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

A

accept(T) - Method in interface org.genantics.access.Filter

Access<V> - Interface in org.genantics.access

Element access and data common to all immutable collections.

add(T) - Method in class org.genantics.set.KeyedSet

Add an element to the set.

add(T, boolean[]) - Method in class org.genantics.set.KeyedSet

Convenience method for java.util.Set, which returns true if the element was not already present in the tree.

addAll(Iterable<T>) - Method in class org.genantics.set.KeyedSet

Add all elements in iterable to set.

addElement(T, boolean[]) - Method in class org.genantics.set.KeyedSet

addEntry returns this tree with added element

addElement(T, boolean[]) - Method in class org.genantics.set.KeyedSet.Empty

Array<V> - Class in org.genantics.array

Array() - Constructor for class org.genantics.array.Array

Array.ArrayState - Class in org.genantics.array

Array.ArrayState(Array<V>, int) - Constructor for class org.genantics.array.Array.ArrayState

Array.Empty<V> - Class in org.genantics.array

Empty is a singleton object representing the empty array.

Array.Empty() - Constructor for class org.genantics.array.Array.Empty

Array.References<V> - Class in org.genantics.array

A references array contains references to References or, at height 2, Values.

Array.Values<V> - Class in org.genantics.array

A values array contains actual data.

B

balanceTree(KeyedSet<K, T>) - Method in class org.genantics.set.KeyedSet

C

checkNull(V) - Method in class org.genantics.array.Array.Values

clear() - Method in class org.genantics.set.KeyedSet

Vacuous method for compatibility.

CList<V> - Interface in org.genantics.list

Classical List interface.

CodedList<V> - Class in org.genantics.list

CodedList implements a "CDR-coded" list.

CodedList(V, CList<V>) - Constructor for class org.genantics.list.CodedList

Constructor.

CodedList(V, CodedList<V>, int) - Constructor for class org.genantics.list.CodedList

CodedList(CodedList<V>) - Constructor for class org.genantics.list.CodedList

CodedList.CListIterator<V> - Class in org.genantics.list

CodedList.CListReverseIterator<V> - Class in org.genantics.list

collect(Collection<T>) - Method in class org.genantics.set.KeyedSet

Add all elements to collection.

collect(Collection<T>) - Method in class org.genantics.set.KeyedSet.Empty

ConditionalVisitor<V> - Interface in org.genantics.access

Conditional visitor.

cons(V) - Method in interface org.genantics.list.CList

Add an element to the head of the list.

cons(V) - Method in class org.genantics.list.CodedList

cons(V) - Method in class org.genantics.list.ConsList

cons(V) - Method in class org.genantics.list.Nil

ConsList<V> - Class in org.genantics.list

Classical immutable list.

ConsList(V, ConsList<V>) - Constructor for class org.genantics.list.ConsList

contains(V) - Method in interface org.genantics.access.Access

Test if collection contains value.

contains(V) - Method in class org.genantics.array.Array.Empty

contains(V) - Method in class org.genantics.array.Array.References

contains(V) - Method in class org.genantics.array.Array.Values

contains(V) - Method in interface org.genantics.list.CList

Test for element.

contains(V) - Method in class org.genantics.list.CodedList

contains(V, int) - Method in class org.genantics.list.CodedList

contains(V) - Method in class org.genantics.list.ConsList

contains(V) - Method in class org.genantics.list.Nil

contains(T) - Method in class org.genantics.set.KeyedSet

containsAll(Iterable<T>) - Method in class org.genantics.set.KeyedSet

containsAll(Iterable<T>) - Method in class org.genantics.set.KeyedSet.Empty

containsAny(Iterable<T>) - Method in class org.genantics.set.KeyedSet

containsAny(Iterable<T>) - Method in class org.genantics.set.KeyedSet.Empty

containsKey(K) - Method in class org.genantics.set.KeyedSet

Test if tree contains the specified key.

containsKey(T) - Method in class org.genantics.set.KeyedSet

containsKey(K) - Method in class org.genantics.set.KeyedSet.Empty

containsKey(T) - Method in class org.genantics.set.KeyedSet.Empty

D

DefaultIterator<V> - Class in org.genantics.access

Default iterator for immutable classes, which never support remove().

