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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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@@ -28,7 +28,7 @@
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<archive>
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<manifest>
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<addClasspath>true</addClasspath>
31-
<mainClass>org.biojava3.aaproperties.CommandPrompt</mainClass>
31+
<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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@@ -12,8 +12,8 @@
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<!-- <useAllReactorProjects>true</useAllReactorProjects> -->
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<includes>
15-
<include>org.biojava:biojava3-core</include>
16-
<include>org.biojava:biojava3-structure</include>
15+
<include>org.biojava:biojava-core</include>
16+
<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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@@ -19,10 +19,10 @@
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*
2020
*/
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package demo;
22-
import org.biojava3.aaproperties.IPeptideProperties;
23-
import org.biojava3.aaproperties.PeptidePropertiesImpl;
24-
import org.biojava3.core.exceptions.CompoundNotFoundException;
25-
import org.biojava3.core.sequence.ProteinSequence;
22+
import org.biojava.nbio.aaproperties.IPeptideProperties;
23+
import org.biojava.nbio.aaproperties.PeptidePropertiesImpl;
24+
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
25+
import org.biojava.nbio.core.sequence.ProteinSequence;
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/**
2828
* 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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@@ -18,16 +18,16 @@
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* http://www.biojava.org/
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*
2020
*/
21-
package org.biojava3.aaproperties;
21+
package org.biojava.nbio.aaproperties;
2222

23-
import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
24-
import org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet;
25-
import org.biojava3.core.exceptions.CompoundNotFoundException;
26-
import org.biojava3.core.sequence.ProteinSequence;
27-
import org.biojava3.core.sequence.compound.AminoAcidCompound;
28-
import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
29-
import org.biojava3.core.sequence.io.*;
30-
import org.biojava3.core.sequence.template.CompoundSet;
23+
import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
24+
import org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet;
25+
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
26+
import org.biojava.nbio.core.sequence.ProteinSequence;
27+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
28+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
29+
import org.biojava.nbio.core.sequence.io.*;
30+
import org.biojava.nbio.core.sequence.template.CompoundSet;
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import java.io.File;
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import java.io.FileInputStream;
@@ -39,6 +39,7 @@
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import java.util.Map;
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import java.util.Map.Entry;
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42+
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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;
21+
package org.biojava.nbio.aaproperties;
2222

23-
import org.biojava3.aaproperties.PeptideProperties.SingleLetterAACode;
24-
import org.biojava3.core.sequence.compound.AminoAcidCompound;
25-
import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
23+
import org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode;
24+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
25+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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import java.util.HashMap;
2828
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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*
2222
*/
23-
package org.biojava3.aaproperties;
23+
package org.biojava.nbio.aaproperties;
2424

25-
import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
26-
import org.biojava3.core.sequence.ProteinSequence;
27-
import org.biojava3.core.sequence.compound.AminoAcidCompound;
25+
import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
26+
import org.biojava.nbio.core.sequence.ProteinSequence;
27+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import javax.xml.bind.JAXBException;
3030
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;
21+
package org.biojava.nbio.aaproperties;
2222

23-
import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
24-
import org.biojava3.core.exceptions.CompoundNotFoundException;
25-
import org.biojava3.core.sequence.ProteinSequence;
26-
import org.biojava3.core.sequence.compound.AminoAcidCompound;
27-
import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
23+
import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
24+
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
25+
import org.biojava.nbio.core.sequence.ProteinSequence;
26+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
27+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
2828
import org.slf4j.Logger;
2929
import org.slf4j.LoggerFactory;
3030

‎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;
21+
package org.biojava.nbio.aaproperties;
2222

23-
import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
24-
import org.biojava3.aaproperties.xml.ElementTable;
25-
import org.biojava3.aaproperties.xml.MyValidationEventHandler;
26-
import org.biojava3.core.sequence.ProteinSequence;
27-
import org.biojava3.core.sequence.compound.AminoAcidCompound;
28-
import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
23+
import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
24+
import org.biojava.nbio.aaproperties.xml.ElementTable;
25+
import org.biojava.nbio.aaproperties.xml.MyValidationEventHandler;
26+
import org.biojava.nbio.core.sequence.ProteinSequence;
27+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
28+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
2929
import org.slf4j.Logger;
3030
import org.slf4j.LoggerFactory;
3131

