Index (intermine-model 5.0.2 API)

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

A

addCollectionElement(Object, String, Object) - Static method in class org.intermine.metadata.TypeUtil: Adds an element to a public or protected collection of an Object given the field name.
addModel(String, Model) - Static method in class org.intermine.metadata.Model: Adds model to known models.
addProblem(String) - Method in class org.intermine.metadata.Model: Add a problem to the model that doesn't prevent it from being created for backwards compatibility but should be checked when creating a new model.
addRow(String...) - Method in class org.intermine.metadata.TextTable: Adds a single row to the table.
addToListMap(Map<K, List<V>>, K, V) - Static method in class org.intermine.metadata.Util: Add a value to a Map from keys to Set of values, creating the value list as needed.
addToSetMap(Map<K, Set<V>>, K, Collection<V>) - Static method in class org.intermine.metadata.Util: Add values to a Map from keys to Set of values, creating the value list as needed.
addToSetMap(Map<K, Set<V>>, K, V) - Static method in class org.intermine.metadata.Util: Add a value to a Map from keys to Set of values, creating the value list as needed.
allDigits(String) - Static method in class org.intermine.metadata.StringUtil: Return true if all characters in a given String are digits.
AND - Static variable in class org.intermine.metadata.ConstraintOp: Combine constraints with the AND operation
append(boolean) - Method in class org.intermine.model.StringConstructor: Appends a boolean onto the end of this object.
append(double) - Method in class org.intermine.model.StringConstructor: Appends a double onto the end of this object.
append(float) - Method in class org.intermine.model.StringConstructor: Appends a float onto the end of this object.
append(int) - Method in class org.intermine.model.StringConstructor: Appends an int onto the end of this object.
append(long) - Method in class org.intermine.model.StringConstructor: Appends a long onto the end of this object.
append(Object) - Method in class org.intermine.model.StringConstructor: Appends an Object onto the end of this object.
append(String) - Method in class org.intermine.model.StringConstructor: Appends a String onto the end of this object.
AttributeDescriptor - Class in org.intermine.metadata: Describes an attribute of a class - i.e.
AttributeDescriptor(String, String, String) - Constructor for class org.intermine.metadata.AttributeDescriptor: Construct, name and type cannot be null.

B

bufferToHexString(byte[]) - Static method in class org.intermine.metadata.StringUtil: Convert a byte buffer to a hexadecimal string.

C

capitalise(String) - Static method in class org.intermine.metadata.StringUtil: Returns a capitalised version of the given String
charAt(int) - Method in class org.intermine.model.StringConstructor
ClassDescriptor - Class in org.intermine.metadata: Describe a business model class.
ClassDescriptor(String, String, boolean, Collection<AttributeDescriptor>, Collection<ReferenceDescriptor>, Collection<CollectionDescriptor>, String) - Constructor for class org.intermine.metadata.ClassDescriptor: Construct a ClassDescriptor.
cld - Variable in class org.intermine.metadata.FieldDescriptor
CollectionDescriptor - Class in org.intermine.metadata: Describes a field that references a collection of other objects.
CollectionDescriptor(String, String, String) - Constructor for class org.intermine.metadata.CollectionDescriptor: Construct a CollectionDescriptor.
colonsToDots(String) - Static method in class org.intermine.metadata.StringUtil: Converts all the colons in a String into dots.
compareTo(ClassDescriptor) - Method in class org.intermine.metadata.ClassDescriptor
ConstraintOp - Class in org.intermine.metadata: Operations used in building constraints.
CONTAINS - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument contains the second
countOccurances(String, String) - Static method in class org.intermine.metadata.StringUtil: Returns the number of occurances of str in target
createNew(String) - Static method in class org.intermine.metadata.TypeUtil: Encapsulate the logic of requesting an object of a class named name where that class has a default no-arguments constructor.

D

decapitalise(String) - Static method in class org.intermine.metadata.StringUtil: Returns a decapitalised version of the given String unless string is an acronym.
decomposeClass(Class<?>) - Static method in class org.intermine.metadata.Util: Convert a dynamic Class into a Set of Class objects that comprise it.
DELIM - Static variable in class org.intermine.codegen.JavaModelOutput: The string that delimits the sections of the NotXml.
DescriptorUtils - Class in org.intermine.metadata
destDir - Variable in class org.intermine.task.ModelOutputTask
DOES_NOT_CONTAIN - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument does not contain the second
DOES_NOT_EXIST - Static variable in class org.intermine.metadata.ConstraintOp: Subquery does not exist
DOES_NOT_MATCH - Static variable in class org.intermine.metadata.ConstraintOp: Require that the two arguments do not match
DOES_NOT_OVERLAP - Static variable in class org.intermine.metadata.ConstraintOp: Require that a range does not overlap another range
duplicateQuotes(String) - Static method in class org.intermine.metadata.StringUtil: Duplicates single quotes in Strings for correct storage in postgres.

