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A
- addAttributeComments(Vector, StringBuffer, String) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Adds the documentation for the attributes passed in.
C
- CreateWriteFiles(Vector) - Method in class org.biomage.tools.generate_dtd.WriteDTDFile
- Description: Create the write classes for each of the class files.
- comment - Variable in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: The documentation for this class.
- createAttrs(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates the attribute entity for the class.
- createAttrsEntity(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates the attribute entity for the class.
- createChoices(StringBuffer, Vector, String) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates all the possibilities of ordering the vector of choices.
- createClassesEntity(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates the classes entity and, if not owned, the ref entity.
- createClassesOrRefEntity(StringBuffer, String) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates either classes entity or the ref entity, depending on adornment parameter.
- createComment() - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates the documentation for the class.
- createContainer(CreateFile.AssociationAttrInformation) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates the name of the container for the association passed in.
- createContent(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates the content entity for the class.
- createContentEntity(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates the content entity for the class.
- createElementAndAttlist(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: If not owned, creates the *_ref element and attlist then creates the element and attlist declarations for the class.
- createElementAndAttlists() - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates the different element and attlist declarations for the class.
- createEntities() - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates the different entities for the class.
- createFile - Variable in class org.biomage.tools.generate_dtd.WriteDTDElement
- Description: The createFile this class will.
- createFiles - Variable in class org.biomage.tools.generate_dtd.WriteDTDFile.PackageDependencies
- Description: The classes that belong to this package.
- createReference(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: If not owned, creates the *_ref element and attlist then creates the element and attlist declarations for the class.
- createRoleDeclarations(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates the element and attlist declarations for the role names of the class.
- createXMLStrings(Element) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Creates the different entities, elements and attlists for the class.
- createXMLStrings(Element) - Method in class org.biomage.tools.generate_dtd.WriteDTDElement
- Description: Creates the different entities, elements and attlists for the class.
- createXMLStrings(Element) - Method in class org.biomage.tools.generate_dtd.WriteDTDMageElement
- Description: Creates the element declaration for the top-level model.
- createXMLStrings(Element) - Method in class org.biomage.tools.generate_dtd.WriteDTDPackageElement
- Description: Creates the element declaration for the package.
D
- dependentOn - Variable in class org.biomage.tools.generate_dtd.WriteDTDFile.PackageDependencies
- Description: Names of packages this package is dependent on..
E
- elements - Variable in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: The element and Attlist declarations.
- entities - Variable in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: If this is a base class, will contain the string to use for the entity.
- entityPrefix - Variable in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: String to use as prefix for the entities for this class.
I
- isReferencedClass(CreateFile) - Static method in class org.biomage.tools.generate_dtd.WriteDTDFile
- Description: Utility method to verify whether class has roles or is top-level.
M
- mageML - Variable in class org.biomage.tools.generate_dtd.WriteDTDMageElement
- Description: For outputting the MAGE-OM element to the file.
N
- NEWLINE - Static variable in class org.biomage.tools.generate_dtd.WriteDTDClassElement
O
- orderPackages() - Method in class org.biomage.tools.generate_dtd.WriteDTDMageElement
- Description: Creates an orderd map to order the packages based on packageOrder then returns the values from that map as a Vector.
- orderedClasses(Element) - Method in class org.biomage.tools.generate_dtd.WriteDTDPackageElement
- Description: Method to read the XML configuration for the ordering of the lists for this package.
- org.biomage.tools.generate_dtd - package org.biomage.tools.generate_dtd
P
- packageElement - Variable in class org.biomage.tools.generate_dtd.WriteDTDPackageElement
- Description: For outputting the MAGE-OM element to the file.
- packageOrder - Variable in class org.biomage.tools.generate_dtd.WriteDTDMageElement
- Description: Map that specifies the order of the packages.
S
- setPackageOrder(Element) - Method in class org.biomage.tools.generate_dtd.WriteDTDMageElement
- Description: Method to read the XML configuration for the ordering of the packages.
