ontologizer.io.annotation

Class AssociationParser

java.lang.Object

ontologizer.io.annotation.AssociationParser

public class AssociationParser
extends Object

This class is responsible for parsing GO association files. One object is made for each entry; since genes can have 0, 1, or more than one synonyms, we also parse the synonym field and create a mapping from each synonym to the gene-association object. Therefore, if the user enters the synonym of a gene, we may still be able to identify it.

Author:

Peter Robinson, Sebastian Bauer

See Also:

Association, www.geneontology.org

Constructor Summary

Constructors

Constructor and Description
AssociationParser(IParserInput input, TermMap terms) Construct the association parser object.
AssociationParser(IParserInput input, TermMap terms, HashSet<ByteString> names) Construct the association parser object.
AssociationParser(IParserInput input, TermMap terms, HashSet<ByteString> names, Collection<String> evidences, IAssociationParserProgress progress) Construct the association parser object.
AssociationParser(IParserInput input, TermMap terms, HashSet<ByteString> names, Collection<String> evidences, IAssociationParserProgress progress, boolean iterative) Construct the association parser object.
AssociationParser(IParserInput input, TermMap terms, HashSet<ByteString> names, IAssociationParserProgress progress) Construct the association parser object.

Method Summary

Modifier and Type	Method and Description
AnnotationContext	getAnnotationMapping()
ArrayList<Association>	getAssociations()
ontologizer.io.annotation.AssociationParser.Type	getFileType()
List<ByteString>	getListOfObjectSymbols()
boolean	parse() Start or continue to parse the associations.

Methods inherited from class java.lang.Object

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

Constructor Detail

AssociationParser

public AssociationParser(IParserInput input,
                         TermMap terms)
                  throws IOException

Construct the association parser object. The given file name will parsed. Convenience constructor when not using progress monitor.

Parameters:

input -

terms -

Throws:

IOException

AssociationParser

public AssociationParser(IParserInput input,
                         TermMap terms,
                         HashSet<ByteString> names)
                  throws IOException

Construct the association parser object. The given file name will parsed. Convenience constructor when not using progress monitor.

Parameters:

input -

terms -

names -

Throws:

IOException

AssociationParser

public AssociationParser(IParserInput input,
                         TermMap terms,
                         HashSet<ByteString> names,
                         IAssociationParserProgress progress)
                  throws IOException

Construct the association parser object. The given file name will parsed.

Parameters:

input - specifies wrapping input that contains association of genes to GO terms.

terms - the container of the GO terms

names - list of genes from which the associations should be gathered. If null all associations are taken,

progress -

Throws:

IOException

AssociationParser

public AssociationParser(IParserInput input,
                         TermMap terms,
                         HashSet<ByteString> names,
                         Collection<String> evidences,
                         IAssociationParserProgress progress)
                  throws IOException

Construct the association parser object. The given file name will parsed.

Parameters:

input - specifies wrapping input that contains association of genes to GO terms.

terms - the container of the GO terms

names - list of genes from which the associations should be gathered. If null all associations are taken,

progress -

Throws:

IOException

AssociationParser

public AssociationParser(IParserInput input,
                         TermMap terms,
                         HashSet<ByteString> names,
                         Collection<String> evidences,
                         IAssociationParserProgress progress,
                         boolean iterative)
                  throws IOException

Construct the association parser object. The given file name will parsed.

Parameters:

input - specifies wrapping input that contains association of genes to GO terms.

terms - the container of the GO terms

names - list of genes from which the associations should be gathered. If null all associations are taken,

evidences - keep only the annotation whose evidence match the given ones. If null, all annotations are used. Note that this field is currently used when the filenames referes to a GAF file.

progress -

iterative - set to true if no actual parsing should be done in the constructor.

Throws:

IOException

Method Detail

parse

public boolean parse()
              throws IOException

Start or continue to parse the associations. This needs only to be called when the parser was created with the iterative flag set to true.

Returns:

true if parsing is completed. Otherwise, false is returned in which case you must call parse() again.

Throws:

IOException

getAssociations

public ArrayList<Association> getAssociations()

Returns:

all parsed associations.

getAnnotationMapping

public AnnotationContext getAnnotationMapping()

getListOfObjectSymbols

public List<ByteString> getListOfObjectSymbols()

Returns:

the list of object symbols of all associations.

getFileType

public ontologizer.io.annotation.AssociationParser.Type getFileType()

Returns:

the file type of the associations.