// Path: biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.java
// public class AminoAcidCompound extends AbstractCompound implements Serializable {
// 
// 	/**
// 	 *
// 	 */
// private static final long serialVersionUID = -1955116496725902319L;
// private final AminoAcidCompoundSet compoundSet;
// 
// 
// 	public AminoAcidCompound(AminoAcidCompoundSet compoundSet, String shortName,
// 			String longName, String description, Float molecularWeight) {
// 		super(shortName);
// 		setShortName(shortName);
// 		setLongName(longName);
// 		setDescription(description);
// 		setMolecularWeight(molecularWeight);
// 		this.compoundSet = compoundSet;
// 	}
// 
// 	// TODO need to allow for modified name; that's not equality though is it?
// 	@Override
// public boolean equals(Object obj) {
// 		if (obj == null) {
// 			return false;
// 		}
// 		if (!(obj instanceof AminoAcidCompound)) {
// 			return false;
// 		}
// 		AminoAcidCompound them = (AminoAcidCompound) obj;
// 		if (toString().equals(them.toString())) {
// 			return true;
// 		}
// 		return getLongName().equals(them.getLongName());
// 
// 	}
// 
// 	@Override
// public int hashCode() {
// 		return toString().hashCode();
// 	}
// 
// 	@Override
// public boolean equalsIgnoreCase(Compound compound) {
// 		if (compound == null) {
// 			return false;
// 		}
// 		if (!(compound instanceof AminoAcidCompound)) {
// 			return false;
// 		}
// 		AminoAcidCompound them = (AminoAcidCompound) compound;
// 		if (toString().equalsIgnoreCase(them.toString())) {
// 			return true;
// 		}
// 		return getLongName().equalsIgnoreCase(them.getLongName());
// 	}
// 
// 	public CompoundSet<AminoAcidCompound> getCompoundSet() {
// 		return compoundSet;
// 	}
// }


import org.biojava.nbio.core.sequence.location.SimpleLocation;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import java.util.Arrays;
import static org.junit.Assert.*;
import org.biojava.nbio.core.alignment.template.AlignedSequence;
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.Strand;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on June 15, 2010
 * Author: Mark Chapman
 */

package org.biojava.nbio.core.alignment;




public class SimpleAlignedSequenceTest {

	private ProteinSequence go, lo;
// Path: biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.java
// public class AminoAcidCompound extends AbstractCompound implements Serializable {
// 
// 	/**
// 	 *
// 	 */
// private static final long serialVersionUID = -1955116496725902319L;
// private final AminoAcidCompoundSet compoundSet;
// 
// 
// 	public AminoAcidCompound(AminoAcidCompoundSet compoundSet, String shortName,
// 			String longName, String description, Float molecularWeight) {
// 		super(shortName);
// 		setShortName(shortName);
// 		setLongName(longName);
// 		setDescription(description);
// 		setMolecularWeight(molecularWeight);
// 		this.compoundSet = compoundSet;
// 	}
// 
// 	// TODO need to allow for modified name; that's not equality though is it?
// 	@Override
// public boolean equals(Object obj) {
// 		if (obj == null) {
// 			return false;
// 		}
// 		if (!(obj instanceof AminoAcidCompound)) {
// 			return false;
// 		}
// 		AminoAcidCompound them = (AminoAcidCompound) obj;
// 		if (toString().equals(them.toString())) {
// 			return true;
// 		}
// 		return getLongName().equals(them.getLongName());
// 
// 	}
// 
// 	@Override
// public int hashCode() {
// 		return toString().hashCode();
// 	}
// 
// 	@Override
// public boolean equalsIgnoreCase(Compound compound) {
// 		if (compound == null) {
// 			return false;
// 		}
// 		if (!(compound instanceof AminoAcidCompound)) {
// 			return false;
// 		}
// 		AminoAcidCompound them = (AminoAcidCompound) compound;
// 		if (toString().equalsIgnoreCase(them.toString())) {
// 			return true;
// 		}
// 		return getLongName().equalsIgnoreCase(them.getLongName());
// 	}
// 
// 	public CompoundSet<AminoAcidCompound> getCompoundSet() {
// 		return compoundSet;
// 	}
// }


// Path: biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java
import org.biojava.nbio.core.sequence.location.SimpleLocation;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import java.util.Arrays;
import static org.junit.Assert.*;
import org.biojava.nbio.core.alignment.template.AlignedSequence;
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.Strand;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;

/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on June 15, 2010
 * Author: Mark Chapman
 */

package org.biojava.nbio.core.alignment;




public class SimpleAlignedSequenceTest {

	private ProteinSequence go, lo;
	private AlignedSequence<ProteinSequence, AminoAcidCompound> global, local, local2;