uk.ac.ebi.arrayexpress2.magetab.datamodel

Class ADF

java.lang.Object

uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph<ADFNode>

uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF

All Implemented Interfaces:

Graph<ADFNode>

public class ADF
extends AbstractGraph<ADFNode>

A datastructure that models the ADF in the MAGE-TAB spec. Fields for the header part (which resembles the IDF arrangement) are public. Methods are provided for accessing the graph part (resembling SDRF) by retrieving nodes by type.

Author:

Tony Burdett

See Also:

IDF, SDRF

Field Summary

Fields

Modifier and Type	Field and Description
String	accession
String	arrayDesignName
String	magetabVersion
String	printingProtocol
String	provider
List<String>	sequencePolymerType
List<String>	sequencePolymerTypeTermAccession
List<String>	sequencePolymerTypeTermSourceRef
List<String>	substrateType
List<String>	substrateTypeTermAccession
List<String>	substrateTypeTermSourceRef
List<String>	surfaceType
List<String>	surfaceTypeTermAccession
List<String>	surfaceTypeTermSourceRef
List<String>	technologyType
List<String>	technologyTypeTermAccession
List<String>	technologyTypeTermSourceRef
List<String>	termSourceFile
List<String>	termSourceName
List<String>	termSourceVersion
String	version

Constructor Summary

Constructors

Constructor and Description
ADF()

Method Summary

Methods

Modifier and Type	Method and Description
void	addComment(String type, String comment) Add a comment to the array design, keyed by type.
Map<String,Set<String>>	getComments() Get the map of all current comments.
ADFLayout	getLayout() Get the layout of this SDRF.
URL	getLocation() Get the known location of this SDRF, being the location of the file which was parsed to generate it.
boolean	hasBeenHandled(String nodeName, Class<? extends ADFNode> nodeType) Determine whether a given node has been handled already, and exists in the graph.
<T extends ADFNode> T	lookupNode(String nodeName, Class<T> nodeType) Deprecated. since version 1.1, use AbstractGraph.getNode(String, Class) instead
ADFNode	lookupNode(String nodeName, String nodeType) Deprecated. since version 1.1, use AbstractGraph.getNode(String, String) instead
<T extends ADFNode> Collection<T>	lookupNodes(Class<T> nodeType) Deprecated. since version 1.1, use AbstractGraph.getNodes(Class) instead
Collection<? extends ADFNode>	lookupNodes(String nodeType) Deprecated. since version 1.1, use AbstractGraph.getNodes(String) instead
void	removeNodeFromGraph(ADFNode node) Deprecated. since version 1.1, use AbstractGraph.removeNode(uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node) instead
void	setLocation(URL location) Get the known location of this SDRF, being the location of the file which was parsed to generate it.
void	storeNode(ADFNode node) Deprecated. since version 1.1, use AbstractGraph.addNode(uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node) instead

Methods inherited from class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph

addNode, checkForCycles, getAllNodes, getLog, getNode, getNode, getNodeCount, getNodes, getNodes, getRootNodes, removeNode, resolveGraphStructure, updateNode

Methods inherited from class java.lang.Object

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

Field Detail

magetabVersion

public volatile String magetabVersion

accession

public volatile String accession

arrayDesignName

public volatile String arrayDesignName

version

public volatile String version

provider

public volatile String provider

printingProtocol

public volatile String printingProtocol

technologyType

public volatile List<String> technologyType

technologyTypeTermSourceRef

public volatile List<String> technologyTypeTermSourceRef

technologyTypeTermAccession

public volatile List<String> technologyTypeTermAccession

surfaceType

public volatile List<String> surfaceType

surfaceTypeTermSourceRef

public volatile List<String> surfaceTypeTermSourceRef

surfaceTypeTermAccession

public volatile List<String> surfaceTypeTermAccession

substrateType

public volatile List<String> substrateType

substrateTypeTermSourceRef

public volatile List<String> substrateTypeTermSourceRef

substrateTypeTermAccession

public volatile List<String> substrateTypeTermAccession

sequencePolymerType

public volatile List<String> sequencePolymerType

sequencePolymerTypeTermSourceRef

public volatile List<String> sequencePolymerTypeTermSourceRef

sequencePolymerTypeTermAccession

public volatile List<String> sequencePolymerTypeTermAccession

termSourceName

public volatile List<String> termSourceName

termSourceFile

public volatile List<String> termSourceFile

termSourceVersion

public volatile List<String> termSourceVersion

Constructor Detail

ADF

public ADF()

Method Detail

getLocation

public URL getLocation()

Get the known location of this SDRF, being the location of the file which was parsed to generate it. This may be used by handlers wishing to read files declared with some relative location to the SDRF.

