A B C D E F G H I J K L M N O P Q R S T U V W X

A

AbstractTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

AbstractTagValueHandler(String, OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
addAnnotation(String, String, OWLLiteral) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
addEscapes(String) - Static method in error org.coode.owlapi.obo.parser.TokenMgrError
Replaces unprintable characters by their escaped (or unicode escaped) equivalents in the given string
addException(OBOStorageException) - Method in interface org.coode.owlapi.obo.renderer.OBOExceptionHandler
 
addException(OBOStorageException) - Method in class org.coode.owlapi.obo.renderer.OBOFlatFileRenderer
 
addIntersectionOfOperand(OWLClassExpression) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
addModifier(String, String) - Method in class org.coode.owlapi.obo.parser.Modifiers
Adds a modifier
addPair(OBOVocabulary, String) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList
 
addPair(IRI, String) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList
 
addSymbolicIdMapping(String, IRI) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
addUnionOfOperand(OWLClassExpression) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
adjustBeginLineColumn(int, int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream
Method to adjust line and column numbers for the start of a token.
AdjustBuffSize() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
 
AltIdTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 10/05/2012
AltIdTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.AltIdTagValueHandler
 
ANNOTATION_URI_BASE - Static variable in enum org.coode.owlapi.obo.parser.OBOVocabulary
Deprecated. Use OBOVocabulary.OBO_IRI_BASE
applyChange(OWLOntologyChange) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
AsymmetricHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

AsymmetricHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.AsymmetricHandler
 

B

backup(int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream
Retreat.
beginColumn - Variable in class org.coode.owlapi.obo.parser.Token
The column number of the first character of this Token.
beginLine - Variable in class org.coode.owlapi.obo.parser.Token
The line number of the first character of this Token.
BeginToken() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
 
bufcolumn - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 
buffer - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 
bufline - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 
bufpos - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
Position in buffer.

C

canStoreOntology(OWLOntologyFormat) - Method in class org.coode.owlapi.obo.renderer.OBOFlatFileOntologyStorer
 
clear() - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator
 
CLOSE_SQUARE_BRACKET - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
column - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 
Comment() - Method in class org.coode.owlapi.obo.parser.OBOParser
 
COMMENT - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
COMMENT_END - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
COMMENT_START - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
createParser(OWLOntologyManager) - Method in class org.coode.owlapi.obo.parser.OBOParserFactory
 
curChar - Variable in class org.coode.owlapi.obo.parser.OBOParserTokenManager
 
currentToken - Variable in exception org.coode.owlapi.obo.parser.ParseException
This is the last token that has been consumed successfully.

D

DataVersionTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 19/04/2012
DataVersionTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.DataVersionTagValueHandler
 
debugStream - Variable in class org.coode.owlapi.obo.parser.OBOParserTokenManager
Debug output.
DEFAULT - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
Lexical state.
DefaultNamespaceTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Information Management Group
Date: 01-Sep-2008

OBO Namespaces are NOT like XML Namespaces.

DefaultNamespaceTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.DefaultNamespaceTagValueHandler
 
DefTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012
DefTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.DefTagValueHandler
 
disable_tracing() - Method in class org.coode.owlapi.obo.parser.OBOParser
Disable tracing.
DisjointFromHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

DisjointFromHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.DisjointFromHandler
 
DomainHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 20-May-2007

DomainHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.DomainHandler
 
Done() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
Set buffers back to null when finished.

E

enable_tracing() - Method in class org.coode.owlapi.obo.parser.OBOParser
Enable tracing.
endColumn - Variable in class org.coode.owlapi.obo.parser.Token
The column number of the last character of this Token.
endFrame() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
endFrame() - Method in interface org.coode.owlapi.obo.parser.OBOParserHandler
 
endFrame() - Method in class org.coode.owlapi.obo.parser.OBOParserHandlerAdapter
 
endFrame() - Method in class org.coode.owlapi.obo.parser.RawFrameHandler
 
endHeader() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
endHeader() - Method in interface org.coode.owlapi.obo.parser.OBOParserHandler
 
