<commit_before>package am.application.mappingEngine;

import am.application.ontology.*;

import java.util.ArrayList;


public class AlignmentSet
{
    private ArrayList<Alignment> collection = null;

    public AlignmentSet()
    {
        collection = new ArrayList<Alignment>();
    }

    public void addAlignment(Alignment alignment)
    {
        collection.add(alignment);
    }
    
    public void addAll(AlignmentSet a)
    {
    	if(a != null) {
    		for(int i= 0; i<a.size();i++) {
    			Alignment alignment = a.getAlignment(i);
    			collection.add(alignment);
    		}
    	}
        
    }<commit_msg>AlignmentSet should now be able to handle null values in the AlignmentMatrix<commit_after>package am.application.mappingEngine;

import am.application.ontology.*;

import java.util.ArrayList;


public class AlignmentSet
{
    private ArrayList<Alignment> collection = null;

    public AlignmentSet()
    {
        collection = new ArrayList<Alignment>();
    }

    public void addAlignment(Alignment alignment)
    {
        if( alignment != null ) collection.add(alignment);
    }
    
    public void addAll(AlignmentSet a)
    {
    	if(a != null) {
    		for(int i= 0; i<a.size();i++) {
    			Alignment alignment = a.getAlignment(i);
    			collection.add(alignment);
    		}
    	}
        
    }
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