‎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
*/
21-
package org.biojava3.aaproperties;
21+
package org.biojava.nbio.aaproperties;
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import org.slf4j.Logger;
2424
import org.slf4j.LoggerFactory;
@@ -172,7 +172,7 @@ public static final String checkSequence(String sequence, Set<Character> cSet){
172172
if(containInvalid){
173173
String cSeq = cleanSequence(sequence, cSet);
174174
logger.warn("There exists invalid characters in the sequence. Computed results might not be precise.");
175-
logger.warn("To remove this warning: Please use org.biojava3.aaproperties.Utils.cleanSequence to clean sequence.");
175+
logger.warn("To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence.");
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177177
return cSeq;
178178
}

‎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
2727
* @since 3.0.2
2828
*/
29-
package org.biojava3.aaproperties;
29+
package org.biojava.nbio.aaproperties;
3030

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

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* http://www.biojava.org/
1919
*
2020
*/
21-
package org.biojava3.aaproperties.profeat;
21+
package org.biojava.nbio.aaproperties.profeat;
2222

23-
import org.biojava3.core.sequence.ProteinSequence;
23+
import org.biojava.nbio.core.sequence.ProteinSequence;
2424

2525
import java.util.Map;
2626

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

+6-6
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* http://www.biojava.org/
1919
*
2020
*/
21-
package org.biojava3.aaproperties.profeat;
21+
package org.biojava.nbio.aaproperties.profeat;
2222

23-
import org.biojava3.aaproperties.profeat.IProfeatProperties.ATTRIBUTE;
24-
import org.biojava3.aaproperties.profeat.IProfeatProperties.DISTRIBUTION;
25-
import org.biojava3.aaproperties.profeat.IProfeatProperties.GROUPING;
26-
import org.biojava3.aaproperties.profeat.IProfeatProperties.TRANSITION;
27-
import org.biojava3.core.sequence.ProteinSequence;
23+
import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE;
24+
import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION;
25+
import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING;
26+
import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION;
27+
import org.biojava.nbio.core.sequence.ProteinSequence;
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import java.util.Map;
3030

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

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* http://www.biojava.org/
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*
2020
*/
21-
package org.biojava3.aaproperties.profeat;
21+
package org.biojava.nbio.aaproperties.profeat;
2222

23-
import org.biojava3.aaproperties.profeat.convertor.*;
24-
import org.biojava3.core.sequence.ProteinSequence;
23+
import org.biojava.nbio.aaproperties.profeat.convertor.*;
24+
import org.biojava.nbio.core.sequence.ProteinSequence;
2525

2626
import java.util.HashMap;
2727
import java.util.Map;

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2Charge.java renamed to ‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Charge.java

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* http://www.biojava.org/
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*
2020
*/
21-
package org.biojava3.aaproperties.profeat.convertor;
21+
package org.biojava.nbio.aaproperties.profeat.convertor;
2222

2323
public class Convert2Charge extends Convertor{
2424
/**

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2Hydrophobicity.java renamed to ‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Hydrophobicity.java

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* http://www.biojava.org/
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*
2020
*/
21-
package org.biojava3.aaproperties.profeat.convertor;
21+
package org.biojava.nbio.aaproperties.profeat.convertor;
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2323
public class Convert2Hydrophobicity extends Convertor {
2424
/**

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2NormalizedVanDerWaalsVolume.java renamed to ‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2NormalizedVanDerWaalsVolume.java

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* http://www.biojava.org/
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*
2020
*/
21-
package org.biojava3.aaproperties.profeat.convertor;
21+
package org.biojava.nbio.aaproperties.profeat.convertor;
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2323
public class Convert2NormalizedVanDerWaalsVolume extends Convertor{
2424
/**

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2Polarity.java renamed to ‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarity.java

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* http://www.biojava.org/
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*
2020
*/
21-
package org.biojava3.aaproperties.profeat.convertor;
21+
package org.biojava.nbio.aaproperties.profeat.convertor;
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2323
public class Convert2Polarity extends Convertor{
2424
/**