DefaultIterator() - Constructor for class org.genantics.access.DefaultIterator

delete(K) - Method in class org.genantics.set.KeyedSet

Delete the element with matching key.

delete(K, boolean[]) - Method in class org.genantics.set.KeyedSet

Delete the element with matching key.

deleteFirst() - Method in class org.genantics.set.KeyedSet

Delete the first element of the tree.

deleteFirst() - Method in class org.genantics.set.KeyedSet.Empty

deleteKey(K, boolean[]) - Method in class org.genantics.set.KeyedSet

deleteKey(K, boolean[]) - Method in class org.genantics.set.KeyedSet.Empty

deleteLast() - Method in class org.genantics.set.KeyedSet

Delete the last element of the tree.

deleteLast() - Method in class org.genantics.set.KeyedSet.Empty

E

elements() - Method in class org.genantics.set.KeyedSet

Return an iterable that can be used in foreach to obtain elements in ascending order.

elements() - Method in class org.genantics.set.KeyedSet.Empty

EMPTY - Static variable in class org.genantics.array.Array

An empty array suitable for growing.

EMPTY - Static variable in class org.genantics.set.KeyedSet

equals(Object) - Method in class org.genantics.set.KeyedSet.Empty

equals(Object) - Method in class org.genantics.set.KeyedSet

Compare sets.

F

Filter<T> - Interface in org.genantics.access

filter(Filter) - Method in class org.genantics.set.KeyedSet.Empty

filter(Filter) - Method in class org.genantics.set.KeyedSet

Filter the set, removing all elements for which the test method returns false.

find(V) - Method in class org.genantics.array.Array.Empty

find(V) - Method in class org.genantics.array.Array.References

find(V) - Method in class org.genantics.array.Array.Values

find(V) - Method in interface org.genantics.array.IndexedAccess

G

get(int) - Method in class org.genantics.array.Array.Empty

get(int) - Method in class org.genantics.array.Array.References

get(int) - Method in class org.genantics.array.Array.Values

get(int) - Method in interface org.genantics.array.IndexedAccess

get(K) - Method in class org.genantics.set.KeyedSet.Empty

get(K) - Method in class org.genantics.set.KeyedSet

Get the element with matching key.

getBalance() - Method in class org.genantics.set.KeyedSet

getFirst() - Method in class org.genantics.set.KeyedSet.Empty

getFirst() - Method in class org.genantics.set.KeyedSet

Get the first element in the tree.

getKey() - Method in interface org.genantics.set.Keyed

getLast() - Method in class org.genantics.set.KeyedSet.Empty

getLast() - Method in class org.genantics.set.KeyedSet

Get the last element in the tree.

getNext(int, Stack<Array<V>.ArrayState>) - Method in class org.genantics.array.Array.Empty

getNext(int, Stack<Array<V>.ArrayState>) - Method in class org.genantics.array.Array

getNext(int, Stack<Array<V>.ArrayState>) - Method in class org.genantics.array.Array.References

getNext(int, Stack<Array<V>.ArrayState>) - Method in class org.genantics.array.Array.Values

getPrev(int, Stack<Array<V>.ArrayState>) - Method in class org.genantics.array.Array.Empty

getPrev(int, Stack<Array<V>.ArrayState>) - Method in class org.genantics.array.Array

getPrev(int, Stack<Array<V>.ArrayState>) - Method in class org.genantics.array.Array.References

getPrev(int, Stack<Array<V>.ArrayState>) - Method in class org.genantics.array.Array.Values

H

hashCode() - Method in class org.genantics.set.KeyedSet.Empty

hashCode() - Method in class org.genantics.set.KeyedSet

Get the hashCode for the set.

hasNext() - Method in class org.genantics.list.CodedList.CListIterator

hasNext() - Method in class org.genantics.list.CodedList.CListReverseIterator

hasNext() - Method in class org.genantics.set.KeyedSet.ReverseTreeIterator

hasNext() - Method in class org.genantics.set.KeyedSet.ReverseValueIterator

hasNext() - Method in class org.genantics.set.KeyedSet.ValueIterator

head() - Method in interface org.genantics.list.CList

Get the head of the list.

head() - Method in class org.genantics.list.CodedList

head() - Method in class org.genantics.list.ConsList

head() - Method in class org.genantics.list.Nil

height - Variable in class org.genantics.set.KeyedSet

I

IndexedAccess<V> - Interface in org.genantics.array

init() - Method in class org.genantics.set.KeyedSet.Empty

init() - Method in class org.genantics.set.KeyedSet

isEmpty() - Method in interface org.genantics.access.Access

Test if empty.

isEmpty() - Method in class org.genantics.array.Array.Empty

isEmpty() - Method in class org.genantics.array.Array.References

isEmpty() - Method in class org.genantics.array.Array.Values

isEmpty() - Method in class org.genantics.list.CodedList

isEmpty() - Method in class org.genantics.list.ConsList

isEmpty() - Method in class org.genantics.list.Nil

isEmpty() - Method in class org.genantics.set.KeyedSet.Empty

isEmpty() - Method in class org.genantics.set.KeyedSet

iterator() - Method in interface org.genantics.access.Access

Get the elements in order.