E

ENCODED_DELIM - Static variable in class org.intermine.codegen.JavaModelOutput: The character that denotes an encoded delimiter in the string.
ENDL - Static variable in class org.intermine.codegen.JavaModelOutput
ENDL - Static variable in class org.intermine.metadata.ClassDescriptor
ENDL - Static variable in class org.intermine.metadata.Model
equals(Object) - Method in class org.intermine.metadata.AttributeDescriptor
equals(Object) - Method in class org.intermine.metadata.ClassDescriptor
equals(Object) - Method in class org.intermine.metadata.CollectionDescriptor
equals(Object) - Method in class org.intermine.metadata.Model
equals(Object) - Method in class org.intermine.metadata.PrimaryKey
equals(Object) - Method in class org.intermine.metadata.ReferenceDescriptor
equals(Object) - Method in class org.intermine.metadata.StringUtil.LineWrappedString
equals(Object, Object) - Static method in class org.intermine.metadata.Util: Compare two objects, using their .equals method, but comparing null to null as equal.
EQUALS - Static variable in class org.intermine.metadata.ConstraintOp: Require that the two arguments are equal, regardless of case for strings
escapeBackslash(String) - Static method in class org.intermine.metadata.StringUtil: Escape single backslash with single forwardslash for correct storage in postgres.
escapeWithBackslashes(String) - Static method in class org.intermine.metadata.StringUtil: Escapes single quotes and backslashes, with backslashes.
EXACT_MATCH - Static variable in class org.intermine.metadata.ConstraintOp: Require that the two arguments are exactly equal
execute() - Method in class org.intermine.task.ModelOutputTask
EXISTS - Static variable in class org.intermine.metadata.ConstraintOp: Subquery exists

F

fairTerm - Variable in class org.intermine.metadata.AttributeDescriptor
FastPathObject - Interface in org.intermine.model: A root interface for all objects that can be stored in a InterMine database.
FieldDescriptor - Class in org.intermine.metadata: Abstract representation of a field within a class - could be an attribute, an object reference or a collection.
FieldDescriptor(String) - Constructor for class org.intermine.metadata.FieldDescriptor: Construct, name of field must not be null and must be a valid Java variable name.
FieldInfo(String, Method, Method, Method, Method, Method) - Constructor for class org.intermine.metadata.TypeUtil.FieldInfo: Construct a new FieldInfo object.
file - Variable in class org.intermine.codegen.JavaModelOutput
findCommonClasses(Collection<ClassDescriptor>) - Static method in class org.intermine.metadata.DescriptorUtils: Return a list of the classes which present in the inheritance tree of all the given classes.
findFairTerm(Model, String) - Static method in class org.intermine.metadata.ClassDescriptor: Return the fair term for the given class name defined in the model.
findInherithance(Model, String, String) - Static method in class org.intermine.metadata.ClassDescriptor: Return true if the superClassName given in input is a super class of className
findIntersectionType(Collection<ClassDescriptor>) - Static method in class org.intermine.metadata.DescriptorUtils: Find the ClassDescriptor for the type that any two or more objects must be of where those objects are randomly selected from a collection containing objects which are of the types represented by the class descriptors in the provided collection.
findReferencedDescriptor() - Method in class org.intermine.metadata.ReferenceDescriptor: sort out references from this class
findSumType(Collection<ClassDescriptor>) - Static method in class org.intermine.metadata.DescriptorUtils: Find the ClassDescriptor for the type that any random element selected from a collection of objects must be an instance of, where each object is an instance of one of the classes represented by the class descriptors in the input collection.
findSuperClassNames(Model, String) - Static method in class org.intermine.metadata.ClassDescriptor: Return a list of the super class names for the given class name.
flatten(Object) - Static method in class org.intermine.metadata.TypeUtil: Make all nested objects top-level in returned collection

