A C D E F G I N O P R S T U W X

A

AbstractByteLineScanner - Class in ontologizer.io.linescanner

This is a simple class that can be used to read an input stream in byte representation in a line-based manner.

AbstractByteLineScanner(InputStream) - Constructor for class ontologizer.io.linescanner.AbstractByteLineScanner

AbstractDotAttributesProvider - Class in ontologizer.io.dot

Default implementation of the interface providing attributes for dot graph.

AbstractDotAttributesProvider() - Constructor for class ontologizer.io.dot.AbstractDotAttributesProvider

AffyParser - Class in ontologizer.io.annotation

Parser of affymetrix annotation files.

AffyParser() - Constructor for class ontologizer.io.annotation.AffyParser

ALT_ID_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

AssociationParser - Class in ontologizer.io.annotation

This class is responsible for parsing GO association files.

AssociationParser(IParserInput, TermMap) - Constructor for class ontologizer.io.annotation.AssociationParser

Construct the association parser object.

AssociationParser(IParserInput, TermMap, HashSet<ByteString>) - Constructor for class ontologizer.io.annotation.AssociationParser

Construct the association parser object.

AssociationParser(IParserInput, TermMap, HashSet<ByteString>, IAssociationParserProgress) - Constructor for class ontologizer.io.annotation.AssociationParser

Construct the association parser object.

AssociationParser(IParserInput, TermMap, HashSet<ByteString>, Collection<String>, IAssociationParserProgress) - Constructor for class ontologizer.io.annotation.AssociationParser

Construct the association parser object.

AssociationParser(IParserInput, TermMap, HashSet<ByteString>, Collection<String>, IAssociationParserProgress, boolean) - Constructor for class ontologizer.io.annotation.AssociationParser

Construct the association parser object.

available() - Method in class ontologizer.io.linescanner.AbstractByteLineScanner

Returns the number of bytes that are still available in the buffer after the reading has been aborted.

availableBuffer() - Method in class ontologizer.io.linescanner.AbstractByteLineScanner

Returns the bytes that are still available in the buffer after the reading has been aborted.

C

close() - Method in interface ontologizer.io.obo.IParserInput

Close the associated input streams.

close() - Method in class ontologizer.io.obo.OBOParserFileInput

D

DATA_VERSION_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

DATE_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

decodeTermID(String) - Static method in class ontologizer.io.dot.GODOTWriter

Decode the string that was encoded via GODOTWriter.encodeTermID(TermID)

DEF_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

DescriptionParser - Class in ontologizer.io.obo

This is a simple parser for descriptions used in OBO.

DescriptionParser() - Constructor for class ontologizer.io.obo.DescriptionParser

DescriptionParser.IDescriptionPartCallback - Interface in ontologizer.io.obo

doParse() - Method in class ontologizer.io.obo.OBOParser

The main parsing routine for the gene_ontology.obo file

doParse(IOBOParserProgress) - Method in class ontologizer.io.obo.OBOParser

The main parsing routine for the gene_ontology.obo file

DOTWriter - Class in ontologizer.io.dot

DOTWriter() - Constructor for class ontologizer.io.dot.DOTWriter

E

encodeTermID(TermID) - Static method in class ontologizer.io.dot.GODOTWriter

Encode the term id string of the given term id.

EQUIVALENT_TO_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

F

FORMAT_VERSION_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

G

getAnnotationMapping() - Method in class ontologizer.io.annotation.AssociationParser

getAssociations() - Method in class ontologizer.io.annotation.AffyParser

getAssociations() - Method in class ontologizer.io.annotation.AssociationParser

getDataVersion() - Method in class ontologizer.io.obo.OBOParser

getDate() - Method in class ontologizer.io.obo.OBOParser

getDotEdgeAttributes(TermID, TermID) - Method in class ontologizer.io.dot.AbstractDotAttributesProvider

getDotEdgeAttributes(TermID, TermID) - Method in interface ontologizer.io.dot.IDotAttributesProvider

getDotNodeAttributes(TermID) - Method in class ontologizer.io.dot.AbstractDotAttributesProvider

Returns the dot attributes for the given term.

getDotNodeAttributes(TermID) - Method in interface ontologizer.io.dot.IDotAttributesProvider

getFilename() - Method in interface ontologizer.io.obo.IParserInput

getFilename() - Method in class ontologizer.io.obo.OBOParserFileInput

getFileType() - Method in class ontologizer.io.annotation.AssociationParser

getFormatVersion() - Method in class ontologizer.io.obo.OBOParser

getLine() - Method in exception ontologizer.io.obo.OBOParserException

getLineNum() - Method in exception ontologizer.io.obo.OBOParserException

getListOfObjectSymbols() - Method in class ontologizer.io.annotation.AssociationParser

getPosition() - Method in interface ontologizer.io.obo.IParserInput

getPosition() - Method in class ontologizer.io.obo.OBOParserFileInput

getSize() - Method in interface ontologizer.io.obo.IParserInput

getSize() - Method in class ontologizer.io.obo.OBOParserFileInput

getSynonym2Symbol() - Method in class ontologizer.io.annotation.AffyParser

getTermMap() - Method in class ontologizer.io.obo.OBOParser

GODOTWriter - Class in ontologizer.io.dot

GODOTWriter() - Constructor for class ontologizer.io.dot.GODOTWriter

I

IAssociationParserProgress - Interface in ontologizer.io.annotation

ID_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

IDotAttributesProvider - Interface in ontologizer.io.dot

An interface for providing attributes for dot graph.