iterator() - Method in class org.genantics.array.Array.Empty

iterator() - Method in class org.genantics.array.Array.References

iterator() - Method in class org.genantics.array.Array.Values

iterator() - Method in interface org.genantics.list.CList

Iterate through the elements in the list.

iterator() - Method in class org.genantics.list.CodedList

iterator() - Method in class org.genantics.list.ConsList

iterator() - Method in class org.genantics.list.Nil

iterator() - Method in class org.genantics.set.KeyedSet.Empty

iterator() - Method in class org.genantics.set.KeyedSet

Return an iterator over the elements of the set in ascending order.

iterator() - Method in class org.genantics.set.KeyedSet.ReverseTreeIterable

iterator() - Method in class org.genantics.set.KeyedSet.ReverseValueIterable

iterator() - Method in class org.genantics.set.KeyedSet.TreeIterable

iterator() - Method in class org.genantics.set.KeyedSet.ValueIterable

J

JAVA_8 - Static variable in interface org.genantics.access.Access

K

Keyed<T extends Comparable<T>> - Interface in org.genantics.set

Interface implemented by KeyedSet elements.

KeyedSet<K extends Comparable<K>,T extends Keyed<K>> - Class in org.genantics.set

Immutable set based on AVL tree.

KeyedSet(Iterable<T>) - Constructor for class org.genantics.set.KeyedSet

Construct set from iterable.

KeyedSet(T, KeyedSet<K, T>, KeyedSet<K, T>) - Constructor for class org.genantics.set.KeyedSet

Constructor.

KeyedSet.Empty<T extends Keyed<K>,K extends Comparable<K>> - Class in org.genantics.set

Empty is a singleton object representing the empty set.

KeyedSet.Empty() - Constructor for class org.genantics.set.KeyedSet.Empty

KeyedSet.ReverseTreeIterable - Class in org.genantics.set

KeyedSet.ReverseTreeIterable() - Constructor for class org.genantics.set.KeyedSet.ReverseTreeIterable

KeyedSet.ReverseTreeIterator - Class in org.genantics.set

KeyedSet.ReverseTreeIterator() - Constructor for class org.genantics.set.KeyedSet.ReverseTreeIterator

KeyedSet.ReverseValueIterable - Class in org.genantics.set

KeyedSet.ReverseValueIterable() - Constructor for class org.genantics.set.KeyedSet.ReverseValueIterable

KeyedSet.ReverseValueIterator - Class in org.genantics.set

KeyedSet.ReverseValueIterator() - Constructor for class org.genantics.set.KeyedSet.ReverseValueIterator

KeyedSet.TreeIterable - Class in org.genantics.set

KeyedSet.TreeIterable() - Constructor for class org.genantics.set.KeyedSet.TreeIterable

KeyedSet.TreeState - Class in org.genantics.set

KeyedSet.TreeState(KeyedSet<K, T>, int) - Constructor for class org.genantics.set.KeyedSet.TreeState

KeyedSet.ValueIterable - Class in org.genantics.set

KeyedSet.ValueIterable() - Constructor for class org.genantics.set.KeyedSet.ValueIterable

KeyedSet.ValueIterator - Class in org.genantics.set

KeyedSet.ValueIterator() - Constructor for class org.genantics.set.KeyedSet.ValueIterator

keys() - Method in class org.genantics.set.KeyedSet

Get an iterable that can be used in foreach to obtain keys in ascending order.

L

left - Variable in class org.genantics.set.KeyedSet

LEFT - Static variable in class org.genantics.set.KeyedSet.TreeState

loopTraversal(KeyedSet<K, T>) - Method in class org.genantics.set.KeyedSet.ReverseTreeIterator

Implements the recursive generator schema:

M

member - Variable in class org.genantics.set.KeyedSet

N

newArray(int, Object) - Static method in class org.genantics.array.Array

newTree(T, KeyedSet<K, T>, KeyedSet<K, T>) - Method in class org.genantics.set.KeyedSet

Function that wraps constructor.