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2Polarizability.java renamed to ‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarizability.java

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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties.profeat.convertor;
21+
package org.biojava.nbio.aaproperties.profeat.convertor;
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2323
public class Convert2Polarizability extends Convertor{
2424
/**

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2SecondaryStructure.java renamed to ‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SecondaryStructure.java

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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties.profeat.convertor;
21+
package org.biojava.nbio.aaproperties.profeat.convertor;
2222

2323
public class Convert2SecondaryStructure extends Convertor{
2424
/**

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2SolventAccessibility.java renamed to ‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SolventAccessibility.java

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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties.profeat.convertor;
21+
package org.biojava.nbio.aaproperties.profeat.convertor;
2222

2323
public class Convert2SolventAccessibility extends Convertor{
2424
/**

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convertor.java renamed to ‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java

+2-2
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* http://www.biojava.org/
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*
2020
*/
21-
package org.biojava3.aaproperties.profeat.convertor;
21+
package org.biojava.nbio.aaproperties.profeat.convertor;
2222

23-
import org.biojava3.core.sequence.ProteinSequence;
23+
import org.biojava.nbio.core.sequence.ProteinSequence;
2424

2525
public abstract class Convertor {
2626
/**

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

+1-1
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3434
* @version 2011.08.22
3535
* @since 3.0.2
3636
*/
37-
package org.biojava3.aaproperties.profeat.convertor;
37+
package org.biojava.nbio.aaproperties.profeat.convertor;
3838

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

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* @version 2011.08.22
2929
* @since 3.0.2
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*/
31-
package org.biojava3.aaproperties.profeat;
31+
package org.biojava.nbio.aaproperties.profeat;
3232

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

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* http://www.biojava.org/
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*
2020
*/
21-
package org.biojava3.aaproperties.xml;
21+
package org.biojava.nbio.aaproperties.xml;
2222

2323
import javax.xml.bind.annotation.*;
2424
import java.util.List;

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

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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties.xml;
21+
package org.biojava.nbio.aaproperties.xml;
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2323
import javax.xml.bind.annotation.XmlAccessType;
2424
import javax.xml.bind.annotation.XmlAccessorType;

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

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*
2020
* Created on 01-21-2010
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*/
22-
package org.biojava3.aaproperties.xml;
22+
package org.biojava.nbio.aaproperties.xml;
2323

24-
import org.biojava3.core.sequence.compound.AminoAcidCompound;
25-
import org.biojava3.core.sequence.template.CompoundSet;
26-
import org.biojava3.core.sequence.template.Sequence;
24+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
25+
import org.biojava.nbio.core.sequence.template.CompoundSet;
26+
import org.biojava.nbio.core.sequence.template.Sequence;
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import java.util.*;
2929

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

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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties.xml;
21+
package org.biojava.nbio.aaproperties.xml;
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2323
import javax.xml.bind.annotation.XmlAccessType;
2424
import javax.xml.bind.annotation.XmlAccessorType;

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

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* http://www.biojava.org/
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*
2020
*/
21-
package org.biojava3.aaproperties.xml;
21+
package org.biojava.nbio.aaproperties.xml;
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import javax.xml.bind.annotation.XmlRootElement;
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import java.util.HashMap;

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

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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties.xml;
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package org.biojava.nbio.aaproperties.xml;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;

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

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@@ -18,11 +18,11 @@
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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties.xml;
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package org.biojava.nbio.aaproperties.xml;
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import org.biojava3.core.sequence.compound.AminoAcidCompound;
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import org.biojava3.core.sequence.template.CompoundSet;
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import org.biojava3.core.sequence.template.Sequence;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.template.CompoundSet;
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import org.biojava.nbio.core.sequence.template.Sequence;
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import java.util.*;
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‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/xml/MyValidationEventHandler.java renamed to ‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java

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@@ -18,7 +18,7 @@
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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties.xml;
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package org.biojava.nbio.aaproperties.xml;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/xml/Name2Count.java renamed to ‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java

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@@ -18,7 +18,7 @@
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* http://www.biojava.org/
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*
2020
*/
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package org.biojava3.aaproperties.xml;
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package org.biojava.nbio.aaproperties.xml;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;

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