ubic.erminej.data

Class GeneSetTerms

java.lang.Object

ubic.erminej.data.GeneSetTerms

public class GeneSetTerms
extends Object

Maintain information on GeneSetTerms (including but not limited GO terms). Note that this does not keep track of which genes are annotated with these terms.

Version:

$Id: GeneSetTerms.java,v 1.17 2013/05/20 05:21:15 paul Exp $

Author:

Paul Pavlidis, Homin Lee

See Also:

GeneAnnotations, which represents the actual annotations (and Gene and Probes also keep track of their own), which provides convenient methods to work with the sets themselves., which helps deal with ones the user has stored separately from GO

Field Summary

Fields

Modifier and Type	Field and Description
protected static org.apache.commons.logging.Log	log
static String	NO_ASPECT_AVAILABLE Name for aspect when none is defined.
static String	USER_DEFINED Name for root of tree representing user-defined gene sets.

Constructor Summary

Constructors

Constructor and Description
GeneSetTerms(Collection<GeneSetTerm> terms) Create based only on 'user defined', without reading in GO.
GeneSetTerms(InputStream inputStream)
GeneSetTerms(InputStream i, boolean oldFormat)
GeneSetTerms(String fileName, boolean oldFormat)
GeneSetTerms(String fileName, Settings settings)

Method Summary

Methods

Modifier and Type	Method and Description
protected GeneSetTerm	get(String geneSetId) Note that it is probably preferable to use findTerm from GeneAnnotations; this is used while setting that up.
Set<GeneSetTerm>	getAllChildren(GeneSetTerm term)
Collection<GeneSetTerm>	getAllParents(GeneSetTerm id)
Set<GeneSetTerm>	getChildren(GeneSetTerm id)
Set<GeneSetTerm>	getGeneSets()
DirectedGraph<String,GeneSetTerm>	getGraph()
Collection<GeneSetTerm>	getParents(GeneSetTerm id)
Collection<GeneSetTerm>	getTerms()
DefaultTreeModel	getTreeModel()
boolean	isLeaf(GeneSetTerm id)
boolean	isParent(GeneSetTerm p, GeneSetTerm c)
protected void	removeUserDefined(GeneSetTerm id)

Methods inherited from class java.lang.Object

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

Field Detail

NO_ASPECT_AVAILABLE

public static final String NO_ASPECT_AVAILABLE

Name for aspect when none is defined.

See Also:

Constant Field Values

USER_DEFINED

public static final String USER_DEFINED

Name for root of tree representing user-defined gene sets.

See Also:

Constant Field Values

log

protected static final org.apache.commons.logging.Log log

Constructor Detail

GeneSetTerms

public GeneSetTerms(InputStream inputStream)
             throws IOException,
                    SAXException

Parameters:

inputStream - assumed to be in recent format.

Throws:

IOException

SAXException

GeneSetTerms

public GeneSetTerms(String fileName,
            Settings settings)
             throws SAXException,
                    IOException

Parameters:

fileNamefilename - String The XML file containing class to name mappings.

Throws:

SAXException

IOException

GeneSetTerms

public GeneSetTerms(String fileName,
            boolean oldFormat)
             throws SAXException,
                    IOException

Parameters:

filename - String The XML file containing class to name mappings.

oldFormat - set to true to indicate that the RDF is 'old style' (pre ~2008)

Throws:

IOException

SAXException

GeneSetTerms

public GeneSetTerms(Collection<GeneSetTerm> terms)

Create based only on 'user defined', without reading in GO. Unless you construct the terms specially, this will be a flat set (not a hierarchy)

Parameters:

terms -

GeneSetTerms

public GeneSetTerms(InputStream i,
            boolean oldFormat)
             throws SAXException,
                    IOException

Throws:

SAXException

IOException

Method Detail

removeUserDefined

protected void removeUserDefined(GeneSetTerm id)

Parameters:

id -

get

protected GeneSetTerm get(String geneSetId)

Note that it is probably preferable to use findTerm from GeneAnnotations; this is used while setting that up.

Parameters:

geneSetId -

Returns:

GeneSetTerm

isLeaf

public boolean isLeaf(GeneSetTerm id)

Parameters:

id -

Returns:

true if this term has no children

getChildren

public Set<GeneSetTerm> getChildren(GeneSetTerm id)

Parameters:

id -

Returns:

a Set containing the ids of geneSets which are immediately below the selected one in the hierarchy.

getGeneSets

public Set<GeneSetTerm> getGeneSets()

Returns:

all the geneset terms.

getGraph

public DirectedGraph<String,GeneSetTerm> getGraph()

Returns:

graph representation of the term hierarchy

getParents

public Collection<GeneSetTerm> getParents(GeneSetTerm id)

Parameters:

id - GO id

Returns:

a Set containing the ids of geneSets which are immediately above the selected one in the hierarchy - but excluding the aspect or the root. Thus if the parameter is an aspect, nothing will be returned.

getAllParents

public Collection<GeneSetTerm> getAllParents(GeneSetTerm id)

Parameters:

id -

Returns:

all parents EXCEPT for obsolete terms, aspect and root.

getTerms

public Collection<GeneSetTerm> getTerms()

Returns:

getTreeModel

public DefaultTreeModel getTreeModel()

getAllChildren

public Set<GeneSetTerm> getAllChildren(GeneSetTerm term)

Parameters:

term -

Returns:

isParent

public boolean isParent(GeneSetTerm p,
               GeneSetTerm c)

Parameters:

p -

c -

Returns:

true if p is a parent of c (somewhere in the hierarchy.