A C E F G H I L M N P R S T U

A

Annotation - class Annotation.
An example of the kind of information that can be attached to the nodes of the suffix tree: here, the sum of the length of all the labels on the path from the root to the current node.
Annotation(int) - Constructor for class Annotation
Stores pathLen in this Annotation object.
addCoordinates(int) - Method in class LeafNode
prepends the current coordinates (an object that contains the starting index of the current added suffix) to the list of coordinates - that in case two strings have the same suffix
addPathLength(SuffixTree) - Static method in class Annotation
A class method to decorate a tree with pathLen information at each node.
addPathLength(int, NodeInterface) - Static method in class Annotation
 
addToken(String) - Method in class SuffixTree
adds a new string to the suffix tree
addToken(String) - Method in class TreeBuilder
add a string to the tree this builder is constructed for
alphabet - Variable in class SuffixTree
permitted characters in the strings

C

coordinates - Variable in class LeafNode
the coordinates of one of the suffixes ending at this leaf node
current - Variable in class TreeBuilder
the current node; it is always the node where the substring S[ j..i] ends (where j is the index of the previous phase)

E

extend(int, int) - Method in class TreeBuilder
 

F

findChild(char) - Method in class TreeBuilder
finds the child of the current node that has branchStart as its first character; this function will succeed in finding the child since the string S[j-1..i] is already in the tree returns true if there are more branches to be followed
firstChild - Variable in class InternalNode
Link to the first child of this node.

G

gamma - Variable in class TreeBuilder
if the current internal node was just inserted, it does not have a suffix link attached to it; in this case, we have to remeber the string that labels the branch leading to this node (gamma will be followed down from the node at the end of the suffix link starting form the parent of this node
gammaLen - Variable in class TreeBuilder
store the gamma length, so that we don't have to call gamma.length() each time (expensive)
getCoordinates() - Method in class LeafNode
Returns the first coordinate object.
getFirstChild() - Method in class InternalNode
 
getIndex(int) - Method in class ListOfTokens
Returns the index of the string that contains position.
getIndex(int) - Method in class SuffixTree
Returns the index of the token that contains position.
getInfo() - Method in class InternalNode
 
getInfo() - Method in class LeafNode
Returns the first info object.
getInfo() - Method in interface NodeInterface
 
getLCE(String, int, int, int) - Method in class ListOfTokens
Returns the length of the Longest Common Extension (LCE), starting at position i of p, and j within the list of tokens.
getLCE(String, int, NodeInterface) - Method in class SuffixTree
Returns the length of the Longest Common Extension (LCE), starting at position pos of the pattern, and leftIndex from the string collection.
getLeftIndex() - Method in class InternalNode
 
getLeftIndex() - Method in class LeafNode
 
getLeftIndex() - Method in interface NodeInterface
 
getLen() - Method in class Token
 
getLength() - Method in class InternalNode
 
getLength() - Method in class LeafNode
 
getLength() - Method in interface NodeInterface
 
getNext() - Method in class SuffixCoordinates
returns the next coordinate object
getNext() - Method in class Token
 
getNextInfo() - Method in class Annotation
Returns the next element of information stored at that node.
getNextInfo() - Method in interface Info
 
getNoNodes() - Method in class SuffixTree
returns the total no of nodes in the tree
getPathLength() - Method in class Annotation
Returns the pathLen.
getPosition() - Method in class SuffixCoordinates
returns the position of the suffix
getRightSybling() - Method in class InternalNode
 
getRightSybling() - Method in class LeafNode
 
getRightSybling() - Method in interface NodeInterface
 
getRoot() - Method in class SuffixTree
returns the root of the tree
getStart(int) - Method in class ListOfTokens
returns the starting index of the string containing "position"
getStart(int) - Method in class SuffixTree
returns the starting index of the token at indexToken
getSubstring(int, int) - Method in class ListOfTokens
returns the substring at the position "position", where position is counted from the first symbol of the first token (cumulative position)
getSubstring(int) - Method in class ListOfTokens
returns the substring at the position "position", to the end of the string, where position is counted from the first symbol of the first token (cumulative position)
getSubstring(int, int) - Method in class SuffixTree
returns the substring starting at leftIndex and having length length from the string collection
getSubstring(int) - Method in class SuffixTree
returns the suffix starting at leftIndex
getSuffixLink() - Method in class InternalNode
 
getToken() - Method in class Token
 
getTotalLength() - Method in class ListOfTokens
returns the total length of the strings contained in this list
getTotalLength() - Method in class SuffixTree
returns the total length of the strings in the tree
goDown() - Method in class TreeBuilder
walks down from node s(v) along the path gamma, using skip/count trick
goToLastExplicit() - Method in class TreeBuilder
just before ending the current phase, after an implicit extension was made
goUp(int, int) - Method in class TreeBuilder
currentSuffix is the j index of the current phase, and the last explicit extension index + 1

H

head - Variable in class ListOfTokens
head of the list

I

Info - interface Info.
This interface is to be implemented by new classes that need to add their own information to the tree nodes.
InternalNode - class InternalNode.
 