endHeader() - Method in class org.coode.owlapi.obo.parser.OBOParserHandlerAdapter
 
endHeader() - Method in class org.coode.owlapi.obo.parser.RawFrameHandler
 
endLine - Variable in class org.coode.owlapi.obo.parser.Token
The line number of the last character of this Token.
EOF - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
End of File.
eol - Variable in exception org.coode.owlapi.obo.parser.ParseException
The end of line string for this machine.
ERROR - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
ExpandBuff(boolean) - Method in class org.coode.owlapi.obo.parser.JavaCharStream
 
expectedTokenSequences - Variable in exception org.coode.owlapi.obo.parser.ParseException
Each entry in this array is an array of integers.

F

FillBuff() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
 

G

generateParseException() - Method in class org.coode.owlapi.obo.parser.OBOParser
Generate ParseException.
getAnnotationForTagValuePair(String, String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
Gets an OWLAnnotation for a tag value pair.
getBeginColumn() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
 
getBeginLine() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
 
getBooleanConstant(boolean) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getCardinality() - Method in class org.coode.owlapi.obo.renderer.OBORelationship
 
getCauses() - Method in exception org.coode.owlapi.obo.renderer.OBOStorageIncompleteException
 
getClassFromId(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getColumn() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
Deprecated. 
getComment() - Method in class org.coode.owlapi.obo.parser.OBOTagValuePair
 
getConsumer() - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getCurrentClass() - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getCurrentClass() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
getCurrentEntity() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
getCurrentId() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
getDataFactory() - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getDefaultIRIPrefix() - Method in class org.coode.owlapi.obo.parser.IDSpaceManager
Gets the default IRI prefix (which is returned by the IDSpaceManager.getIRIPrefix(String) for unregistered id prefixes.
getDefaultNamespaceTagValue() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
Gets the default-namespace tag value for the current ontology.
getEndColumn() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
Get end column.
getEndLine() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
Get end line.
getExceptions() - Method in interface org.coode.owlapi.obo.renderer.OBOExceptionHandler
 
getExceptions() - Method in class org.coode.owlapi.obo.renderer.OBOFlatFileRenderer
 
getFiller() - Method in class org.coode.owlapi.obo.renderer.OBORelationship
 
getFrameType() - Method in class org.coode.owlapi.obo.parser.OBOFrame
 
getHeaderFrame() - Method in class org.coode.owlapi.obo.parser.RawFrameHandler
 
getHeaderTags() - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary
 
getIdSpaceManager() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
Gets a COPY of the IDSpaceManager held by this OBOConsumer.
getIdSpaceManager() - Method in class org.coode.owlapi.obo.parser.OBOOntologyFormat
Gets the OBO id-space manager.
getIdType(String) - Static method in enum org.coode.owlapi.obo.parser.OBOIdType
Gets the OBOIdType for a given OBO ID.
GetImage() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
 
getInstanceStanzaTags() - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary
 
getIRI() - Method in enum org.coode.owlapi.obo.parser.OBOVocabulary
 
getIRIFromOBOId(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getIRIFromOBOId(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
Gets an IRI from an OBO ID.
getIRIFromOBOId(String) - Method in class org.coode.owlapi.obo.parser.OBOIdTranslator
 
getIRIFromOBOId(OWLOntologyID, IDSpaceManager, String) - Method in enum org.coode.owlapi.obo.parser.OBOIdType
 
getIRIFromTagName(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
Gets an IRI from a tag name.
getIRIPrefix(String) - Method in class org.coode.owlapi.obo.parser.IDSpaceManager
Gets an IRI prefix from an id prefix.
getLine() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
Deprecated. 
getMaxCardinality() - Method in class org.coode.owlapi.obo.renderer.OBORelationship
 
getMessage() - Method in error org.coode.owlapi.obo.parser.TokenMgrError
You can also modify the body of this method to customize your error messages.
getMessage() - Method in exception org.coode.owlapi.obo.renderer.OBOStorageIncompleteException
 