- setTopElements(Element) - Method in class org.biomage.tools.generate_dtd.WriteDTDFile
- sortWriteFiles(Vector) - Static method in class org.biomage.tools.generate_dtd.WriteDTDFile
- Description: Create the write classes for each of the class files.
T
- TransformBioAssayData - class org.biomage.tools.generate_dtd.TransformBioAssayData.
- Description: Class that is resposible for transforming the class list passed in.
- TransformBioAssayData() - Constructor for class org.biomage.tools.generate_dtd.TransformBioAssayData
- topElementNames - Static variable in class org.biomage.tools.generate_dtd.WriteDTDFile
- Description: The top level class.
- transform(Vector) - Method in class org.biomage.tools.generate_dtd.TransformBioAssayData
- Description: Transform the BioAssayData class for producing modified DTD for its associations and attributes.
- transform(Vector) - Method in interface org.biomage.tools.generate_dtd.WriteDTDFile.CreateClassTransformer
- transformer - Variable in class org.biomage.tools.generate_dtd.WriteDTDFile
- Description: A class that implements the transformation interface.
W
- WriteDTDClassElement - class org.biomage.tools.generate_dtd.WriteDTDClassElement.
- Description: Class that is resposible for generating the DTD entities, if base class, and element and attribute if not abstract for the CreateClassFile passed into the c'tor.
- WriteDTDClassElement(CreateFile) - Constructor for class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Constructor for classes for the DTD file generator.
- WriteDTDElement - class org.biomage.tools.generate_dtd.WriteDTDElement.
- Description: Class that is resposible for generating a DTD file for the classes represented by the list of class nodes passed into the constructor.
- WriteDTDElement(CreateFile) - Constructor for class org.biomage.tools.generate_dtd.WriteDTDElement
- Description: Constructor for the DTD file generator.
- WriteDTDFile - class org.biomage.tools.generate_dtd.WriteDTDFile.
- Description: Class that is resposible for generating a DTD file for the classes represented by the list of class nodes passed into the constructor.
- WriteDTDFile(Vector, String, String, File, String, Element, Element) - Constructor for class org.biomage.tools.generate_dtd.WriteDTDFile
- Description: Constructor for the DTD file generator.
- WriteDTDFile.CreateClassTransformer - interface org.biomage.tools.generate_dtd.WriteDTDFile.CreateClassTransformer.
- Description: An interface implemented by classes that take a class list and transform the members by either changing the relationships or adding or subtracting classes.
- WriteDTDFile.PackageDependencies - class org.biomage.tools.generate_dtd.WriteDTDFile.PackageDependencies.
- Description: An inner class to hold the inter and intra package dependencies.
- WriteDTDFile.PackageDependencies() - Constructor for class org.biomage.tools.generate_dtd.WriteDTDFile.PackageDependencies
- WriteDTDMageElement - class org.biomage.tools.generate_dtd.WriteDTDMageElement.
- Description: Class that is resposible for generating a DTD file for the classes represented by the list of class nodes passed into the constructor.
- WriteDTDMageElement(CreateFile) - Constructor for class org.biomage.tools.generate_dtd.WriteDTDMageElement
- Description: Constructor for the DTD file generator.
- WriteDTDPackageElement - class org.biomage.tools.generate_dtd.WriteDTDPackageElement.
- Description: Class that is resposible for generating a DTD file for the classes represented by the list of class nodes passed into the constructor.
- WriteDTDPackageElement(CreateFile) - Constructor for class org.biomage.tools.generate_dtd.WriteDTDPackageElement
- Description: Constructor for the DTD file generator.
- writeBody(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Method to write out entities.
- writeBody(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDElement
- Description: Method to write out the body.
- writeBody(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDMageElement
- Description: Method to write out the body.
- writeBody(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDPackageElement
- Description: Method to write out the body.
- writeEntities(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
- Description: Method to write out entities.
- writeEntities(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDElement
- Description: Method to write out entities.
- writeEntities(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDPackageElement
- Description: Method to write out entities.
- writeHeader(FileWriter, File) - Method in class org.biomage.tools.generate_dtd.WriteDTDFile
- Description: Writes the header information out to the file.
A C D E I M N O P S T W
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