next() - Method in class org.genantics.list.CodedList.CListIterator

next() - Method in class org.genantics.list.CodedList.CListReverseIterator

next() - Method in class org.genantics.set.KeyedSet.ReverseTreeIterator

next() - Method in class org.genantics.set.KeyedSet.ReverseValueIterator

next() - Method in class org.genantics.set.KeyedSet.ValueIterator

NIL - Static variable in interface org.genantics.list.CList

Nil<V> - Class in org.genantics.list

NONE - Static variable in class org.genantics.set.KeyedSet.TreeState

O

org.genantics.access - package org.genantics.access

org.genantics.array - package org.genantics.array

org.genantics.list - package org.genantics.list

org.genantics.set - package org.genantics.set

P

prettyPrint() - Method in class org.genantics.set.KeyedSet.Empty

prettyPrint() - Method in class org.genantics.set.KeyedSet

prettyPrint(String) - Method in class org.genantics.set.KeyedSet

R

remove() - Method in class org.genantics.access.DefaultIterator

remove(T) - Method in class org.genantics.set.KeyedSet

Remove an element if the keys match and the values are equal.

remove(T, boolean[]) - Method in class org.genantics.set.KeyedSet

Remove an element if the keys match and the values are equal.

remove() - Method in class org.genantics.set.KeyedSet.ReverseTreeIterator

remove() - Method in class org.genantics.set.KeyedSet.ReverseValueIterator

remove() - Method in class org.genantics.set.KeyedSet.ValueIterator

removeAll(Iterable<T>) - Method in class org.genantics.set.KeyedSet.Empty

removeAll(Iterable<T>) - Method in class org.genantics.set.KeyedSet

Remove all elements in iterable from tree.

removeElement(T, boolean[]) - Method in class org.genantics.set.KeyedSet.Empty

removeElement(T, boolean[]) - Method in class org.genantics.set.KeyedSet

removeFirst() - Method in class org.genantics.list.Nil

removeHigh(KeyedSet<K, T>, KeyedSet<K, T>) - Method in class org.genantics.set.KeyedSet

retainAll(Iterable<T>) - Method in class org.genantics.set.KeyedSet.Empty

retainAll(Iterable<T>) - Method in class org.genantics.set.KeyedSet

Get all elements in both set and iterable.

reverseElements() - Method in class org.genantics.set.KeyedSet.Empty

reverseElements() - Method in class org.genantics.set.KeyedSet

Return an iterable that can be used in foreach to obtain elements in descending order.

reverseIterator() - Method in interface org.genantics.access.Access

Get the elements in reverse order.

reverseIterator() - Method in class org.genantics.array.Array.Empty

reverseIterator() - Method in class org.genantics.array.Array.References

reverseIterator() - Method in class org.genantics.array.Array.Values

reverseIterator() - Method in class org.genantics.list.CodedList

reverseIterator() - Method in class org.genantics.list.ConsList

reverseIterator() - Method in class org.genantics.list.Nil

reverseIterator() - Method in class org.genantics.set.KeyedSet.Empty

reverseIterator() - Method in class org.genantics.set.KeyedSet

Return an iterator over the elements of the set in descending order.

reverseKeys() - Method in class org.genantics.set.KeyedSet

Get an iterable that can be used in foreach to obtain keys in descending order.

reverseVisit(Visitor<V>) - Method in interface org.genantics.access.Access

Visit all elements in reverse order.

reverseVisit(ConditionalVisitor<V>) - Method in interface org.genantics.access.Access

Visit all elements in reverse order until visitor.visit() returns true;

reverseVisit(Visitor<V>) - Method in class org.genantics.array.Array.Empty

reverseVisit(ConditionalVisitor<V>) - Method in class org.genantics.array.Array.Empty

reverseVisit(Visitor<V>) - Method in class org.genantics.array.Array.References

reverseVisit(ConditionalVisitor<V>) - Method in class org.genantics.array.Array.References

reverseVisit(Visitor<V>) - Method in class org.genantics.array.Array.Values

reverseVisit(ConditionalVisitor<V>) - Method in class org.genantics.array.Array.Values

reverseVisit(Visitor<V>, int, CList<V>) - Method in class org.genantics.list.CodedList

reverseVisit(ConditionalVisitor<V>, int, CList<V>) - Method in class org.genantics.list.CodedList

reverseVisit(Visitor<V>) - Method in class org.genantics.list.CodedList

reverseVisit(ConditionalVisitor<V>) - Method in class org.genantics.list.CodedList

reverseVisit(Visitor<V>) - Method in class org.genantics.list.ConsList

reverseVisit(ConditionalVisitor<V>) - Method in class org.genantics.list.ConsList

reverseVisit(Visitor<V>) - Method in class org.genantics.list.Nil

reverseVisit(ConditionalVisitor<V>) - Method in class org.genantics.list.Nil

right - Variable in class org.genantics.set.KeyedSet

RIGHT - Static variable in class org.genantics.set.KeyedSet.TreeState

S

set(int, V) - Method in class org.genantics.array.Array.Empty

set(int, V) - Method in class org.genantics.array.Array.References

set(int, V) - Method in class org.genantics.array.Array.Values

set(int, V) - Method in interface org.genantics.array.IndexedAccess

setLeft(KeyedSet<K, T>) - Method in class org.genantics.set.KeyedSet

setRight(KeyedSet<K, T>) - Method in class org.genantics.set.KeyedSet

size() - Method in interface org.genantics.access.Access

Get the number of elements in the collection.