getMinCardinality() - Method in class org.coode.owlapi.obo.renderer.OBORelationship
 
getModifierNames() - Method in class org.coode.owlapi.obo.parser.Modifiers
Returns the names of modifiers stored in this modifier object
getModifierValues(String) - Method in class org.coode.owlapi.obo.parser.Modifiers
 
getName() - Method in enum org.coode.owlapi.obo.parser.OBOVocabulary
 
getNextToken() - Method in class org.coode.owlapi.obo.parser.OBOParser
Get the next Token.
getNextToken() - Method in class org.coode.owlapi.obo.parser.OBOParserTokenManager
Get the next Token.
getNonTypeDefFrames() - Method in class org.coode.owlapi.obo.parser.RawFrameHandler
 
getOBOIdFromIRI() - Method in class org.coode.owlapi.obo.parser.OBOIdTranslator
 
getOBORelationships() - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator
 
getOntology() - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getOntology() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
getOWLClass(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getOWLClassOrRestriction(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getOWLObjectProperty(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getOWLOntologyManager() - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getOWLOntologyManager() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
getPattern() - Method in enum org.coode.owlapi.obo.parser.OBOIdType
 
getPrefix() - Method in enum org.coode.owlapi.obo.parser.OBOPrefix
 
getProperty() - Method in class org.coode.owlapi.obo.renderer.OBORelationship
 
getQualifier() - Method in class org.coode.owlapi.obo.parser.OBOTagValuePair
 
getRelationIRIFromSymbolicIdOrOBOId(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
getStanzaType() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
GetSuffix(int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream
 
getTabSize(int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream
 
getTagIRI(OBOVocabulary) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getTagIRI(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
Gets an IRI for a tag name.
getTagName() - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getTagName() - Method in class org.coode.owlapi.obo.parser.OBOTagValuePair
 
getTagName() - Method in interface org.coode.owlapi.obo.parser.TagValueHandler
Gets the name of the tag handled by this tag value handler
getTagValuePairs() - Method in class org.coode.owlapi.obo.parser.OBOFrame
 
getTermStanzaTags() - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary
 
getToken(int) - Method in class org.coode.owlapi.obo.parser.OBOParser
Get the specific Token.
getTypeDefFrames() - Method in class org.coode.owlapi.obo.parser.RawFrameHandler
 
getTypeDefStanzaTags() - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary
 
getUnquotedString(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler
 
getValue() - Method in class org.coode.owlapi.obo.parser.OBOTagValuePair
 
getValue() - Method in class org.coode.owlapi.obo.parser.Token
An optional attribute value of the Token.
getValues(OBOVocabulary) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList
 

H

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.AltIdTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.AsymmetricHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.DataVersionTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.DefaultNamespaceTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.DefTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.DisjointFromHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.DomainHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.IDSpaceTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.IDTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.IntersectionOfHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.InverseHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.IsATagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.IsObsoleteTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.NameTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.OntologyTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.PartOfTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.ReflexiveHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.RelationshipTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.SymmetricTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.SynonymTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.SynonymTypeDefTagHandler
 
handle(String, String, String, String) - Method in interface org.coode.owlapi.obo.parser.TagValueHandler
Handles a tag.
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.TransitiveOverHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.TransitiveTagValueHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.UnionOfHandler
 
handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.XRefTagHandler
 
handleTagValue(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
handleTagValue(String, String, String, String) - Method in interface org.coode.owlapi.obo.parser.OBOParserHandler
 
handleTagValue(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.OBOParserHandlerAdapter
 
handleTagValue(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.RawFrameHandler
 
Header() - Method in class org.coode.owlapi.obo.parser.OBOParser
 

I

IDSpaceManager - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012
IDSpaceManager() - Constructor for class org.coode.owlapi.obo.parser.IDSpaceManager
 
IDSpaceManager(IDSpaceManager) - Constructor for class org.coode.owlapi.obo.parser.IDSpaceManager
Creates an IDSpaceManager and copying the id prefix to IRI prefix mappings contained in some other IDSpaceManager.
IDSpaceTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012
IDSpaceTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.IDSpaceTagValueHandler
 
IDTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

IDTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.IDTagValueHandler
 
image - Variable in class org.coode.owlapi.obo.parser.Token
The string image of the token.
IN_COMMENT - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
Lexical state.
IN_QUOTED_STRING - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
Lexical state.
IN_STANZA_HEADER - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
Lexical state.
IN_TAG_VALUE - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
Lexical state.
IN_TAG_VALUE_PAIR - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
Lexical state.
inBuf - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 
input_stream - Variable in class org.coode.owlapi.obo.parser.OBOParserTokenManager
 
inputStream - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 
IntersectionOfHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

IntersectionOfHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.IntersectionOfHandler
 
InverseHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

InverseHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.InverseHandler
 
IsATagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

IsATagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.IsATagValueHandler
 
isHeaderFrame() - Method in class org.coode.owlapi.obo.parser.OBOFrame
 
isInstanceType() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
isOBOIRI(IRI) - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary
 
IsObsoleteTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012
IsObsoleteTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.IsObsoleteTagValueHandler
 
isTerm() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
isTypedef() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
isTypeDefFrame() - Method in class org.coode.owlapi.obo.parser.OBOFrame
 

J

JavaCharStream - Class in org.coode.owlapi.obo.parser
An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (with java-like unicode escape processing).
JavaCharStream(Reader, int, int, int) - Constructor for class org.coode.owlapi.obo.parser.JavaCharStream
Constructor.
JavaCharStream(Reader, int, int) - Constructor for class org.coode.owlapi.obo.parser.JavaCharStream
Constructor.
JavaCharStream(InputStream, String, int, int, int) - Constructor for class org.coode.owlapi.obo.parser.JavaCharStream
Constructor.
JavaCharStream(InputStream, String, int, int) - Constructor for class org.coode.owlapi.obo.parser.JavaCharStream
Constructor.
jj_nt - Variable in class org.coode.owlapi.obo.parser.OBOParser
Next token.
jjFillToken() - Method in class org.coode.owlapi.obo.parser.OBOParserTokenManager
 
jjnewLexState - Static variable in class org.coode.owlapi.obo.parser.OBOParserTokenManager
Lex State array.
jjstrLiteralImages - Static variable in class org.coode.owlapi.obo.parser.OBOParserTokenManager
Token literal values.

K

kind - Variable in class org.coode.owlapi.obo.parser.Token
An integer that describes the kind of this token.

L

LEGACY_OBO_IRI_BASE - Static variable in enum org.coode.owlapi.obo.parser.OBOVocabulary
 
LexicalError(boolean, int, int, int, String, char) - Static method in error org.coode.owlapi.obo.parser.TokenMgrError
Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.
lexStateNames - Static variable in class org.coode.owlapi.obo.parser.OBOParserTokenManager
Lexer state names.
line - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 
LINE_COMMENTED_OUT - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.

M

maxNextCharInd - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 
Modifiers - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University of Manchester
Bio-Health Informatics Group
Date: 03/02/2011
Modifiers() - Constructor for class org.coode.owlapi.obo.parser.Modifiers
 

N

NameTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

NameTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.NameTagValueHandler
 
newToken(int, String) - Static method in class org.coode.owlapi.obo.parser.Token
Returns a new Token object, by default.
newToken(int) - Static method in class org.coode.owlapi.obo.parser.Token
 
next - Variable in class org.coode.owlapi.obo.parser.Token
A reference to the next regular (non-special) token from the input stream.
nextCharBuf - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 
nextCharInd - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 

O

OBO_ID_PATTERN - Static variable in enum org.coode.owlapi.obo.parser.OBOVocabulary
The pattern for OBO IDs.
OBO_IRI_BASE - Static variable in enum org.coode.owlapi.obo.parser.OBOVocabulary
 
OBO_IRI_PATTERN - Static variable in enum org.coode.owlapi.obo.parser.OBOVocabulary
 
