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Refactoring of all package names according to biojava#245 biojava#242 biojava#240 
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‎biojava-aa-prop/pom.xml‎

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<archive>
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<manifest>
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<addClasspath>true</addClasspath>
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<mainClass>org.biojava3.aaproperties.CommandPrompt</mainClass>
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<mainClass>org.biojava.nbio.aaproperties.CommandPrompt</mainClass>
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</manifest>
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</archive>
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<descriptorRefs>

‎biojava-aa-prop/src/main/assembly/assembly.xml‎

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<!-- <useAllReactorProjects>true</useAllReactorProjects> -->
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<includes>
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<include>org.biojava:biojava3-core</include>
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<include>org.biojava:biojava3-structure</include>
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<include>org.biojava:biojava-core</include>
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<include>org.biojava:biojava-structure</include>
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</includes>
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<binaries>

‎biojava-aa-prop/src/main/java/demo/BioJavaAADemo.java‎

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*
2020
*/
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package demo;
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import org.biojava3.aaproperties.IPeptideProperties;
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import org.biojava3.aaproperties.PeptidePropertiesImpl;
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import org.biojava3.core.exceptions.CompoundNotFoundException;
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import org.biojava3.core.sequence.ProteinSequence;
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import org.biojava.nbio.aaproperties.IPeptideProperties;
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import org.biojava.nbio.aaproperties.PeptidePropertiesImpl;
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import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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/**
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* Created by andreas on 8/9/14.

biojava-aa-prop/src/main/java/org/biojava3/aaproperties/CommandPrompt.java renamed to biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java

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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties;
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package org.biojava.nbio.aaproperties;
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import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
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import org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet;
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import org.biojava3.core.exceptions.CompoundNotFoundException;
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import org.biojava3.core.sequence.ProteinSequence;
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import org.biojava3.core.sequence.compound.AminoAcidCompound;
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import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
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import org.biojava3.core.sequence.io.*;
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import org.biojava3.core.sequence.template.CompoundSet;
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import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
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import org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet;
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import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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import org.biojava.nbio.core.sequence.io.*;
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import org.biojava.nbio.core.sequence.template.CompoundSet;
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import java.io.File;
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import java.io.FileInputStream;
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import java.util.Map;
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import java.util.Map.Entry;
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public class CommandPrompt {
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/**

biojava-aa-prop/src/main/java/org/biojava3/aaproperties/Constraints.java renamed to biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java

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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties;
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package org.biojava.nbio.aaproperties;
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import org.biojava3.aaproperties.PeptideProperties.SingleLetterAACode;
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import org.biojava3.core.sequence.compound.AminoAcidCompound;
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import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
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import org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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import java.util.HashMap;
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import java.util.Map;

biojava-aa-prop/src/main/java/org/biojava3/aaproperties/IPeptideProperties.java renamed to biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java

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2020
* Created on 2011.05.09 by kohchuanhock
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*
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*/
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package org.biojava3.aaproperties;
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package org.biojava.nbio.aaproperties;
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import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
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import org.biojava3.core.sequence.ProteinSequence;
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import org.biojava3.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import javax.xml.bind.JAXBException;
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import java.io.File;

biojava-aa-prop/src/main/java/org/biojava3/aaproperties/PeptideProperties.java renamed to biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java

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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties;
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package org.biojava.nbio.aaproperties;
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import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
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import org.biojava3.core.exceptions.CompoundNotFoundException;
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import org.biojava3.core.sequence.ProteinSequence;
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import org.biojava3.core.sequence.compound.AminoAcidCompound;
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import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
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import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
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import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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biojava-aa-prop/src/main/java/org/biojava3/aaproperties/PeptidePropertiesImpl.java renamed to biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java

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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties;
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package org.biojava.nbio.aaproperties;
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import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
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import org.biojava3.aaproperties.xml.ElementTable;
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import org.biojava3.aaproperties.xml.MyValidationEventHandler;
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import org.biojava3.core.sequence.ProteinSequence;
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import org.biojava3.core.sequence.compound.AminoAcidCompound;
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import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
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import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
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import org.biojava.nbio.aaproperties.xml.ElementTable;
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import org.biojava.nbio.aaproperties.xml.MyValidationEventHandler;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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biojava-aa-prop/src/main/java/org/biojava3/aaproperties/Utils.java renamed to biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java

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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties;
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package org.biojava.nbio.aaproperties;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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if(containInvalid){
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String cSeq = cleanSequence(sequence, cSet);
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logger.warn("There exists invalid characters in the sequence. Computed results might not be precise.");
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logger.warn("To remove this warning: Please use org.biojava3.aaproperties.Utils.cleanSequence to clean sequence.");
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logger.warn("To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence.");
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return cSeq;
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}

biojava-aa-prop/src/main/java/org/biojava3/aaproperties/package-info.java renamed to biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/package-info.java

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* @version 2011.08.22
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* @since 3.0.2
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*/
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package org.biojava3.aaproperties;
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package org.biojava.nbio.aaproperties;
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