IGNORE_SYNONYMS - Static variable in class ontologizer.io.obo.OBOParser

Ignore synonyms

init(int) - Method in interface ontologizer.io.annotation.IAssociationParserProgress

Called upon initialization.

init(int) - Method in interface ontologizer.io.obo.IOBOParserProgress

Called upon initialization.

inputStream() - Method in interface ontologizer.io.obo.IParserInput

inputStream() - Method in class ontologizer.io.obo.OBOParserFileInput

IOBOParserProgress - Interface in ontologizer.io.obo

IParserInput - Interface in ontologizer.io.obo

An interface wrapping the input for miscellaneous parsers.

IS_A_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

IS_OBSOLETE_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

N

NAME_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

NAMESPACE_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

NEGATIVELY_REGULATES_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

newLine(byte[], int, int) - Method in class ontologizer.io.linescanner.AbstractByteLineScanner

Called whenever a new line was encountered.

O

OBOKeywords - Class in ontologizer.io.obo

OBOKeywords() - Constructor for class ontologizer.io.obo.OBOKeywords

OBOParser - Class in ontologizer.io.obo

OBOParser parses the Gene Ontology OBO term definition file.

OBOParser(IParserInput) - Constructor for class ontologizer.io.obo.OBOParser

Construct an obo parser.

OBOParser(IParserInput, int) - Constructor for class ontologizer.io.obo.OBOParser

Constructs an obo parser for a particular input.

OBOParserException - Exception in ontologizer.io.obo

An exception which may be thrown by the OBOParser class.

OBOParserException(String, String, int) - Constructor for exception ontologizer.io.obo.OBOParserException

OBOParserException(String) - Constructor for exception ontologizer.io.obo.OBOParserException

OBOParserFileInput - Class in ontologizer.io.obo

An OBOParserInput for a local file.

OBOParserFileInput(String) - Constructor for class ontologizer.io.obo.OBOParserFileInput

ontologizer.io.annotation - package ontologizer.io.annotation

ontologizer.io.dot - package ontologizer.io.dot

ontologizer.io.linescanner - package ontologizer.io.linescanner

ontologizer.io.obo - package ontologizer.io.obo

P

parse(IParserInput, byte[], HashSet<ByteString>, TermMap, IAssociationParserProgress) - Method in class ontologizer.io.annotation.AffyParser

parse() - Method in class ontologizer.io.annotation.AssociationParser

Start or continue to parse the associations.

parse(String, DescriptionParser.IDescriptionPartCallback) - Static method in class ontologizer.io.obo.DescriptionParser

Parse the given description.

parse(String) - Static method in class ontologizer.io.obo.DescriptionParser

Parse the given description using the default filter.

PARSE_DEFINITIONS - Static variable in class ontologizer.io.obo.OBOParser

Flag to keep the definitions

PARSE_INTERSECTIONS - Static variable in class ontologizer.io.obo.OBOParser

Flag to keep the intersections

PARSE_XREFS - Static variable in class ontologizer.io.obo.OBOParser

Flag to keep the xrefs

part(String, String) - Method in interface ontologizer.io.obo.DescriptionParser.IDescriptionPartCallback

PART_OF_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

POSITIVELY_REGULATES_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

push(byte[]) - Method in class ontologizer.io.linescanner.AbstractByteLineScanner

Push the given bytes such that they are read first before the bytes at the input stream.

R

REGULATES_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

RELATIONSHIP_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

S

scan() - Method in class ontologizer.io.linescanner.AbstractByteLineScanner

SETNAMEEQUALTOID - Static variable in class ontologizer.io.obo.OBOParser

Takes the id as name, if the name is not present

SUBSET_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

SUBSETDEF_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

SYNONYM_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

T

TERM_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

TERM_KEYWORDS - Static variable in class ontologizer.io.obo.OBOKeywords

toString() - Method in exception ontologizer.io.obo.OBOParserException

TRUE_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

TYPEDEF_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

U

update(int) - Method in interface ontologizer.io.annotation.IAssociationParserProgress

Called arbitrary.

update(int, int) - Method in interface ontologizer.io.obo.IOBOParserProgress

Called arbitrary.

W

warning(String) - Method in interface ontologizer.io.annotation.IAssociationParserProgress

In case of a warning.

write(AbstractGraph<V>, OutputStream, Iterable<V>, AbstractGraph.DotAttributesProvider<V>, double, double) - Static method in class ontologizer.io.dot.DOTWriter

Writes out a graph as a dot file.

write(AbstractGraph<V>, OutputStream, Iterable<V>, AbstractGraph.DotAttributesProvider<V>) - Static method in class ontologizer.io.dot.DOTWriter

Writes out a graph as a dot file.

writeDOT(Ontology, File, TermID, Set<TermID>, IDotAttributesProvider) - Static method in class ontologizer.io.dot.GODOTWriter

Writes out a basic dot file which can be used within graphviz.

writeDOT(Ontology, File, TermID, Set<TermID>, IDotAttributesProvider, String, boolean, boolean, Set<TermID>) - Static method in class ontologizer.io.dot.GODOTWriter

Writes out a basic dot file which can be used within graphviz.

X

XREF_KEYWORD - Static variable in class ontologizer.io.obo.OBOKeywords

A C D E F G I N O P R S T U W X