diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 70ab1fa759..908f2d28c2 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -105,8 +105,8 @@ - javax.xml.bind - jaxb-api + jakarta.xml.bind + jakarta.xml.bind-api org.glassfish.jaxb diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java index 5499509820..e90e7bd568 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java @@ -26,7 +26,7 @@ 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; diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java index edf76339d9..da0cef9997 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java @@ -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; @@ -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. diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java index c75554f9e6..fc31b9510b 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java @@ -29,9 +29,9 @@ 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; diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java index 9004426ff5..034df5fb12 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java @@ -20,7 +20,7 @@ */ 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") diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java index 6c90355296..c0b2e1489d 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java @@ -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.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; diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java index b03d15d1ac..4fc5f5ad66 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java @@ -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; diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java index efac678f23..acdcee25d9 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java @@ -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; diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java index 493bf938a3..cc0682f084 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java @@ -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.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"}) diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java index 2f49bb5c18..9430090436 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java @@ -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{ diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java index 431cc3e48c..b30e4c6dd2 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java @@ -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{ diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java index 8005bf3bac..5ca2b550ed 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java @@ -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; diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java index 25ebf3abed..bbde2c1e30 100644 --- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java +++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java @@ -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; diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java index 4f0439a5d4..8c79e3b078 100644 --- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java +++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java @@ -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; diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java index 528192dcb4..49947c1f50 100644 --- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java +++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java @@ -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; diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java index 37376b6bd0..26de47bf03 100644 --- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java +++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java @@ -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; diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 0fe122bf49..fb44bbadd3 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -74,8 +74,8 @@ log4j-core - javax.xml.bind - jaxb-api + jakarta.xml.bind + jakarta.xml.bind-api org.glassfish.jaxb diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index a87767f8a9..ff8771babc 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -54,8 +54,8 @@ log4j-core - javax.xml.bind - jaxb-api + jakarta.xml.bind + jakarta.xml.bind-api org.glassfish.jaxb diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 51053cc428..c86173990f 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -85,8 +85,8 @@ log4j-core - javax.xml.bind - jaxb-api + jakarta.xml.bind + jakarta.xml.bind-api org.glassfish.jaxb diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/FastaSequence.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/FastaSequence.java index 6af6f13712..f53d236b89 100644 --- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/FastaSequence.java +++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/FastaSequence.java @@ -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; diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index ecb43920a0..bd779d4ba0 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -67,11 +67,9 @@ 1.4.0 - - javax.xml.bind - jaxb-api + jakarta.xml.bind + jakarta.xml.bind-api org.glassfish.jaxb diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java index 878ec29686..635f8bad94 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java @@ -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; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDescription.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDescription.java index b85845ce2c..b7ef2881f7 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDescription.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDescription.java @@ -20,9 +20,9 @@ */ 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; /** Contains data from diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java index 7d1446cb9d..34e7702e23 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java @@ -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; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopNode.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopNode.java index 8faf5dd6c7..40012d8d52 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopNode.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopNode.java @@ -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; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java index b7be721a87..caeaf6c9ee 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java @@ -30,13 +30,13 @@ 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; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java index 93896000b1..d0ff2cf4eb 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java @@ -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; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java index 6c068f51e3..aab18d3ff0 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java @@ -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; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapElements.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapElements.java index 6572570964..49170edf16 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapElements.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapElements.java @@ -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 { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java index e7998ee8dd..eaf23f6d6e 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java @@ -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; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java index 7e707002d8..c1416b7fad 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java @@ -24,7 +24,7 @@ package org.biojava.nbio.structure.xtal.io; -import javax.xml.bind.annotation.adapters.XmlAdapter; +import jakarta.xml.bind.annotation.adapters.XmlAdapter; import java.util.ArrayList; import java.util.List; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.java index 8aabe9b2f1..5a438b55d7 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.java @@ -26,13 +26,13 @@ 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.XmlAccessType; -import javax.xml.bind.annotation.XmlAccessorType; -import javax.xml.bind.annotation.XmlRootElement; +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.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlRootElement; import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; import java.io.PrintStream; diff --git a/pom.xml b/pom.xml index a418dfea5a..1b079ca711 100644 --- a/pom.xml +++ b/pom.xml @@ -462,14 +462,14 @@ 1.039 - javax.xml.bind - jaxb-api - 2.3.1 + jakarta.xml.bind + jakarta.xml.bind-api + 4.0.0 org.glassfish.jaxb jaxb-runtime - 2.3.5 + 4.0.3 runtime