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TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
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/*
 *  GenericArrayPositions
 * 
 *  Created on Oct 31, 2016
 */

package net.maizegenetics.analysis.avro;

import java.util.Collection;
import java.util.Iterator;
import java.util.List;
import java.util.ListIterator;
import net.maizegenetics.dna.map.PositionList;
import org.apache.avro.Schema;
import org.apache.avro.generic.GenericArray;
import org.apache.avro.generic.GenericRecord;

/**
 *
 * @author Terry Casstevens
 */
public class GenericArrayPositions implements GenericArray {
    
    private final PositionList myPositions;
    private final int myNumSites;
    
    public GenericArrayPositions(PositionList positions) {
        myPositions = positions;
        myNumSites = myPositions.numberOfSites();
    }
    
    @Override
    public GenericRecord peek() {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public void reverse() {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public int size() {
        return myNumSites;
    }
    
    @Override
    public boolean isEmpty() {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public boolean contains(Object o) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public Iterator iterator() {
        
        return new Iterator() {
            
            private int myIndex = 0;
            
            @Override
            public boolean hasNext() {
                return myIndex < myNumSites;
            }
            
            @Override
            public GenericRecord next() {
                return new GenericRecordPosition(myPositions.get(myIndex++));
            }
        };
        
    }
    
    @Override
    public Object[] toArray() {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public  T[] toArray(T[] a) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public boolean add(GenericRecord e) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public boolean remove(Object o) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public boolean containsAll(Collection c) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public boolean addAll(Collection c) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public boolean addAll(int index, Collection c) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public boolean removeAll(Collection c) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public boolean retainAll(Collection c) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public void clear() {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public GenericRecord get(int index) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public GenericRecord set(int index, GenericRecord element) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public void add(int index, GenericRecord element) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public GenericRecord remove(int index) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public int indexOf(Object o) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public int lastIndexOf(Object o) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public ListIterator listIterator() {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public ListIterator listIterator(int index) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public List subList(int fromIndex, int toIndex) {
        throw new UnsupportedOperationException("Not supported yet.");
    }
    
    @Override
    public Schema getSchema() {
        return AvroConstants.POSITIONS_SCHEMA;
    }
    
}