OBOConsumer - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

OBOConsumer(OWLOntology, OWLOntologyLoaderConfiguration, IRI) - Constructor for class org.coode.owlapi.obo.parser.OBOConsumer
 
OBOConsumer(OWLOntologyManager, OWLOntology, OWLOntologyLoaderConfiguration, IRI) - Constructor for class org.coode.owlapi.obo.parser.OBOConsumer
 
OBOExceptionHandler - Interface in org.coode.owlapi.obo.renderer
Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 19, 2008

OBOFlatFileOntologyStorer - Class in org.coode.owlapi.obo.renderer
Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 17, 2008

OBOFlatFileOntologyStorer() - Constructor for class org.coode.owlapi.obo.renderer.OBOFlatFileOntologyStorer
 
OBOFlatFileRenderer - Class in org.coode.owlapi.obo.renderer
Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 17, 2008

Renders OBO 1.2 flat file format.
OBOFlatFileRenderer(OWLOntologyManager) - Constructor for class org.coode.owlapi.obo.renderer.OBOFlatFileRenderer
 
OBOFrame - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 19/04/2012
OBOFrame(List<OBOTagValuePair>) - Constructor for class org.coode.owlapi.obo.parser.OBOFrame
 
OBOFrame(String, List<OBOTagValuePair>) - Constructor for class org.coode.owlapi.obo.parser.OBOFrame
 
OBOIdTranslator - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 19/04/2012
OBOIdTranslator() - Constructor for class org.coode.owlapi.obo.parser.OBOIdTranslator
 
OBOIdType - Enum in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 19/04/2012
OBOOntologyFormat - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

OBOOntologyFormat() - Constructor for class org.coode.owlapi.obo.parser.OBOOntologyFormat
 
OBOOntologyFormat(IDSpaceManager) - Constructor for class org.coode.owlapi.obo.parser.OBOOntologyFormat
Constructs an OBOOntologyFormat object.
OBOParser - Class in org.coode.owlapi.obo.parser
 
OBOParser(InputStream) - Constructor for class org.coode.owlapi.obo.parser.OBOParser
Constructor with InputStream.
OBOParser(InputStream, String) - Constructor for class org.coode.owlapi.obo.parser.OBOParser
Constructor with InputStream and supplied encoding
OBOParser(Reader) - Constructor for class org.coode.owlapi.obo.parser.OBOParser
Constructor.
OBOParser(OBOParserTokenManager) - Constructor for class org.coode.owlapi.obo.parser.OBOParser
Constructor with generated Token Manager.
OBOParserConstants - Interface in org.coode.owlapi.obo.parser
Token literal values and constants.
OBOParserException - Exception in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 13-Apr-2007

OBOParserException(String) - Constructor for exception org.coode.owlapi.obo.parser.OBOParserException
 
OBOParserException(String, Throwable) - Constructor for exception org.coode.owlapi.obo.parser.OBOParserException
 
OBOParserException(Throwable) - Constructor for exception org.coode.owlapi.obo.parser.OBOParserException
 
OBOParserFactory - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

OBOParserFactory() - Constructor for class org.coode.owlapi.obo.parser.OBOParserFactory
 
OBOParserHandler - Interface in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

OBOParserHandlerAdapter - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

OBOParserHandlerAdapter() - Constructor for class org.coode.owlapi.obo.parser.OBOParserHandlerAdapter
 
OBOParserTokenManager - Class in org.coode.owlapi.obo.parser
Token Manager.
OBOParserTokenManager(JavaCharStream) - Constructor for class org.coode.owlapi.obo.parser.OBOParserTokenManager
Constructor.
OBOParserTokenManager(JavaCharStream, int) - Constructor for class org.coode.owlapi.obo.parser.OBOParserTokenManager
Constructor.
OBOPrefix - Enum in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012
OBORelationship - Class in org.coode.owlapi.obo.renderer
Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 18, 2008

OBORelationship(OWLObjectProperty, OWLNamedIndividual) - Constructor for class org.coode.owlapi.obo.renderer.OBORelationship
 
