned elements, false otherwise

isCompletelyUnassigned

public boolean isCompletelyUnassigned()

Description copied from interface: Layout

Returns true if there is no layout information contained within this layout

Specified by:

isCompletelyUnassigned in interface Layout<SDRF>

Returns:

true if there is no layout information for this datamodel at all

calculateUnassignedLocations

public void calculateUnassignedLocations(SDRF sdrf)

Description copied from interface: Layout

A factory method for calculating the locations of any data items not already assigned. Locations can be assigned during parsing or during any calculation step. If data is subsequently added after calculating locations, it will have an unassigned location. To ensure the layout is changed minimally after adding data, use this method.

Specified by:

calculateUnassignedLocations in interface Layout<SDRF>

Parameters:

sdrf - the datamodel for which to assign layout data for anything that hasn't been laid out previously

calculateLocations

public void calculateLocations(SDRF sdrf)

Description copied from interface: Layout

A factory method for fully calculates the layout of the given datamodel object, using Limpopo's own MAGE-TAB printing algorithms. Any previous location information may become invalid. So, if you use this method to calculate locations on a parsed document, the location information will not be the same as that in the original file.

Specified by:

calculateLocations in interface Layout<SDRF>

Parameters:

sdrf - the datamodel to layout