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Merge pull request #1076 from hilbertglm/20231229-jaxb
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Updated to Jakarta JAXB and Java 17 (ref: #1075)
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@josemduarte
josemduarte committed Jan 5, 2024
2 parents 393a98a + f0320f5 commit 05c229c
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Showing 33 changed files with 88 additions and 98 deletions.
4 changes: 2 additions & 2 deletions biojava-aa-prop/pom.xml
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</dependency>

<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
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2 changes: 1 addition & 1 deletion biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
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import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;

import javax.xml.bind.JAXBException;
import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Map;
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3 changes: 1 addition & 2 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
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Expand Up @@ -28,7 +28,7 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.JAXBException;
import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Arrays;
Expand All @@ -37,7 +37,6 @@
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream;

/**
* This is an adaptor class which enable the ease of generating protein properties.
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6 changes: 3 additions & 3 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java
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import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
import jakarta.xml.bind.JAXBContext;
import jakarta.xml.bind.JAXBException;
import jakarta.xml.bind.Unmarshaller;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
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2 changes: 1 addition & 1 deletion biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java
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*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.annotation.*;
import jakarta.xml.bind.annotation.*;
import java.util.List;

@XmlRootElement(name = "compoundcomposition", namespace ="http://biojava.org")
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8 changes: 4 additions & 4 deletions ...va-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java
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*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlElement;
import jakarta.xml.bind.annotation.XmlRootElement;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
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8 changes: 4 additions & 4 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java
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Expand Up @@ -20,10 +20,10 @@
*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlAttribute;
import jakarta.xml.bind.annotation.XmlElement;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
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2 changes: 1 addition & 1 deletion biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java
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Expand Up @@ -20,7 +20,7 @@
*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.XmlRootElement;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
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8 changes: 4 additions & 4 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java
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*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlAttribute;
import jakarta.xml.bind.annotation.XmlType;


@XmlType(name = "Iostope", propOrder = {"name","neutronsNum","mass"})
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6 changes: 3 additions & 3 deletions ...ava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java
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Expand Up @@ -23,9 +23,9 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.ValidationEvent;
import javax.xml.bind.ValidationEventHandler;
import javax.xml.bind.ValidationEventLocator;
import jakarta.xml.bind.ValidationEvent;
import jakarta.xml.bind.ValidationEventHandler;
import jakarta.xml.bind.ValidationEventLocator;

public class MyValidationEventHandler implements ValidationEventHandler{

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6 changes: 3 additions & 3 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java
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Expand Up @@ -20,9 +20,9 @@
*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlAttribute;

@XmlAccessorType(XmlAccessType.FIELD)
public class Name2Count{
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2 changes: 1 addition & 1 deletion biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java
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Expand Up @@ -20,7 +20,7 @@
*/
package org.biojava.nbio.aaproperties.xml;

import javax.xml.bind.SchemaOutputResolver;
import jakarta.xml.bind.SchemaOutputResolver;
import javax.xml.transform.Result;
import javax.xml.transform.stream.StreamResult;
import java.io.File;
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3 changes: 1 addition & 2 deletions biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java
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Expand Up @@ -20,13 +20,12 @@
*/
package org.biojava.nbio.aaproperties;

import org.biojava.nbio.aaproperties.PeptideProperties;
import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.JAXBException;
import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Map;
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4 changes: 1 addition & 3 deletions biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
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Expand Up @@ -20,14 +20,12 @@
*/
package org.biojava.nbio.aaproperties;

import org.biojava.nbio.aaproperties.PeptideProperties;
import org.biojava.nbio.aaproperties.Utils;
import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.JAXBException;
import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Map;
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8 changes: 4 additions & 4 deletions biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java
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Expand Up @@ -23,10 +23,10 @@
import org.biojava.nbio.aaproperties.PeptideProperties;
import org.junit.Test;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import jakarta.xml.bind.JAXBContext;
import jakarta.xml.bind.JAXBException;
import jakarta.xml.bind.Marshaller;
import jakarta.xml.bind.Unmarshaller;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
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12 changes: 4 additions & 8 deletions biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java
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Expand Up @@ -20,18 +20,14 @@
*/
package org.biojava.nbio.aaproperties.xml;

