ec.gp Class GPTree

java.lang.Object
ec.gp.GPTree

All Implemented Interfaces:
GPNodeParent, Prototype, Setup, java.io.Serializable, java.lang.Cloneable

public class GPTreeextends java.lang.Objectimplements GPNodeParent, Prototype

GPTree is a GPNodeParent which holds the root GPNode of a tree of GPNodes. GPTrees typically fill out an array held in a GPIndividual (their "owner") and their roots are evaluated to evaluate a Genetic programming tree. GPTrees also have constraints, which are shared, and define items shared among several GPTrees.

In addition to serialization for checkpointing, GPTrees may read and write themselves to streams in three ways.

• writeTree(...,DataOutput)/readTree(...,DataInput)   This method transmits or receives a GPTree in binary. It is the most efficient approach to sending GPTrees over networks, etc. The default versions of writeTree/readTree call writeRootedTree/readRootedTree on their respective GPNode roots.
• printTree(...,PrintWriter)/readTree(...,LineNumberReader)   This approach transmits or receives a GPTree in text encoded such that the GPTree is largely readable by humans but can be read back in 100% by ECJ as well. To do this, these methods will typically encode numbers using the ec.util.Code class. These methods are mostly used to write out populations to files for inspection, slight modification, then reading back in later on. readTree largely calls readRootedTree on the GPNode root. Likewise, printTree calls printRootedTree
• printTreeForHumans(...,PrintWriter)   This approach prints a GPTree in a fashion intended for human consumption only. printTreeForHumans calls either makeCTree and prints the result, calls makeLatexTree and prints the result, or calls printRootedTreeForHumans on the root. Which one is called depends on the kind of tree you have chosen to print for humans, as is discussed next.

GPTrees can print themselves for humans in one of three ways:

1. A GPTree can print the tree as a Koza-style Lisp s-expression, which is the default.
2. A GPTree can print itself in pseudo-C format:
1. Terminals can be printed either as variables "a" or as zero-argument functions "a()"
2. One-argument nonterminals are printed as functions "a(b)"
3. Two-argument nonterminals can be printed either as operators "b a c" or as functions "a(b, c)"
4. Nonterminals with more arguments are printed as functions "a(b, c, d, ...)"
3. A GPTree can print the tree as a LaTeX2e code snippet, which can be inserted into a LaTeX2e file and will result in a picture of the tree! Cool, no?

You turn the C-printing feature on with the c parameter, plus certain optional parameters (c-operators, c-variables) as described below. You turn the latex-printing latex parameter below. The C-printing parameter takes precedence.

Here's how the latex system works. To insert the code, you'll need to include the epic,ecltree, and probably the fancybox packages, in that order. You'll also need to define the command \gpbox, which takes one argument (the string name for the GPNode) and draws a box with that node. Lastly, you might want to set a few parameters dealing with the ecltree package.

Here's an example which looks quite good (pardon the double-backslashes in front of the usepackage statements -- javadoc is freaking out if I put a single backslash. So you'll need to remove the extra backslash in order to try out this example):

  \documentclass[]{article} \ \usepackage{epic} % required by ecltree and fancybox packages \ \usepackage{ecltree} % to draw the GP trees \ \usepackage{fancybox} % required by \Ovalbox \begin{document} % minimum distance between nodes on the same line \setlength{\GapWidth}{1em} % draw with a thick dashed line, very nice looking \thicklines \drawwith{\dottedline{2}} % draw an oval and center it with the rule. You may want to fool with the % rule values, though these seem to work quite well for me. If you make the % rule smaller than the text height, then the GP nodes may not line up with % each other horizontally quite right, so watch out. \newcommand{\gpbox}[1]{\Ovalbox{#1\rule[-.7ex]{0ex}{2.7ex}}} % Here's the tree which the GP system spat out \begin{bundle}{\gpbox{progn3}}\chunk{\begin{bundle}{\gpbox{if-food-ahead}} \chunk{\begin{bundle}{\gpbox{progn3}}\chunk{\gpbox{right}} \chunk{\gpbox{left}}\chunk{\gpbox{move}}\end{bundle}} \chunk{\begin{bundle}{\gpbox{if-food-ahead}}\chunk{\gpbox{move}} \chunk{\gpbox{left}}\end{bundle}}\end{bundle}}\chunk{\begin{bundle}{\gpbox{progn2}} \chunk{\begin{bundle}{\gpbox{progn2}}\chunk{\gpbox{move}} \chunk{\gpbox{move}}\end{bundle}}\chunk{\begin{bundle}{\gpbox{progn2}} \chunk{\gpbox{right}}\chunk{\gpbox{left}}\end{bundle}}\end{bundle}} \chunk{\begin{bundle}{\gpbox{if-food-ahead}}\chunk{\begin{bundle}{\gpbox{if-food-ahead}} \chunk{\gpbox{move}}\chunk{\gpbox{left}}\end{bundle}} \chunk{\begin{bundle}{\gpbox{if-food-ahead}}\chunk{\gpbox{left}}\chunk{\gpbox{right}} \end{bundle}}\end{bundle}}\end{bundle} \end{document} 