InternalNode() - Constructor for class InternalNode
 
InternalNode(int, int, Object, Object) - Constructor for class InternalNode
 
info - Variable in class InternalNode
Contains additinaol information about this node (such as lca info).
info - Variable in class LeafNode
May contain additional information about this node (such as lca info).
insertToken(String) - Method in class ListOfTokens
returns token position inserts token as string if the token is not already there

L

LeafNode - class LeafNode.
 
LeafNode(int, int, Object) - Constructor for class LeafNode
 
LeafNode() - Constructor for class LeafNode
 
ListOfTokens - class ListOfTokens.
 
ListOfTokens() - Constructor for class ListOfTokens
 
lastExtPhase - Variable in class TreeBuilder
records the last extension phase, so that we know where to start form when inserting a new suffix in the tree
leftIndex - Variable in class InternalNode
The starting index of the branch that leads to this node.
leftIndex - Variable in class LeafNode
The starting index of the branch that leads to this node.
length - Variable in class InternalNode
The length of the branch leading to this node.
length - Variable in class LeafNode
The length of the branch leading to this node.

M

myTree - Variable in class TreeBuilder
the tree in which the string is added

N

NodeInterface - interface NodeInterface.
Interface to access the node information.
next - Variable in class Annotation
 
next - Variable in class Token
 
nextCoordinates - Variable in class SuffixCoordinates
the next coordinate object
noNodes - Variable in class SuffixTree
total number of nodes in the tree
noNodes - Variable in class TreeBuilder
number of nodes added to the tree during the insertion of this string

P

pathLength - Variable in class Annotation
 
position - Variable in class SuffixCoordinates
the position of the suffix associated with this leaf node Note that the position is calculated relatively to the first char of the first string added to the tree
prettyPrint(NodeInterface, String) - Method in class TreePrinter
 
prettyPrint() - Method in class TreePrinter
 
previous - Variable in class TreeBuilder
preserves the internal node that was previously added to the tree, as well as its parent this is necesary when the chain of explicit extensions ends in the current phase, so that we can restore the starting point for the next phase

R

rightSybling - Variable in class InternalNode
Link to the right sybling of this node (if there is one).
rightSybling - Variable in class LeafNode
Link to the right sybling of this node (if there is one).
root - Variable in class SuffixTree
the root of the tree

S

SuffixCoordinates - class SuffixCoordinates.
Holds the coordinates of this leaf can have more than one set of coordinates, since this suffix can be suffix to more than one string.
SuffixCoordinates(int, SuffixCoordinates) - Constructor for class SuffixCoordinates
 
SuffixTree - class SuffixTree.
 
SuffixTree(String) - Constructor for class SuffixTree
Alphabet specifies what characters are allowed in the strings added to the suffix tree.
setFirstChild(Object) - Method in class InternalNode
 
setInfo(Info) - Method in class InternalNode
sets an Info object to this node.
setInfo(Info) - Method in class LeafNode
prepends the current info to the list of already existing info objects
setInfo(Info) - Method in interface NodeInterface
 
setLeftIndex(int) - Method in class InternalNode
 
setLeftIndex(int) - Method in class LeafNode
 
setLength(int) - Method in class InternalNode
 
setLength(int) - Method in class LeafNode
 
setNext(Token) - Method in class Token
 
setNextInfo(Info) - Method in class Annotation
Add an element of information to this node.
setNextInfo(Info) - Method in interface Info
 
setRightSybling(Object) - Method in class InternalNode
 
setRightSybling(Object) - Method in class LeafNode
 
setSuffixLink(Object) - Method in class InternalNode
 
setToken(String) - Method in class Token
 
startPos - Variable in class TreeBuilder
the index of the first char ofthis string, relatively to the first char of the first string inserted in the tree
suffixLink - Variable in class InternalNode
An internal node always has a sufix link.

T

Token - class Token.
Simple object that contains a string, and a link to the next token.
Token() - Constructor for class Token
 
Token(String, Token) - Constructor for class Token
 
TreeBuilder - class TreeBuilder.
Used to build the tree; the tree structure itself is very simple.
TreeBuilder(SuffixTree) - Constructor for class TreeBuilder
Initialized always at the root of the tree, each time a new string is added to the tree.
TreePrinter - class TreePrinter.
 
TreePrinter(SuffixTree) - Constructor for class TreePrinter
 
toString() - Method in class Annotation
Returns a String representation of this and the following elements of information.
toString() - Method in class SuffixCoordinates
 
token - Variable in class Token
 
token - Variable in class TreeBuilder
the string that is currently inserted
tokenIndex - Variable in class TreeBuilder
the index of the current token; it is assigned in the order of insertion of the strings in the tree
tokenLen - Variable in class TreeBuilder
store the token length, so that we don't have to call token.length() each time (expensive)
tokens - Variable in class SuffixTree
the strings in the tree
tree - Variable in class TreePrinter
 

U

updateNoNodes(int) - Method in class SuffixTree
updates the total no of nodes in the tree, after a new string was inserted

A C E F G H I L M N P R S T U