size() - Method in class org.genantics.array.Array.Empty

size() - Method in class org.genantics.array.Array.References

size() - Method in class org.genantics.array.Array.Values

size() - Method in class org.genantics.list.CodedList

size() - Method in class org.genantics.list.ConsList

Return the number of elements in the list.

size() - Method in class org.genantics.list.Nil

size() - Method in class org.genantics.set.KeyedSet.Empty

size() - Method in class org.genantics.set.KeyedSet

Get the tree size.

T

tail() - Method in interface org.genantics.list.CList

Get the rest of the list after the head.

tail() - Method in class org.genantics.list.CodedList

tail() - Method in class org.genantics.list.ConsList

tail() - Method in class org.genantics.list.Nil

THIS - Static variable in class org.genantics.set.KeyedSet.TreeState

toCollection(Collection<V>) - Method in interface org.genantics.list.CList

Copy elements in list to collection in order.

toCollection(Collection<V>, int) - Method in class org.genantics.list.CodedList

toCollection(Collection<V>) - Method in class org.genantics.list.CodedList

toCollection(Collection<V>) - Method in class org.genantics.list.ConsList

toCollection(Collection<V>) - Method in class org.genantics.list.Nil

toString() - Method in class org.genantics.list.ConsList

toString() - Method in class org.genantics.set.KeyedSet.Empty

toString() - Method in class org.genantics.set.KeyedSet

V

visit(Visitor<V>) - Method in interface org.genantics.access.Access

Visit all elements in order.

visit(ConditionalVisitor<V>) - Method in interface org.genantics.access.Access

Visit all elements in order until visitor.visit() returns true;

visit(V) - Method in interface org.genantics.access.ConditionalVisitor

Visit an element.

visit(V) - Method in interface org.genantics.access.Visitor

visit(Visitor<V>) - Method in class org.genantics.array.Array.Empty

visit(ConditionalVisitor<V>) - Method in class org.genantics.array.Array.Empty

visit(Visitor<V>) - Method in class org.genantics.array.Array.References

visit(ConditionalVisitor<V>) - Method in class org.genantics.array.Array.References

visit(Visitor<V>) - Method in class org.genantics.array.Array.Values

visit(ConditionalVisitor<V>) - Method in class org.genantics.array.Array.Values

visit(Visitor<V>) - Method in interface org.genantics.list.CList

Visit each element in order.

visit(ConditionalVisitor<V>) - Method in interface org.genantics.list.CList

Visit each element in order until visit returns false.

visit(Visitor<V>, int) - Method in class org.genantics.list.CodedList

visit(ConditionalVisitor<V>, int) - Method in class org.genantics.list.CodedList

visit(Visitor<V>) - Method in class org.genantics.list.CodedList

visit(ConditionalVisitor<V>) - Method in class org.genantics.list.CodedList

visit(Visitor<V>) - Method in class org.genantics.list.ConsList

visit(ConditionalVisitor<V>) - Method in class org.genantics.list.ConsList

visit(Visitor<V>) - Method in class org.genantics.list.Nil

visit(ConditionalVisitor<V>) - Method in class org.genantics.list.Nil

visitFwd(Visitor) - Method in class org.genantics.set.KeyedSet.Empty

visitFwd(ConditionalVisitor) - Method in class org.genantics.set.KeyedSet.Empty

visitFwd(Visitor) - Method in class org.genantics.set.KeyedSet

Visit all elements in order.

visitFwd(ConditionalVisitor) - Method in class org.genantics.set.KeyedSet

Visit elements in order.

Visitor<V> - Interface in org.genantics.access

visitRev(Visitor) - Method in class org.genantics.set.KeyedSet.Empty

visitRev(ConditionalVisitor) - Method in class org.genantics.set.KeyedSet.Empty

visitRev(Visitor) - Method in class org.genantics.set.KeyedSet

Visit all elements in reverse order.

visitRev(ConditionalVisitor) - Method in class org.genantics.set.KeyedSet

Visit all elements in reverse order.

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