G

gcd(int, int) - Static method in class org.intermine.metadata.Util: Takes two integers, and returns the greatest common divisor, using euclid's algorithm.
generate(AttributeDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput: Generates code for a single attribute.
generate(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput: Generate the output for a ClassDescriptor.
generate(CollectionDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput: Generates code for a single collection.
generate(ReferenceDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput: Generates code for a single reference.
generateAddCollectionElement(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput: Generates the addCollectionElement method.
generateClassDescriptors(Reader, String) - Method in class org.intermine.metadata.InterMineModelParser: Read source model information in InterMine XML format and create a set of ClassDescriptors.
generateClassDescriptors(Reader, String) - Method in interface org.intermine.metadata.ModelParser: Read source information and construct a list of InterMine ClassDescriptors
generateClassName(String, String) - Static method in class org.intermine.metadata.TypeUtil: Generate the full class name, eg.
generateEquals(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput: Generate a .equals() method for the given class.
generateFieldDescriptors(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput: Generate all FieldDescriptors for a class/interface
generateGetElementType(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput: Generates the getElementType method.
generateGetFieldType(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput: Generates the getFieldType method.
generateGetFieldValue(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput: Generates the getFieldValue method.
generateGetObject(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput: Generates the getoBJECT method for producing NotXml.
generateGetSet(FieldDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput: Write code for getters and setters for given field.
generateHashCode(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput: Generate a .hashCode() method for the given class.
generateSetFieldValue(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput: Generates the setFieldValue method.
generateSetObject(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput: Generates the setoBJECT method for deserialising objects.
generateToString(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput: Generate a .toString() method for the given class .
getAdder() - Method in class org.intermine.metadata.TypeUtil.FieldInfo: Returns the adder Method.
getAdder(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil: Returns the Method object that is the adder for the field name
getAllAttributeDescriptors() - Method in class org.intermine.metadata.ClassDescriptor: Gets all AttributeDescriptors for this class and its super classes - i.e.
getAllCollectionDescriptors() - Method in class org.intermine.metadata.ClassDescriptor: Gets all CollectionDescriptors for this class - i.e.
getAllFieldDescriptors() - Method in class org.intermine.metadata.ClassDescriptor: Gets the FieldDescriptors for this class and all superclasses and interfaces.
getAllReferenceDescriptors() - Method in class org.intermine.metadata.ClassDescriptor: Gets all ReferenceDescriptors for this class - i.e.
getAllSubs(ClassDescriptor) - Method in class org.intermine.metadata.Model: Get the ClassDescriptors for the all subclasses of a class
getAllSuperclassNames() - Method in class org.intermine.metadata.ClassDescriptor: Get the full inheritance list for this class.
getAllSuperDescriptors() - Method in class org.intermine.metadata.ClassDescriptor: Get the full inheritance list for this class.
getAttributeDescriptorByName(String) - Method in class org.intermine.metadata.ClassDescriptor: Gets an AttributeDescriptor for a field of the given name.
getAttributeDescriptorByName(String, boolean) - Method in class org.intermine.metadata.ClassDescriptor: Gets an AttributeDescriptor for a field of the given name.
getAttributeDescriptors() - Method in class org.intermine.metadata.ClassDescriptor: Gets AttributeDescriptors for this class - i.e.
getBottomUpLevelTraversal() - Method in class org.intermine.metadata.Model: Return the classes in the model in level order from deepest to shallowest, the order of nodes at any given level is undefined.
getClass(String) - Static method in class org.intermine.metadata.TypeUtil: Instantiate a class by unqualified name The name should be "Date" or that of a primitive container class such as "Integer"
getClass(String, Model) - Static method in class org.intermine.metadata.TypeUtil: Instantiate a class by unqualified name The name should be "InterMineObject" or the name of class in the model provided
getClassDescriptor() - Method in class org.intermine.metadata.FieldDescriptor: Get the ClassDescriptor for this field's class.
getClassDescriptor() - Method in class org.intermine.metadata.PrimaryKey: Return the ClassDescriptor for class this key is defined for
getClassDescriptorByName(String) - Method in class org.intermine.metadata.Model: Get a ClassDescriptor by name, null if no ClassDescriptor of given name in Model.
getClassDescriptors() - Method in class org.intermine.metadata.Model: Get all ClassDescriptors in this model.
getClassDescriptorsForClass(Class<?>) - Method in class org.intermine.metadata.Model: Takes a Class, and generates a Set of all ClassDescriptors that are the Class or any of its parents.
getClasses() - Method in class org.intermine.metadata.Model.ModelAST
getClassFromString(String) - Static method in class org.intermine.metadata.Util: Returns the class (not primitive) associated with the given String type.
getClassNames() - Method in class org.intermine.metadata.Model: Get a Set of fully qualified class names in this model (i.e.
getCollectionDescriptorByName(String) - Method in class org.intermine.metadata.ClassDescriptor: Gets a CollectionDescriptor for a collection of the given name.
getCollectionDescriptorByName(String, boolean) - Method in class org.intermine.metadata.ClassDescriptor: Gets a CollectionDescriptor for a field of the given name.
getCollectionDescriptors() - Method in class org.intermine.metadata.ClassDescriptor: Gets CollectionDescriptors for this class.
getCollectionsForClass(Class<?>) - Method in class org.intermine.metadata.Model: Takes a Class, and generates a Map of all the collections that are in the Class or any of its parents.
getConstraintOp(String) - Static method in class org.intermine.metadata.ConstraintOp: Get ConstraintOp for given operation code.
getDirectSubs(ClassDescriptor) - Method in class org.intermine.metadata.Model: Get the ClassDescriptors for the direct subclasses of a class
getElementType() - Method in class org.intermine.metadata.TypeUtil.FieldInfo: Returns the collection element type of the field.
getElementType(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil: Returns the element type of a collection given the field name.
getElementType(String) - Method in interface org.intermine.model.InterMineFastPathObject: Returns the element type of a collection by name.
getFairTerm() - Method in class org.intermine.metadata.AttributeDescriptor: Get the term for the attribute - a URI pointing to an ontology term describing this attribute.
getFairTerm() - Method in class org.intermine.metadata.ClassDescriptor: Returns the URI for this data type.
getFieldDescriptorByName(String) - Method in class org.intermine.metadata.ClassDescriptor: Retrieve a FieldDescriptor by name.
getFieldDescriptors() - Method in class org.intermine.metadata.ClassDescriptor: Gets the FieldDescriptors for this class (but not superclasses).
getFieldDescriptorsForClass(Class<?>) - Method in class org.intermine.metadata.Model: Takes a Class, and generates a Map of all FieldDescriptors that are the class fields or any of its parents.
getFieldInfo(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil: Returns a FieldInfo object for the given class and field name.
getFieldInfos(Class<?>) - Static method in class org.intermine.metadata.TypeUtil: Returns the Map from field name to TypeUtil.FieldInfo objects for all the fields in a given class.
getFieldNames() - Method in class org.intermine.metadata.PrimaryKey: Return the Set of field names