OBORelationship(OWLObjectProperty, OWLClass) - Constructor for class org.coode.owlapi.obo.renderer.OBORelationship
 
OBORelationshipGenerator - Class in org.coode.owlapi.obo.renderer
Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 18, 2008

OBORelationshipGenerator(OBOExceptionHandler) - Constructor for class org.coode.owlapi.obo.renderer.OBORelationshipGenerator
 
OBOStorageException - Exception in org.coode.owlapi.obo.renderer
Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 19, 2008

OBOStorageException(OWLObject, OWLObject, String) - Constructor for exception org.coode.owlapi.obo.renderer.OBOStorageException
 
OBOStorageIncompleteException - Exception in org.coode.owlapi.obo.renderer
Author: drummond
http://www.cs.man.ac.uk/~drummond/

The University Of Manchester
Bio Health Informatics Group
Date: Apr 9, 2009

OBOStorageIncompleteException(List<OBOStorageException>) - Constructor for exception org.coode.owlapi.obo.renderer.OBOStorageIncompleteException
 
OBOTagValuePair - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 19/04/2012
OBOTagValuePair(String, String, String, String) - Constructor for class org.coode.owlapi.obo.parser.OBOTagValuePair
 
OBOTagValuePairList - Class in org.coode.owlapi.obo.renderer
Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 19, 2008

An ordered rendering of the Tag Value Pairs that also supports: - default values - unknown tags (which are rendered at the end of the known tags) - extraction of TVPs from annotations

OBOTagValuePairList(List<OBOVocabulary>) - Constructor for class org.coode.owlapi.obo.renderer.OBOTagValuePairList
 
OBOVocabulary - Enum in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

ONTOLOGY_URI_BASE - Static variable in enum org.coode.owlapi.obo.parser.OBOVocabulary
Deprecated. Use OBOVocabulary.OBO_IRI_BASE
OntologyTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University of Manchester
Bio-Health Informatics Group
Date: 03/02/2011
OntologyTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.OntologyTagValueHandler
 
OPEN_SQUARE_BRACKET - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
org.coode.owlapi.obo.parser - package org.coode.owlapi.obo.parser
 
org.coode.owlapi.obo.renderer - package org.coode.owlapi.obo.renderer
 
OWLOBOParser - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

OWLOBOParser() - Constructor for class org.coode.owlapi.obo.parser.OWLOBOParser
 

P

parse() - Method in class org.coode.owlapi.obo.parser.OBOParser
 
parse(OWLOntologyDocumentSource, OWLOntology) - Method in class org.coode.owlapi.obo.parser.OWLOBOParser
 
parse(OWLOntologyDocumentSource, OWLOntology, OWLOntologyLoaderConfiguration) - Method in class org.coode.owlapi.obo.parser.OWLOBOParser
 
ParseException - Exception in org.coode.owlapi.obo.parser
This exception is thrown when parse errors are encountered.
ParseException(Token, int[][], String[]) - Constructor for exception org.coode.owlapi.obo.parser.ParseException
This constructor is used by the method "generateParseException" in the generated parser.
ParseException() - Constructor for exception org.coode.owlapi.obo.parser.ParseException
The following constructors are for use by you for whatever purpose you can think of.
ParseException(String) - Constructor for exception org.coode.owlapi.obo.parser.ParseException
Constructor with message.
parseModifiers(String) - Static method in class org.coode.owlapi.obo.parser.Modifiers
Parses a list of modifiers.
parseXRef(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
PartOfTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

PartOfTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.PartOfTagValueHandler
 
PATTERN - Static variable in class org.coode.owlapi.obo.parser.SynonymTypeDefTagHandler
 
prevCharIsCR - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 
prevCharIsLF - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 

Q

QUOTED_STRING - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
QUOTED_STRING_DBL_QUOTE_TERMINATOR - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
QUOTED_STRING_NEW_LINE_TERMINATOR - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
QUOTED_STRING_START - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.

