source: branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/Node.java @ 1612

// Node.java
//
// (c) 1999-2001 PAL Development Core Team
//
// This package may be distributed under the
// terms of the Lesser GNU General Public License (LGPL)


package de.ugoe.cs.autoquest.tasktrees.alignment.pal.tree;


import java.util.ArrayList;

import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.Identifier;



/**
 * interface for a node (includes branch) in a binary/non-binary
 * rooted/unrooted tree
 *
 * @version $Id: Node.java,v 1.20 2001/11/20 07:35:44 matt Exp $
 *
 * @author Alexei Drummond
 * @author Korbinian Strimmer
 *
 */

public interface Node {

        /** Returns the parent node of this node. */
        Node getParent();

        /** Set the parent node of this node. */
        void setParent(Node node);

        /** Returns the sequence at this node */
        NumberSequence getSequence(int index);

        /** Sets the sequence using an array of bytes. */
        void setSequence(int index,NumberSequence seq);

        /** return the index of this node */
        int getNumber();

        /** set the index of this node */
        void setNumber(int number);

        /** Get the length of the branch attaching this node to its parent. */
        double getBranchLength();

        /** Set the length of the branch attaching this node to its parent. */
        void setBranchLength(double value);

        /** Get the length SE of the branch attaching this node to its parent. */
        double getBranchLengthSE();

        /** Set the length SE of the branch attaching this node to its parent. */
        void setBranchLengthSE(double value);

        /** Get the height of this node relative to the most recent node. */
        double getNodeHeight();

        /** Set the height of this node relative to the most recent node. */
        void setNodeHeight(double value);

        /** Returns the identifier for this node. */
        Identifier getIdentifier();

        /** Set identifier for this node. */
        Identifier setIdentifier(Identifier id);

        /**
         * Returns the number of children this node has.
         */
        int getChildCount();

        /**
         * check whether this node is an external node
         *
         * @return result (true or false)
         */
        boolean isLeaf();

        /**
         * check whether this node is a root node
         *
         * @return result (true or false)
         */
        boolean isRoot();

        /**
         * get child node
         *
         * @param n number of child
         *
         * @return child node
         */
        Node getChild(int n);

        /**
         * set child node
         *
         * @param n number
         * @node node new child node
         */
        void setChild(int n, Node node);

        /**
         * add new child node
         *
         * @param c new child node
         */
        void addChild(Node c);

        /**
         * add new child node (insertion at a specific position)
         *
         * @param c new child node
         + @param pos position
         */
        void insertChild(Node c, int pos);


        /**
         * remove child
         *
         * @param n number of child to be removed
         */
        Node removeChild(int n);

        
        ArrayList<NumberSequence> getSequences();
        
        Node joinChildren( int n1, int n2);

        void addSequence(NumberSequence numberSequence);

        void setSequences(ArrayList<NumberSequence> alignSequences);





        
}