getFieldProxy(Object, String) - Static method in class org.intermine.metadata.TypeUtil: Returns the value of a public or protected Field of an Object given by the field name without dereferencing any ProxyReference objects.
getFieldProxy(String) - Method in interface org.intermine.model.FastPathObject: Returns the value of a field without dereferencing any ProxyReference objects.
getFieldType(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil: Returns the type of a field given the field name.
getFieldType(String) - Method in interface org.intermine.model.FastPathObject: Returns the type of a field by name.
getFieldValue(Object, String) - Static method in class org.intermine.metadata.TypeUtil: Returns the value of a public or protected Field of an Object given the field name
getFieldValue(String) - Method in interface org.intermine.model.FastPathObject: Returns the value of a field by name.
getFilename(String, String) - Static method in class org.intermine.metadata.Util: Given a key and model name, return filename for reading/writing.
getFlattenedSourceName(String) - Static method in class org.intermine.metadata.StringUtil: Flattens source name.
getFriendlyName(Class<?>) - Static method in class org.intermine.metadata.Util: Creates a friendly name for a given class.
getGetter() - Method in class org.intermine.metadata.TypeUtil.FieldInfo: Returns the getter Method.
getGetter(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil: Returns the Method object that is the getter for the field name.
getGetters(Class<?>) - Static method in class org.intermine.metadata.TypeUtil: Gets the getter methods for the bean properties of a class
getHumanReadableText() - Method in class org.intermine.metadata.ClassDescriptor: Returns a String that contains a multi-line human-readable description of the ClassDescriptor.
getId() - Method in interface org.intermine.model.InterMineFastPathObject: Getter for the ID field - ensures that every object in the database has an ID.
getIndex() - Method in class org.intermine.metadata.ConstraintOp: Get an index for this ConstraintOp TODO: expunge this horror.
getInstanceByName(String) - Static method in class org.intermine.metadata.Model: Return a Model for specified model name (loading Model if necessary)
getKeyProperties(String) - Static method in class org.intermine.metadata.PrimaryKeyUtil: Return the Properties that specify the key fields for the classes in this Model
getMd5checksum(String) - Static method in class org.intermine.metadata.Util
getModel() - Method in class org.intermine.metadata.ClassDescriptor: Return the model this class is a part of.
getName() - Method in class org.intermine.metadata.ClassDescriptor: Returns the fully qualified class name described by this ClassDescriptor.
getName() - Method in class org.intermine.metadata.FieldDescriptor: Get the name of the described field.
getName() - Method in class org.intermine.metadata.Model: Get the name of this model - i.e.
getName() - Method in class org.intermine.metadata.PrimaryKey: Return the name
getName() - Method in class org.intermine.metadata.TypeUtil.FieldInfo: Returns the field name
getoBJECT() - Method in interface org.intermine.model.InterMineFastPathObject: Returns the NotXml serialised version of this object.
getOpForIndex(Integer) - Static method in class org.intermine.metadata.ConstraintOp: Convert an index to a ConstraintOp (Only for use in webapp)
getPackageName() - Method in class org.intermine.metadata.Model: Return name of the model's package.
getPrimaryKeys(ClassDescriptor) - Static method in class org.intermine.metadata.PrimaryKeyUtil: Retrieve a map from key name to PrimaryKey object.
getProblems() - Method in class org.intermine.metadata.Model: Return a list of problems with the model or an empty list.
getPropertiesStartingWith(String, Properties) - Static method in class org.intermine.metadata.Util: Returns all Properties in props that begin with str
getProxyGetter() - Method in class org.intermine.metadata.TypeUtil.FieldInfo: Returns the proxyGetter Method.
getProxyGetter(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil: Returns the Method object that is the proxyGetter for the field name
getProxySetter() - Method in class org.intermine.metadata.TypeUtil.FieldInfo: Returns the proxySetter Method.
getProxySetter(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil: Returns the Method object that is the proxySetter for the field name
getQualifiedTypeName(String) - Method in class org.intermine.metadata.Model: Return the qualified name of the given unqualified class name.
getReferencedClassDescriptor() - Method in class org.intermine.metadata.ReferenceDescriptor: Returns a ClassDescriptor for the object referenced by this field.
getReferencedClassName() - Method in class org.intermine.metadata.ReferenceDescriptor: Returns the class name of the object referenced by this field.
getReferenceDescriptorByName(String) - Method in class org.intermine.metadata.ClassDescriptor: Gets a ReferenceDescriptor for a field of the given name.
getReferenceDescriptorByName(String, boolean) - Method in class org.intermine.metadata.ClassDescriptor: Gets a ReferenceDescriptor for a field of the given name.
getReferenceDescriptors() - Method in class org.intermine.metadata.ClassDescriptor: Gets the descriptors for the external object references in this class.
getReverseReferenceDescriptor() - Method in class org.intermine.metadata.ReferenceDescriptor: Gets the field in the referenced object that refers back to this class.
getReverseReferenceFieldName() - Method in class org.intermine.metadata.ReferenceDescriptor: Gets the name of the reverse reference field.
getSetter() - Method in class org.intermine.metadata.TypeUtil.FieldInfo: Returns the setter Method.
getSetter(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil: Returns the Method object that is the setter for the field name
getSimpleName() - Method in class org.intermine.metadata.ClassDescriptor: Returns the simple class name described by this ClassDescriptor.
getSimpleObjectClassDescriptors() - Method in class org.intermine.metadata.Model: Return ClassDescriptors for simple objects only - simple objects are light weight objects without an id and with no inheritance.
getString() - Method in class org.intermine.metadata.StringUtil.LineWrappedString: Returns the wrapped String.
getStrings() - Method in class org.intermine.model.StringConstructor: Returns a Collection containing the Strings that form this object, in the correct order.
getSubDescriptors() - Method in class org.intermine.metadata.ClassDescriptor: Return a Set of ClassDescriptors for all classes that directly extend or implement this class or interface.
getSuperclassDescriptor() - Method in class org.intermine.metadata.ClassDescriptor: Get the super class of this class (may be null).
getSuperclassNames() - Method in class org.intermine.metadata.ClassDescriptor: Return set of superclass class names.
getSuperDescriptors() - Method in class org.intermine.metadata.ClassDescriptor: Get a set of ClassDescriptors for the interfaces superclasses that this class implements.
getTopDownLevelTraversal() - Method in class org.intermine.metadata.Model: Return the classes in the model in level order from shallowest to deepest, the order of nodes at any given level is undefined.
getType() - Method in class org.intermine.metadata.AttributeDescriptor: Get the type of the attribute - either name of primitive or fully qualified class name.
getType() - Method in class org.intermine.metadata.ClassDescriptor: Returns the Class described by this ClassDescriptor.
getType() - Method in class org.intermine.metadata.TypeUtil.FieldInfo: Returns the type of the field.
getType(FieldDescriptor) - Method in class org.intermine.codegen.JavaModelOutput: Return the java type of a particular field.
getTypeByName(String) - Static method in class org.intermine.metadata.TypeUtil: Returns the Class for a given name (promoting primitives to their container class) and returning null if the name does not refer to any known class.
getUnqualifiedName() - Method in class org.intermine.metadata.ClassDescriptor: Returns unqualified name of class described by this ClassDescriptor.
getValues() - Static method in class org.intermine.metadata.ConstraintOp: Get the the internal list of ConstraintOps (Only for use in webapp)
getVersion() - Method in class org.intermine.metadata.Model
GREATER_THAN - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument is greater than the second
GREATER_THAN_EQUALS - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument is greater than or equal to the second