Returns:

the location of the SDRF file

setLocation

public void setLocation(URL location)

Get the known location of this SDRF, being the location of the file which was parsed to generate it. This may be used by handlers wishing to read files declared with some relative location to the SDRF.

Parameters:

location - the full URL of the SDRF file represented by this SDRF object

getLayout

public ADFLayout getLayout()

Get the layout of this SDRF. This layout can be used for tracking error locations or writing an SDRF to file.

Returns:

the layout of this SDRF in it's file form

addComment

public void addComment(String type,
              String comment)

Add a comment to the array design, keyed by type.

Parameters:

type - the type of the ADF comment

comment - the value of the comment

getComments

public Map<String,Set<String>> getComments()

Get the map of all current comments.

Returns:

the comments on this IDF

hasBeenHandled

public boolean hasBeenHandled(String nodeName,
                     Class<? extends ADFNode> nodeType)

Determine whether a given node has been handled already, and exists in the graph. Essentially this is a convenience method that delegates to AbstractGraph.getNode(String, Class).

Parameters:

nodeName - the name of the node

nodeType - the class type of the node

Returns:

true if it exists in the graph already, false otherwise

storeNode

@Deprecated
public void storeNode(ADFNode node)
               throws ParseException

Deprecated. since version 1.1, use AbstractGraph.addNode(uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node) instead

Store a node in the ADF graph. This node will be added to the internal graph representation of nodes represented by this ADF object. In this way, this ADF object represents the data encoded by the spreadsheet rather than directly representing the spreadsheet data structure.

Parameters:

node - the node to store

Throws:

ParseException - if the node being stored would violate the principle that the graph is acyclic

removeNodeFromGraph

@Deprecated
public void removeNodeFromGraph(ADFNode node)

Deprecated. since version 1.1, use AbstractGraph.removeNode(uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node) instead

Remove a node that was previously stored in the ADF graph. This node will be taken out of the internal graph representation of nodes represented by this ADF object.

Note: this method also removes any references elsewhere in the graph to this Node, from parent and child nodes. You should relink your ADF graph around the removed node once you have taken it out: but be warned, this may compromise the structure of the graph in terms of Protocol applications either side of the removed node.

Parameters:

node - the node to remove

lookupNode

@Deprecated
public <T extends ADFNode> T lookupNode(String nodeName,
                                          Class<T> nodeType)

Deprecated. since version 1.1, use AbstractGraph.getNode(String, Class) instead

Lookup a node by name and class type in the ADF graph. This will return the node if it exists, or null if not.

Type Parameters:

T - the generic node type to lookup

Parameters:

nodeName - the node name

nodeType - the class type of the node

Returns:

the node, if it exists, or null otherwise

lookupNode

@Deprecated
public ADFNode lookupNode(String nodeName,
                            String nodeType)

Deprecated. since version 1.1, use AbstractGraph.getNode(String, String) instead

Lookup a node by name and type in the ADF graph. This will return the node if it exists, or null if not.

Parameters:

nodeName - the node name

nodeType - the tag that describes the node in the ADF spec

Returns:

the node, if it exists, or null otherwise

lookupNodes

@Deprecated
public <T extends ADFNode> Collection<T> lookupNodes(Class<T> nodeType)

Deprecated. since version 1.1, use AbstractGraph.getNodes(Class) instead

Lookup all nodes of the given class type in the ADF graph. This will return a collection of the nodes of this type, which will be empty if there are none.

Type Parameters:

T - the generic node type to lookup

Parameters:

nodeType - the class type of the node

Returns:

the node, if it exists, or null otherwise

lookupNodes

public Collection<? extends ADFNode> lookupNodes(String nodeType)

Deprecated. since version 1.1, use AbstractGraph.getNodes(String) instead

Lookup all nodes of the given type (by ADF spec name) in the ADF graph. This will return a collection of the nodes of this type, which will be empty if there are none.

Parameters:

nodeType - the class type of the node

Returns:

the node, if it exists, or null otherwise