import org.biojava.nbio.aaproperties.xml.Element;
import org.biojava.nbio.aaproperties.xml.ElementTable;
import org.biojava.nbio.aaproperties.xml.Isotope;
import org.biojava.nbio.aaproperties.xml.SchemaGenerator;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import jakarta.xml.bind.JAXBContext;
import jakarta.xml.bind.JAXBException;
import jakarta.xml.bind.Marshaller;
import jakarta.xml.bind.Unmarshaller;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
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4 changes: 2 additions & 2 deletions biojava-core/pom.xml
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Expand Up @@ -74,8 +74,8 @@
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
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4 changes: 2 additions & 2 deletions biojava-modfinder/pom.xml
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Expand Up @@ -54,8 +54,8 @@
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
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4 changes: 2 additions & 2 deletions biojava-protein-disorder/pom.xml
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Expand Up @@ -85,8 +85,8 @@
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
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4 changes: 2 additions & 2 deletions biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/FastaSequence.java
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Expand Up @@ -24,8 +24,8 @@

package org.biojava.nbio.data.sequence;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

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6 changes: 2 additions & 4 deletions biojava-structure/pom.xml
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Expand Up @@ -67,11 +67,9 @@
<version>1.4.0</version>
</dependency>

<!-- JAXb explicit dependency is needed since Java 9. See https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j
Note versions are set in parent pom in dependency management section -->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
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6 changes: 3 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java
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Expand Up @@ -23,9 +23,9 @@
*/
package org.biojava.nbio.structure.domain.pdp;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlRootElement;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
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6 changes: 3 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDescription.java
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*/
package org.biojava.nbio.structure.scop;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlRootElement;
import java.io.Serializable;

/** Contains data from
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6 changes: 3 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
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Expand Up @@ -26,9 +26,9 @@
import java.util.List;
import java.util.Set;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlRootElement;

import org.biojava.nbio.structure.PdbId;
import org.biojava.nbio.structure.ResidueRange;
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6 changes: 3 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopNode.java
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Expand Up @@ -24,9 +24,9 @@

package org.biojava.nbio.structure.scop;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlRootElement;
import java.io.Serializable;
import java.util.List;

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14 changes: 7 additions & 7 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
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import javax.vecmath.Matrix3d;
import javax.vecmath.Matrix4d;
import javax.vecmath.Vector3d;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import jakarta.xml.bind.JAXBContext;
import jakarta.xml.bind.JAXBException;
import jakarta.xml.bind.Marshaller;
import jakarta.xml.bind.annotation.XmlAccessType;
import jakarta.xml.bind.annotation.XmlAccessorType;
import jakarta.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.adapters.XmlJavaTypeAdapter;

import java.io.ByteArrayOutputStream;
import java.io.PrintStream;
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
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Expand Up @@ -24,7 +24,7 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.bind.JAXBException;
import jakarta.xml.bind.JAXBException;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java
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Expand Up @@ -25,7 +25,7 @@

import org.biojava.nbio.structure.xtal.SpaceGroup;

import javax.xml.bind.annotation.adapters.XmlAdapter;
import jakarta.xml.bind.annotation.adapters.XmlAdapter;
import java.util.Map;
import java.util.TreeMap;

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2 changes: 1 addition & 1 deletion ...ava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapElements.java
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Expand Up @@ -25,7 +25,7 @@

import org.biojava.nbio.structure.xtal.SpaceGroup;

import javax.xml.bind.annotation.XmlElement;
import jakarta.xml.bind.annotation.XmlElement;

public class SpaceGroupMapElements {

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12 changes: 6 additions & 6 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java
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Expand Up @@ -25,12 +25,12 @@

import org.biojava.nbio.structure.xtal.SpaceGroup;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import jakarta.xml.bind.JAXBContext;
import jakarta.xml.bind.JAXBException;
import jakarta.xml.bind.Marshaller;
import jakarta.xml.bind.Unmarshaller;
import jakarta.xml.bind.annotation.XmlRootElement;
import jakarta.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.PrintStream;
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