H

hasClassDescriptor(String) - Method in class org.intermine.metadata.Model: Return true if named ClassDescriptor is found in the model.
hashCode() - Method in class org.intermine.metadata.AttributeDescriptor
hashCode() - Method in class org.intermine.metadata.ClassDescriptor
hashCode() - Method in class org.intermine.metadata.CollectionDescriptor
hashCode() - Method in class org.intermine.metadata.Model
hashCode() - Method in class org.intermine.metadata.PrimaryKey
hashCode() - Method in class org.intermine.metadata.ReferenceDescriptor
hashCode() - Method in class org.intermine.metadata.StringUtil.LineWrappedString
hashCode(Object) - Static method in class org.intermine.metadata.Util: Return a zero hashCode if the object is null, otherwise return the real hashCode
hasProblems() - Method in class org.intermine.metadata.Model: Return true if there are problems with the model despite it's successful creation.

I

IN - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument is IN the second
indefiniteArticle(String) - Static method in class org.intermine.metadata.StringUtil: Return 'a' or 'an' according to first letter of the given article.
INDENT - Static variable in class org.intermine.codegen.JavaModelOutput
instantiate(String) - Static method in class org.intermine.metadata.TypeUtil: Deprecated.
This method is named incorrectly - use getTypeByName instead.
instantiate(String) - Static method in class org.intermine.metadata.Util: Returns the Class for a given name (promoting primitives to their container class)
InterMineException - Exception in org.intermine: An Exception that may be thrown by client facing parts of InterMine code.
InterMineException() - Constructor for exception org.intermine.InterMineException: Constructs an InterMineException
InterMineException(String) - Constructor for exception org.intermine.InterMineException: Constructs an InterMineException with the specified detail message.
InterMineException(String, Throwable) - Constructor for exception org.intermine.InterMineException: Constructs an InterMineException with the specified detail message and nested throwable.
InterMineException(Throwable) - Constructor for exception org.intermine.InterMineException: Constructs an InterMineException with the specified nested throwable.
InterMineFastPathObject - Interface in org.intermine.model: A root interface for all objects that can be stored in a InterMine database.
InterMineModelParser - Class in org.intermine.metadata: Parse InterMine metadata XML to produce an InterMine Model
InterMineModelParser() - Constructor for class org.intermine.metadata.InterMineModelParser
IS_EMPTY - Static variable in class org.intermine.metadata.ConstraintOp: Synonym for IS NULL
IS_NOT_EMPTY - Static variable in class org.intermine.metadata.ConstraintOp: Synonym for IS NOT NULL
IS_NOT_NULL - Static variable in class org.intermine.metadata.ConstraintOp: Require that the argument is not null
IS_NULL - Static variable in class org.intermine.metadata.ConstraintOp: Require that the argument is null
ISA - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument be of the type named by the right argument
isAttribute() - Method in class org.intermine.metadata.FieldDescriptor: Is this FieldDescriptor an attribute?
isCollection() - Method in class org.intermine.metadata.FieldDescriptor: Is this FieldDescriptor a collection?
isGeneratedClassAvailable(String) - Method in class org.intermine.metadata.Model
isGeneratedClassesAvailable() - Method in class org.intermine.metadata.Model
isInstanceOf(FastPathObject, String) - Static method in class org.intermine.metadata.TypeUtil: Return true if and only if the object is an instance of the class given by the className.
isInterface() - Method in class org.intermine.metadata.ClassDescriptor: True if this class is an interface.
ISNT - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument be of the type named by the right argument
isNumeric() - Method in class org.intermine.metadata.AttributeDescriptor: Returns true if the type of the attribute is some kind of number.
isPrimitive() - Method in class org.intermine.metadata.AttributeDescriptor: Returns true if the type of the attribute is a primitive type (rather than object).
isReference() - Method in class org.intermine.metadata.FieldDescriptor: Is this FieldDescriptor a reference?
isTruncated() - Method in class org.intermine.metadata.StringUtil.LineWrappedString: Returns whether the String had to be truncated.

J

javaiseClassName(String) - Static method in class org.intermine.metadata.TypeUtil: Filter a URI fragment to remove illegal characters
javaisePackageName(String) - Static method in class org.intermine.metadata.TypeUtil: Filter a string to remove illegal characters and join the rest in lower case.
JavaModelOutput - Class in org.intermine.codegen: Maps InterMine metadata to Java source files
JavaModelOutput(Model, File) - Constructor for class org.intermine.codegen.JavaModelOutput: Constructor.
join(Collection<?>, String) - Static method in class org.intermine.metadata.StringUtil: Returns a String formed by the delimited results of calling toString over a collection.
join(Collection<?>, String) - Static method in class org.intermine.metadata.Util: Returns a String formed by the delimited results of calling toString over a collection.