Parameters

 base.tc String (The tree's constraints) base.latex bool = true or false (default) (print for humans using latex?) base.c bool = true or false (default) (print for humans using c? Takes precedence over latex) base.c-operators bool = true (default) or false (when printing using c, print two-argument functions operators "b a c"? The alternative is functions "a(b, c)." base.c-variables bool = true (default) or false (when printing using c, print zero-argument functions as variables "a"? The alternative is functions "a()".)

Default Base
gp.tree

Version:
1.0
Author:
Sean Luke
Serialized Form

Field Summary
 GPNode child
the root GPNode in the GPTree
 byte constraints
constraints on the GPTree -- don't access the constraints through this variable -- use the constraints() method instead, which will give the actual constraints object.
static int NO_TREENUM

 GPIndividual owner
the owner of the GPTree
static java.lang.String P_TREE

static java.lang.String P_TREECONSTRAINTS

static java.lang.String P_USEC

static java.lang.String P_USELATEX

static java.lang.String P_USEOPS

static java.lang.String P_USEVARS

 boolean printTerminalsAsVariablesInC
When using c to print for humans, do we print terminals as variables? (as opposed to zero-argument functions)?
 boolean printTwoArgumentNonterminalsAsOperatorsInC
When using c to print for humans, do we print two-argument nonterminals in operator form "a op b"? (as opposed to functions "op(a, b)")?
 boolean useC
Use c to print for humans? Takes precedence over latex.
 boolean useLatex
Use latex to print for humans?

Constructor Summary
GPTree()

Method Summary
 void buildTree(EvolutionState state, int thread)
Builds a new randomly-generated rooted tree and attaches it to the GPTree.
 java.lang.Object clone()
Deep-clones the tree.
 GPTreeConstraints constraints(GPInitializer initializer)

 Parameter defaultBase()
Returns the default base for this prototype.
 GPTree lightClone()
Like clone() but doesn't copy the tree.
 void printTree(EvolutionState state, int log, int verbosity)
Prints out the tree in single-line fashion suitable for reading in later by computer.
 void printTree(EvolutionState state, java.io.PrintWriter writer)
Prints out the tree in single-line fashion suitable for reading in later by computer.
 void printTreeForHumans(EvolutionState state, int log, int verbosity)
Prints out the tree in a readable Lisp-like fashion.
 void readTree(EvolutionState state, java.io.DataInput dataInput)

 void readTree(EvolutionState state, java.io.LineNumberReader reader)
Reads in the tree from a form printed by printTree.
 void setup(EvolutionState state, Parameter base)
Sets up a prototypical GPTree with those features it shares with other GPTrees in its position in its GPIndividual, and nothhing more.
 boolean treeEquals(GPTree tree)
Returns true if I am "genetically" the same as tree, though we may have different owners.
 int treeHashCode()
Returns a hash code for comparing different GPTrees.
 int treeNumber()
An expensive function which determines my tree number -- only use for errors, etc.
 void writeTree(EvolutionState state, java.io.DataOutput dataOutput)

