src/org/gel/mauve/tree/TreeStore.java

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package org.gel.mauve.tree;

import java.io.Serializable;
import java.util.Arrays;

public class TreeStore implements Serializable {
        final static int NULL_REF = -1;

        private final static int INITIAL_SIZE = 10;

        private final static float SCALE_FACTOR = 1.1f;

        private int nodeCount = 0;

        public int [] parent = new int [INITIAL_SIZE];

        public int [] left = new int [INITIAL_SIZE];

        public int [] right = new int [INITIAL_SIZE];

        public long [] length = new long [INITIAL_SIZE];

        public long [] seqLength = new long [INITIAL_SIZE];

        public Key [] key = new Key [INITIAL_SIZE];

        public TreeStore () {
                Arrays.fill (parent, NULL_REF);
                Arrays.fill (left, NULL_REF);
                Arrays.fill (right, NULL_REF);
        }

        public int createGistNode () {
                if (nodeCount >= parent.length) {
                        resizeArrays ();
                }
                int val = nodeCount;
                nodeCount++;
                return val;
        }

        private void resizeArrays () {
                int newSize = (int) (parent.length * SCALE_FACTOR);

                int [] new_parent = new int [newSize];
                Arrays.fill (new_parent, TreeStore.NULL_REF);
                System.arraycopy (parent, 0, new_parent, 0, parent.length);
                parent = new_parent;

                int [] new_left = new int [newSize];
                Arrays.fill (new_left, TreeStore.NULL_REF);
                System.arraycopy (left, 0, new_left, 0, left.length);
                left = new_left;

                int [] new_right = new int [newSize];
                Arrays.fill (new_right, TreeStore.NULL_REF);
                System.arraycopy (right, 0, new_right, 0, right.length);
                right = new_right;

                long [] new_length = new long [newSize];
                System.arraycopy (length, 0, new_length, 0, length.length);
                length = new_length;

                long [] new_seq_length = new long [newSize];
                System.arraycopy (seqLength, 0, new_seq_length, 0, seqLength.length);
                seqLength = new_seq_length;

                Key [] new_key = new Key [newSize];
                System.arraycopy (key, 0, new_key, 0, key.length);
                key = new_key;
        }

        public void pruneArrays () {
                int [] new_parent = new int [nodeCount];
                System.arraycopy (parent, 0, new_parent, 0, nodeCount);
                parent = new_parent;

                int [] new_left = new int [nodeCount];
                System.arraycopy (left, 0, new_left, 0, nodeCount);
                left = new_left;

                int [] new_right = new int [nodeCount];
                System.arraycopy (right, 0, new_right, 0, nodeCount);
                right = new_right;

                long [] new_length = new long [nodeCount];
                System.arraycopy (length, 0, new_length, 0, nodeCount);
                length = new_length;

                long [] new_seq_length = new long [nodeCount];
                System.arraycopy (seqLength, 0, new_seq_length, 0, nodeCount);
                seqLength = new_seq_length;

                Key [] new_key = new Key [nodeCount];
                System.arraycopy (key, 0, new_key, 0, nodeCount);
                key = new_key;
        }
}

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