R

RawFrameHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 19/04/2012
RawFrameHandler() - Constructor for class org.coode.owlapi.obo.parser.RawFrameHandler
 
ReadByte() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
 
readChar() - Method in class org.coode.owlapi.obo.parser.JavaCharStream
Read a character.
ReflexiveHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

ReflexiveHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.ReflexiveHandler
 
registerIdSpace(String, String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
ReInit(Reader, int, int, int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream
Reinitialise.
ReInit(Reader, int, int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream
Reinitialise.
ReInit(InputStream, String, int, int, int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream
Reinitialise.
ReInit(InputStream, String, int, int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream
Reinitialise.
ReInit(InputStream) - Method in class org.coode.owlapi.obo.parser.OBOParser
Reinitialise.
ReInit(InputStream, String) - Method in class org.coode.owlapi.obo.parser.OBOParser
Reinitialise.
ReInit(Reader) - Method in class org.coode.owlapi.obo.parser.OBOParser
Reinitialise.
ReInit(OBOParserTokenManager) - Method in class org.coode.owlapi.obo.parser.OBOParser
Reinitialise.
ReInit(JavaCharStream) - Method in class org.coode.owlapi.obo.parser.OBOParserTokenManager
Reinitialise parser.
ReInit(JavaCharStream, int) - Method in class org.coode.owlapi.obo.parser.OBOParserTokenManager
Reinitialise parser.
RelationshipTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

RelationshipTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.RelationshipTagValueHandler
 
render(OWLOntology, Writer) - Method in class org.coode.owlapi.obo.renderer.OBOFlatFileRenderer
 

S

setCardinality(int) - Method in class org.coode.owlapi.obo.renderer.OBORelationship
 
setClass(OWLClass) - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator
 
setCurrentId(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
setDataVersionTagValue(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
Sets the value of the data-version tag for the current ontology that is being parsed.
setDebugStream(PrintStream) - Method in class org.coode.owlapi.obo.parser.OBOParserTokenManager
Set debug output.
setDefault(OBOVocabulary, String) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList
 
setDefault(IRI, String) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList
 
setDefaultNamespaceTagValue(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
Sets the value of the default-namespace tag for the current ontology being parsed.
setHandler(OBOParserHandler) - Method in class org.coode.owlapi.obo.parser.OBOParser
 
setIRIPrefix(String, String) - Method in class org.coode.owlapi.obo.parser.IDSpaceManager
Sets the IRI prefix for a given id prefix.
setMaxCardinality(int) - Method in class org.coode.owlapi.obo.renderer.OBORelationship
 
setMinCardinality(int) - Method in class org.coode.owlapi.obo.renderer.OBORelationship
 
setOntologyTagValue(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
Sets the value of the ontology tag for the current ontology that is being parsed.
setPair(OBOVocabulary, String) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList
 
setTabSize(int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream
 
specialToken - Variable in class org.coode.owlapi.obo.parser.Token
This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
Stanza() - Method in class org.coode.owlapi.obo.parser.OBOParser
 
STANZA_TYPE - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
startFrame(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
startFrame(String) - Method in interface org.coode.owlapi.obo.parser.OBOParserHandler
 
startFrame(String) - Method in class org.coode.owlapi.obo.parser.OBOParserHandlerAdapter
 
startFrame(String) - Method in class org.coode.owlapi.obo.parser.RawFrameHandler
 
startHeader() - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
startHeader() - Method in interface org.coode.owlapi.obo.parser.OBOParserHandler
 
startHeader() - Method in class org.coode.owlapi.obo.parser.OBOParserHandlerAdapter
 
startHeader() - Method in class org.coode.owlapi.obo.parser.RawFrameHandler
 
staticFlag - Static variable in class org.coode.owlapi.obo.parser.JavaCharStream
Whether parser is static.
storeOntology(OWLOntologyManager, OWLOntology, Writer, OWLOntologyFormat) - Method in class org.coode.owlapi.obo.renderer.OBOFlatFileOntologyStorer
 
STRING - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
SwitchTo(int) - Method in class org.coode.owlapi.obo.parser.OBOParserTokenManager
Switch to specified lex state.
SymmetricTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

SymmetricTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.SymmetricTagValueHandler
 
SYNONYM_TYPE_IRI - Static variable in class org.coode.owlapi.obo.parser.SynonymTagValueHandler
 
SynonymScope - Enum in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012
SynonymTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University of Manchester
Bio-Health Informatics Group
Date: 03/02/2011
SynonymTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.SynonymTagValueHandler
 
SynonymTypeDefTagHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012
SynonymTypeDefTagHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.SynonymTypeDefTagHandler
 

T

tabSize - Variable in class org.coode.owlapi.obo.parser.JavaCharStream
 
TAG_COLON - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
TAG_END - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
TAG_NAME - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
TAG_VALUE_WS - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
RegularExpression Id.
TagValueHandler - Interface in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

Concrete implementations of this interface allow specific behaviour for processing specific tag value pairs in an OBO file to be specified.

TagValuePair() - Method in class org.coode.owlapi.obo.parser.OBOParser
 
token - Variable in class org.coode.owlapi.obo.parser.OBOParser
Current token.
Token - Class in org.coode.owlapi.obo.parser
Describes the input token stream.
Token() - Constructor for class org.coode.owlapi.obo.parser.Token
No-argument constructor
Token(int) - Constructor for class org.coode.owlapi.obo.parser.Token
Constructs a new token for the specified Image.
Token(int, String) - Constructor for class org.coode.owlapi.obo.parser.Token
Constructs a new token for the specified Image and Kind.
token_source - Variable in class org.coode.owlapi.obo.parser.OBOParser
Generated Token Manager.
tokenImage - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants
Literal token values.
tokenImage - Variable in exception org.coode.owlapi.obo.parser.ParseException
This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.
TokenMgrError - Error in org.coode.owlapi.obo.parser
Token Manager Error.
TokenMgrError() - Constructor for error org.coode.owlapi.obo.parser.TokenMgrError
No arg constructor.
TokenMgrError(String, int) - Constructor for error org.coode.owlapi.obo.parser.TokenMgrError
Constructor with message and reason.
TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.coode.owlapi.obo.parser.TokenMgrError
Full Constructor.
toString() - Method in class org.coode.owlapi.obo.parser.OBOOntologyFormat
Returns a string representation of the object.
toString() - Method in enum org.coode.owlapi.obo.parser.OBOVocabulary
 
toString() - Method in class org.coode.owlapi.obo.parser.Token
Returns the image.
TransitiveOverHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

TransitiveOverHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.TransitiveOverHandler
 
TransitiveTagValueHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

TransitiveTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.TransitiveTagValueHandler
 

U

unescapeTagValue(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer
 
UnionOfHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

UnionOfHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.UnionOfHandler
 
UpdateLineColumn(char) - Method in class org.coode.owlapi.obo.parser.JavaCharStream
 

V

valueOf(String) - Static method in enum org.coode.owlapi.obo.parser.OBOIdType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.coode.owlapi.obo.parser.OBOPrefix
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.coode.owlapi.obo.parser.SynonymScope
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.coode.owlapi.obo.parser.OBOIdType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.coode.owlapi.obo.parser.OBOPrefix
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.coode.owlapi.obo.parser.SynonymScope
Returns an array containing the constants of this enum type, in the order they are declared.
visit(OWLObjectSomeValuesFrom) - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator
 
visit(OWLObjectMinCardinality) - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator
 
visit(OWLObjectExactCardinality) - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator
 
visit(OWLObjectMaxCardinality) - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator
 
visit(OWLAnnotation) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList
 

W

write(Writer) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList
 

X

XREF_IRI - Static variable in class org.coode.owlapi.obo.parser.SynonymTagValueHandler
 
XRefTagHandler - Class in org.coode.owlapi.obo.parser
Author: Matthew Horridge
The University of Manchester
Bio-Health Informatics Group
Date: 03/02/2011
XRefTagHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.XRefTagHandler
 

A B C D E F G H I J K L M N O P Q R S T U V W X

Copyright © 2012 The University of Manchester. All Rights Reserved.