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

P_TREE

public static final java.lang.String P_TREE
Constant Field Values

P_TREECONSTRAINTS

public static final java.lang.String P_TREECONSTRAINTS
Constant Field Values

P_USELATEX

public static final java.lang.String P_USELATEX
Constant Field Values

P_USEC

public static final java.lang.String P_USEC
Constant Field Values

P_USEOPS

public static final java.lang.String P_USEOPS
Constant Field Values

P_USEVARS

public static final java.lang.String P_USEVARS
Constant Field Values

NO_TREENUM

public static final int NO_TREENUM
Constant Field Values

child

public GPNode child
the root GPNode in the GPTree

owner

public GPIndividual owner
the owner of the GPTree

constraints

public byte constraints
constraints on the GPTree -- don't access the constraints through this variable -- use the constraints() method instead, which will give the actual constraints object.

useLatex

public boolean useLatex
Use latex to print for humans?

useC

public boolean useC
Use c to print for humans? Takes precedence over latex.

printTerminalsAsVariablesInC

public boolean printTerminalsAsVariablesInC
When using c to print for humans, do we print terminals as variables? (as opposed to zero-argument functions)?

printTwoArgumentNonterminalsAsOperatorsInC

public boolean printTwoArgumentNonterminalsAsOperatorsInC
When using c to print for humans, do we print two-argument nonterminals in operator form "a op b"? (as opposed to functions "op(a, b)")?

Constructor Detail

GPTree

public GPTree()
Method Detail

constraints

public final GPTreeConstraints constraints(GPInitializer initializer)

defaultBase

public Parameter defaultBase()
Description copied from interface: Prototype
Returns the default base for this prototype. This should generally be implemented by building off of the static base() method on the DefaultsForm object for the prototype's package. This should be callable during setup(...).

Specified by:
defaultBase in interface Prototype

treeEquals

public boolean treeEquals(GPTree tree)
Returns true if I am "genetically" the same as tree, though we may have different owners.

treeHashCode

public int treeHashCode()
Returns a hash code for comparing different GPTrees. In general, two trees which are treeEquals(...) should have the same hash code.

lightClone

public GPTree lightClone()
Like clone() but doesn't copy the tree.

clone

public java.lang.Object clone()
Deep-clones the tree. Note that you should not deep-clone trees attached to the prototypical GPIndividual: they are blank trees with no root, and this method will generate a NullPointerException as a result.

Specified by:
clone in interface Prototype
Overrides:
clone in class java.lang.Object

treeNumber

public int treeNumber()
An expensive function which determines my tree number -- only use for errors, etc. Returns ec.gp.GPTree.NO_TREENUM if the tree number could not be determined (might happen if it's not been assigned yet).

setup

public void setup(EvolutionState state,
Parameter base)
Sets up a prototypical GPTree with those features it shares with other GPTrees in its position in its GPIndividual, and nothhing more. This must be called after the GPTypes and GPNodeConstraints have been set up. Presently they're set up in GPInitializer, which gets called before this does, so we're safe.

Specified by:
setup in interface Prototype
Specified by:
setup in interface Setup

printTree

public void printTree(EvolutionState state,
int log,
int verbosity)
Prints out the tree in single-line fashion suitable for reading in later by computer. O(n). The default version of this method simply calls child's printRootedTree(...) method.

printTree

public void printTree(EvolutionState state,
java.io.PrintWriter writer)
Prints out the tree in single-line fashion suitable for reading in later by computer. O(n). The default version of this method simply calls child's printRootedTree(...) method.

public void readTree(EvolutionState state,
throws java.io.IOException
Reads in the tree from a form printed by printTree.

Throws:
java.io.IOException

writeTree

public void writeTree(EvolutionState state,
java.io.DataOutput dataOutput)
throws java.io.IOException
Throws:
java.io.IOException

public void readTree(EvolutionState state,
java.io.DataInput dataInput)
throws java.io.IOException
Throws:
java.io.IOException

printTreeForHumans

public void printTreeForHumans(EvolutionState state,
int log,
int verbosity)
Prints out the tree in a readable Lisp-like fashion. O(n). The default version of this method simply calls child's printRootedTreeForHumans(...) method.

buildTree

public void buildTree(EvolutionState state,
int thread)
Builds a new randomly-generated rooted tree and attaches it to the GPTree.