K

KEY_DEFINITIONS - Static variable in class org.intermine.metadata.Util: Name of the key under which to store the serialized version of the key definitions

L

lcm(int, int) - Static method in class org.intermine.metadata.Util: Takes two integers, and returns the lowest common multiple.
length() - Method in class org.intermine.model.StringConstructor
LESS_THAN - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument is less than the second
LESS_THAN_EQUALS - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument is less than or equal to the second
LineWrappedString(String, boolean) - Constructor for class org.intermine.metadata.StringUtil.LineWrappedString: Constructor.
loadKeyDefinitions(String) - Static method in class org.intermine.metadata.Util: Load the key definitions file for the named model from the classpath
loadModel(String) - Static method in class org.intermine.metadata.ModelFactory: Load a named model from the classpath
loadProperties(String) - Static method in class org.intermine.metadata.Util: Load a specified properties file
LOOKUP - Static variable in class org.intermine.metadata.ConstraintOp: Special operation indicating a bag upload step should be used, for the webapp only.

M

M_N_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor: A M:N relationship.
MATCHES - Static variable in class org.intermine.metadata.ConstraintOp: Require that the two arguments match
MetaDataException - Exception in org.intermine.metadata: An Exception that may be thrown if metadata is in an invalid state.
MetaDataException() - Constructor for exception org.intermine.metadata.MetaDataException: Constructs an MetaDataException
MetaDataException(String) - Constructor for exception org.intermine.metadata.MetaDataException: Constructs an MetaDataException with the specified detail message.
MetaDataException(String, Throwable) - Constructor for exception org.intermine.metadata.MetaDataException: Constructs an MetaDataException with the specified detail message and nested throwable.
MetaDataException(Throwable) - Constructor for exception org.intermine.metadata.MetaDataException: Constructs an MetaDataException with the specified nested throwable.
model - Variable in class org.intermine.codegen.JavaModelOutput
model - Variable in class org.intermine.task.ModelOutputTask
Model - Class in org.intermine.metadata: Represents a named business model, makes available metadata for each class within model.
Model(String, String, int, Collection<ClassDescriptor>) - Constructor for class org.intermine.metadata.Model: Construct a Model with a name and set of ClassDescriptors.
Model(String, String, Collection<ClassDescriptor>) - Constructor for class org.intermine.metadata.Model: Construct a model without a version.
MODEL - Static variable in class org.intermine.metadata.Util: Name of the key under which to store the serialized version of the model
Model.ModelAST - Class in org.intermine.metadata: A Map with slightly more type information.
ModelAST() - Constructor for class org.intermine.metadata.Model.ModelAST
ModelFactory - Class in org.intermine.metadata: A class that loads a model given a name.
modelKeys - Static variable in class org.intermine.metadata.PrimaryKeyUtil
ModelOutputTask - Class in org.intermine.task: Creates and runs a ModelOutput process to generate java or config files.
ModelOutputTask() - Constructor for class org.intermine.task.ModelOutputTask
ModelParser - Interface in org.intermine.metadata: Common interface for parsing source models into InterMine model format.
ModelParserException - Exception in org.intermine.metadata: An Exception that may be thrown by ModelMerger methods.
ModelParserException() - Constructor for exception org.intermine.metadata.ModelParserException: Constructs a ModelParserException
ModelParserException(String) - Constructor for exception org.intermine.metadata.ModelParserException: Constructs a ModelParserException with the specified detail message.
ModelParserException(String, Throwable) - Constructor for exception org.intermine.metadata.ModelParserException: Constructs a ModelParserException with the specified detail message and nested throwable.
ModelParserException(Throwable) - Constructor for exception org.intermine.metadata.ModelParserException: Constructs a ModelParserException with the specified nested throwable.

N

N_ONE_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor: A N:1 relationship.
name - Variable in class org.intermine.metadata.FieldDescriptor
NAND - Static variable in class org.intermine.metadata.ConstraintOp: Combine constraints with the NAND operation
negate() - Method in class org.intermine.metadata.ConstraintOp: Get the negated op
NONE_OF - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument is not one of a list of values
NonFatalMetaDataException - Exception in org.intermine.metadata: An Exception that may be thrown if metadata is in an invalid state.
NonFatalMetaDataException() - Constructor for exception org.intermine.metadata.NonFatalMetaDataException: Constructs an MetaDataException
NonFatalMetaDataException(String) - Constructor for exception org.intermine.metadata.NonFatalMetaDataException: Constructs an MetaDataException with the specified detail message.
NonFatalMetaDataException(String, Throwable) - Constructor for exception org.intermine.metadata.NonFatalMetaDataException: Constructs an MetaDataException with the specified detail message and nested throwable.
NonFatalMetaDataException(Throwable) - Constructor for exception org.intermine.metadata.NonFatalMetaDataException: Constructs an MetaDataException with the specified nested throwable.
NonOverrideableProperties - Class in org.intermine.metadata: Subclass of java.util.Properties that rejects duplicate definitions of a given property.
NonOverrideableProperties() - Constructor for class org.intermine.metadata.NonOverrideableProperties: Empty constructor.
NonOverrideableProperties(Properties) - Constructor for class org.intermine.metadata.NonOverrideableProperties: Constructor with defaults.
NOR - Static variable in class org.intermine.metadata.ConstraintOp: Combine constraints with the NOR operation
NOT_EQUALS - Static variable in class org.intermine.metadata.ConstraintOp: Require that the two arguments are not equal, ignoring case for strings
NOT_IN - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument is NOT IN the second
NOT_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor: Not a relationship between objects

