Documentation of 'ec.gp.GPTree' Java class
GPTree
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ec.gp

Class GPTree

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

    public class GPTree
extends java.lang.Object
implements 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 four styles:

    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 AT&T's Graphviz format. You can snip the code out and save it as a ".dot" file to render in any Graphviz renderer (for example, use this MacOS X front end to the renderer).
    4. 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.print-style
    String, one of: c, dot, latex, lisp    		 (specifies the print style of the tree)
    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

    See Also:
    Serialized Form

    • Field Detail

      • P_TREECONSTRAINTS

        public static final java.lang.String P_TREECONSTRAINTS
        See Also:
        Constant Field Values

      • child

        public GPNode child
        the root GPNode in 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.

      • printStyle

        public int printStyle
        The print style of the GPTree.

      • 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

      • 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

      • verify

        public final void verify(EvolutionState state)
        Verification of validity of the tree -- strictly for debugging purposes only

      • printTree

        public void printTree(EvolutionState state,
                      int log)
        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,
                      int log,
                      int verbosity)
        Deprecated. Verbosity no longer has an effect
        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.

      • readTree

        public void readTree(EvolutionState state,
                     java.io.LineNumberReader reader)
              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

      • readTree

        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)
        Prints out the tree in a readable Lisp-like fashion. O(n). The default version of this method simply calls child's printRootedTreeForHumans(...) method.

      • printTreeForHumans

        public void printTreeForHumans(EvolutionState state,
                               int log,
                               int verbosity)
        Deprecated. Verbosity no longer has an effect.
        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.
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