O

ONE_N_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor: A 1:N relationship.
ONE_OF - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument is one of a list a values
ONE_ONE_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor: A 1:1 relationship
OR - Static variable in class org.intermine.metadata.ConstraintOp: Combine constraints with the OR operation
org.intermine - package org.intermine
org.intermine.codegen - package org.intermine.codegen
org.intermine.metadata - package org.intermine.metadata
org.intermine.model - package org.intermine.model
org.intermine.task - package org.intermine.task
OUTSIDE - Static variable in class org.intermine.metadata.ConstraintOp: Require that some part of the first argument lie outside the second.
OVERLAPS - Static variable in class org.intermine.metadata.ConstraintOp: Require that a range overlaps another range

P

packageName(String) - Static method in class org.intermine.metadata.TypeUtil: Returns the package name from a fully qualified class name
parse(InputSource, DefaultHandler) - Static method in class org.intermine.metadata.SAXParser: Parse the an xml file
parse(InputSource, DefaultHandler, boolean) - Static method in class org.intermine.metadata.SAXParser: Parse the an xml file
pluralise(String) - Static method in class org.intermine.metadata.StringUtil: Returns a pluralised version of the given String
prettyList(Collection<String>) - Static method in class org.intermine.metadata.StringUtil: Take a collection of Strings and return a combined string as a comma separated list with 'and' between the final pair.
prettyList(Collection<String>, boolean) - Static method in class org.intermine.metadata.StringUtil: Take a collection of Strings and return a combined string as a comma separated list with 'and' between the final pair.
PrimaryKey - Class in org.intermine.metadata: Class representing a primary key as a list of field names
PrimaryKey(String, String, ClassDescriptor) - Constructor for class org.intermine.metadata.PrimaryKey: Constructor
primaryKeyCache - Static variable in class org.intermine.metadata.PrimaryKeyUtil
PrimaryKeyUtil - Class in org.intermine.metadata: Utility methods for PrimaryKey objects.
process() - Method in class org.intermine.codegen.JavaModelOutput: Perform the mapping.
process(Reader) - Method in class org.intermine.metadata.InterMineModelParser: Read source model information in InterMine XML format and construct a InterMine Model object.
process(Reader) - Method in interface org.intermine.metadata.ModelParser: Read source model information and construct a InterMine Model object.
put(Object, Object) - Method in class org.intermine.metadata.NonOverrideableProperties: Override put, but do not allow existing values to be changed.

R

referencedClassDesc - Variable in class org.intermine.metadata.ReferenceDescriptor
ReferenceDescriptor - Class in org.intermine.metadata: Describes a field that references a single other class (i.e.
ReferenceDescriptor(String, String, String) - Constructor for class org.intermine.metadata.ReferenceDescriptor: Construct a ReferenceDescriptor.
referencedType - Variable in class org.intermine.metadata.ReferenceDescriptor
relationType() - Method in class org.intermine.metadata.AttributeDescriptor: Return an integer describing the type of relationship this field represents, where relationship types are 1:1, 1:N, N:1, M:N and "not a relationship".
relationType() - Method in class org.intermine.metadata.CollectionDescriptor: Return an integer describing the type of relationship this field represents, where relationship types are 1:1, 1:N, N:1, M:N and "not a relationship".
relationType() - Method in class org.intermine.metadata.FieldDescriptor: Return an integer describing the type of relationship this field represents, where relationship types are 1:1, 1:N, N:1, M:N and "not a relationship".
relationType() - Method in class org.intermine.metadata.ReferenceDescriptor: Return an integer describing the type of relationship this field represents, where relationship types are 1:1, 1:N, N:1, M:N and "not a relationship".
reverseCapitalisation(String) - Static method in class org.intermine.metadata.StringUtil: Reverses the capitalisation of the first character of the given String.
reverseRefDesc - Variable in class org.intermine.metadata.ReferenceDescriptor
reverseRefName - Variable in class org.intermine.metadata.ReferenceDescriptor
ROW_SEPARATOR - Static variable in class org.intermine.metadata.TextTable: An object representing a horizontal line separating two rows - treated as a row.

S

SAXParser - Class in org.intermine.metadata: Basic SAX Parser
serializedSortOrderToMap(String) - Static method in class org.intermine.metadata.StringUtil: Make a Map from the serialized String returned by jQuery.sortable("serialize").
setAllFieldDescriptors() - Method in class org.intermine.metadata.ClassDescriptor: Sets up the object a little.
setClassDescriptor(ClassDescriptor) - Method in class org.intermine.metadata.FieldDescriptor: Set the parent ClassDescriptor - should be called when this is added to a ClassDescriptor.
setClasses(Map<String, Map<String, Object>>) - Method in class org.intermine.metadata.Model.ModelAST
setDestDir(File) - Method in class org.intermine.task.ModelOutputTask: Sets the directory that output should be written to.
setFieldValue(String, Object) - Method in interface org.intermine.model.FastPathObject: Sets the value of a field by name.
setGeneratedClassesAvailable(boolean) - Method in class org.intermine.metadata.Model: Sets if generated classes are available.
setId(Integer) - Method in interface org.intermine.model.InterMineFastPathObject: Setter for the ID field.
setModel(String) - Method in class org.intermine.task.ModelOutputTask: Set the model to be used.
setModel(Model) - Method in class org.intermine.metadata.ClassDescriptor: Set the model for this ClassDescriptor, this is only be called once and will throw an Exception if called again.
setNextUniqueNumber(long) - Static method in class org.intermine.metadata.StringUtil: Sets the number that is used to generate the next uniqueString.
setType(String) - Method in class org.intermine.task.ModelOutputTask: Set the type of model output required.
ShadowClass - Interface in org.intermine.model: A root interface for all shadow classes for performance.
split(String, String) - Static method in class org.intermine.metadata.StringUtil: Returns a list of tokens delimited by delim in String str.
STRICT_NOT_EQUALS - Static variable in class org.intermine.metadata.ConstraintOp: Require that the two arguments are not equal
StringConstructor - Class in org.intermine.model: A CharSequence object representing a String constructed out of a sequence of other Strings.
StringConstructor() - Constructor for class org.intermine.model.StringConstructor: Main constructor - creates an empty object.
stringToObject(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil: Returns an object for a given String.
StringUtil - Class in org.intermine.metadata: Collection of commonly used String utilities
StringUtil.LineWrappedString - Class in org.intermine.metadata: Class for returning multiple values from the wrapLines method.
stripStart(String, Properties) - Static method in class org.intermine.metadata.Util: Strips the given string off the keys of the given Properties, and returns a new set of properties.
subSequence(int, int) - Method in class org.intermine.model.StringConstructor

T

terseClass(String) - Static method in class org.intermine.metadata.ClassDescriptor: Strips everything before the last dot out of a String.
TextTable - Class in org.intermine.metadata: A utility class for generating multi-column aligned text tables.
TextTable(boolean, boolean, boolean) - Constructor for class org.intermine.metadata.TextTable: Creates a new TextTable object, with or without column separating lines.
toAdditionsXML() - Method in class org.intermine.metadata.Model: Used to generate the SO additions file
toJsonAST() - Method in class org.intermine.metadata.Model: Returns a data structure suitable for serialisation, eg.
toJSONString() - Method in class org.intermine.metadata.AttributeDescriptor: Return the JSON representation of this object.
toJSONString() - Method in class org.intermine.metadata.ClassDescriptor
toJSONString() - Method in class org.intermine.metadata.FieldDescriptor: Return the JSON representation of this object.
toJSONString() - Method in class org.intermine.metadata.ReferenceDescriptor: Return the JSON representation of this object.
tokenize(String) - Static method in class org.intermine.metadata.StringUtil: Returns a list of tokens delimited by whitespace in String str (useful when handling XML)
tokenize(String) - Static method in class org.intermine.metadata.Util: Returns a list of tokens delimited by whitespace in String str (useful when handling XML)
tokenize(String, boolean) - Static method in class org.intermine.metadata.StringUtil: Returns a list of tokens delimited by comma.
tokenize(String, String) - Static method in class org.intermine.metadata.StringUtil
toSameInitialCase(String, String) - Static method in class org.intermine.metadata.StringUtil: Returns a string with the same initial letter case as the template string
toString() - Method in class org.intermine.metadata.AttributeDescriptor
toString() - Method in class org.intermine.metadata.ClassDescriptor
toString() - Method in class org.intermine.metadata.CollectionDescriptor
toString() - Method in class org.intermine.metadata.ConstraintOp: Get the String representation of this ConstraintOp
toString() - Method in class org.intermine.metadata.Model
toString() - Method in class org.intermine.metadata.PrimaryKey
toString() - Method in class org.intermine.metadata.ReferenceDescriptor
toString() - Method in class org.intermine.metadata.TextTable: Returns a text-formatted representation of this table.
toString() - Method in class org.intermine.model.StringConstructor: Returns the String that this object represents - note that this method should be avoided, because it defeats the purpose of keeping the constituent Strings separate in the first place.
trimLeft(String) - Static method in class org.intermine.metadata.StringUtil: trim left space in string
trimSlashes(String) - Static method in class org.intermine.metadata.StringUtil: Trim starting and trailing '/' characters from a string if present.
type - Variable in class org.intermine.metadata.AttributeDescriptor
type - Variable in class org.intermine.task.ModelOutputTask
TypeUtil - Class in org.intermine.metadata: Provides utility methods for working with Java types and reflection
TypeUtil.FieldInfo - Class in org.intermine.metadata: Inner class to hold info on a field.

U

uniqueString() - Static method in class org.intermine.metadata.StringUtil: Returns a String that is different every time
unqualifiedName(String) - Static method in class org.intermine.metadata.TypeUtil: Returns the unqualified class name from a fully qualified class name
unqualifiedName(String) - Static method in class org.intermine.metadata.Util: Returns the unqualified class name from a fully qualified class name
Util - Class in org.intermine.metadata: Generic utility functions.

V

VALID_TYPES - Static variable in class org.intermine.metadata.AttributeDescriptor: This is a list of the valid type strings.
verboseException(Exception) - Static method in class org.intermine.metadata.Util: Takes an Exception, and returns an Exception of similar type with all available information in the message.

W

wildcardSqlToUser(String) - Static method in class org.intermine.metadata.Util: Deprecated.
I don't think this is used anymore?
wildcardUserToSql(String) - Static method in class org.intermine.metadata.Util: Turn a user supplied wildcard expression with * into an SQL LIKE/NOT LIKE expression with %'s and other special characters.
WITHIN - Static variable in class org.intermine.metadata.ConstraintOp: Require that the first argument lie entirely within the second.
wrapLines(String, int, int) - Static method in class org.intermine.metadata.StringUtil: Wraps the given String into several lines and ultimately truncates it with an ellipsis.
wrapLines(String, int, int, int) - Static method in class org.intermine.metadata.StringUtil: Wraps the given String into several lines and ultimately truncates it with an ellipsis.

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