From d5ea96c94eff06c6f797f41b1724a7b67e898e75 Mon Sep 17 00:00:00 2001 From: Gary Murphy Date: Fri, 29 Dec 2023 10:30:02 -0600 Subject: [PATCH 1/3] Updated to Jakarta JAXB and Java 17 --- biojava-aa-prop/pom.xml | 13 ++++++++----- .../nbio/aaproperties/IPeptideProperties.java | 2 +- .../nbio/aaproperties/PeptideProperties.java | 3 +-- .../nbio/aaproperties/PeptidePropertiesImpl.java | 6 +++--- .../aaproperties/xml/AminoAcidComposition.java | 2 +- .../xml/AminoAcidCompositionTable.java | 8 ++++---- .../biojava/nbio/aaproperties/xml/Element.java | 8 ++++---- .../nbio/aaproperties/xml/ElementTable.java | 2 +- .../biojava/nbio/aaproperties/xml/Isotope.java | 8 ++++---- .../xml/MyValidationEventHandler.java | 6 +++--- .../biojava/nbio/aaproperties/xml/Name2Count.java | 6 +++--- .../nbio/aaproperties/xml/SchemaGenerator.java | 2 +- .../biojava/nbio/aaproperties/CookBookTest.java | 3 +-- .../aaproperties/PeptidePropertiesImplTest.java | 4 +--- .../nbio/aaproperties/xml/AminoAcidTest.java | 8 ++++---- .../nbio/aaproperties/xml/ElementTest.java | 12 ++++-------- biojava-alignment/pom.xml | 4 ++-- biojava-core/pom.xml | 9 ++++++--- biojava-genome/pom.xml | 6 +++--- biojava-integrationtest/pom.xml | 4 ++-- biojava-modfinder/pom.xml | 11 +++++++---- biojava-ontology/pom.xml | 2 +- biojava-protein-comparison-tool/pom.xml | 10 +++++----- biojava-protein-disorder/pom.xml | 11 +++++++---- .../biojava/nbio/data/sequence/FastaSequence.java | 4 ++-- biojava-structure-gui/pom.xml | 6 +++--- biojava-structure/pom.xml | 15 ++++++++------- .../biojava/nbio/structure/domain/pdp/Domain.java | 6 +++--- .../nbio/structure/scop/ScopDescription.java | 6 +++--- .../biojava/nbio/structure/scop/ScopDomain.java | 6 +++--- .../org/biojava/nbio/structure/scop/ScopNode.java | 6 +++--- .../biojava/nbio/structure/xtal/SpaceGroup.java | 14 +++++++------- .../nbio/structure/xtal/SymoplibParser.java | 2 +- .../structure/xtal/io/SpaceGroupMapAdapter.java | 2 +- .../structure/xtal/io/SpaceGroupMapElements.java | 2 +- .../nbio/structure/xtal/io/SpaceGroupMapRoot.java | 12 ++++++------ .../structure/xtal/io/TransfAlgebraicAdapter.java | 2 +- .../xtal/io/TreeMapSpaceGroupWrapper.java | 14 +++++++------- biojava-survival/pom.xml | 2 +- biojava-ws/pom.xml | 4 ++-- pom.xml | 12 ++++++------ 41 files changed, 135 insertions(+), 130 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 70ab1fa759..6a92d1146b 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT org.biojava biojava-structure - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT @@ -105,12 +105,15 @@ - javax.xml.bind - jaxb-api + jakarta.xml.bind + jakarta.xml.bind-api + 4.0.0 org.glassfish.jaxb jaxb-runtime + 4.0.3 + runtime \ No newline at end of file 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-alignment/pom.xml b/biojava-alignment/pom.xml index 002fbb6b0b..d4af196852 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 0fe122bf49..a2d1f7156f 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT 4.0.0 biojava-core @@ -74,12 +74,15 @@ log4j-core - javax.xml.bind - jaxb-api + jakarta.xml.bind + jakarta.xml.bind-api + 4.0.0 org.glassfish.jaxb jaxb-runtime + 4.0.3 + runtime \ No newline at end of file diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 2b213d7de5..c43b84a4b6 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT 4.0.0 biojava-genome @@ -71,13 +71,13 @@ org.biojava biojava-core - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT compile org.biojava biojava-alignment - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index d02011571c..c7a1975b13 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index a87767f8a9..c228cf38d4 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT jar compile @@ -54,12 +54,15 @@ log4j-core - javax.xml.bind - jaxb-api + jakarta.xml.bind + jakarta.xml.bind-api + 4.0.0 org.glassfish.jaxb jaxb-runtime + 4.0.3 + runtime diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 1fb8967489..393ec45be1 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index 36d3ec3b2b..a0ed12f6bd 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT org.biojava biojava-core - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT org.biojava biojava-structure - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT org.biojava biojava-structure-gui - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 51053cc428..6b1de229a0 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT @@ -85,12 +85,15 @@ log4j-core - javax.xml.bind - jaxb-api + jakarta.xml.bind + jakarta.xml.bind-api + 4.0.0 org.glassfish.jaxb jaxb-runtime + 4.0.3 + runtime 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-gui/pom.xml b/biojava-structure-gui/pom.xml index 8b3522352b..bf6f64246e 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT compile org.biojava biojava-core - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index ecb43920a0..21f5b5ec84 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT biojava-structure biojava-structure @@ -44,13 +44,13 @@ org.biojava biojava-alignment - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT compile org.biojava biojava-core - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT compile @@ -67,15 +67,16 @@ 1.4.0 - - javax.xml.bind - jaxb-api + jakarta.xml.bind + jakarta.xml.bind-api + 4.0.0 org.glassfish.jaxb jaxb-runtime + 4.0.3 + runtime 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/biojava-survival/pom.xml b/biojava-survival/pom.xml index 61bcb2369f..e28fae4370 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 86cf1004f9..8dd7dd399d 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index a418dfea5a..8e4b8ae2a1 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.0.3-SNAPSHOT + 8.0.0.JAXB-SNAPSHOT biojava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the @@ -33,7 +33,7 @@ - 11 + 17 UTF-8 UTF-8 @@ -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 From 171aef0a5512e1cb63f552fd5e04fe66c1226e93 Mon Sep 17 00:00:00 2001 From: Gary Murphy Date: Mon, 1 Jan 2024 10:36:52 -0600 Subject: [PATCH 2/3] Changed the JDK back to Java 11 and reran tests --- biojava-aa-prop/pom.xml | 6 +++--- biojava-alignment/pom.xml | 4 ++-- biojava-core/pom.xml | 2 +- biojava-genome/pom.xml | 6 +++--- biojava-integrationtest/pom.xml | 4 ++-- biojava-modfinder/pom.xml | 4 ++-- biojava-ontology/pom.xml | 2 +- biojava-protein-comparison-tool/pom.xml | 10 +++++----- biojava-protein-disorder/pom.xml | 4 ++-- biojava-structure-gui/pom.xml | 6 +++--- biojava-structure/pom.xml | 6 +++--- biojava-survival/pom.xml | 2 +- biojava-ws/pom.xml | 4 ++-- pom.xml | 4 ++-- 14 files changed, 32 insertions(+), 32 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 6a92d1146b..48c9e35962 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT org.biojava biojava-structure - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index d4af196852..002fbb6b0b 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index a2d1f7156f..c0b3c2ca47 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index c43b84a4b6..2b213d7de5 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT 4.0.0 biojava-genome @@ -71,13 +71,13 @@ org.biojava biojava-core - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT compile org.biojava biojava-alignment - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index c7a1975b13..d02011571c 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index c228cf38d4..44e2e50e4a 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 393ec45be1..1fb8967489 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index a0ed12f6bd..36d3ec3b2b 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT org.biojava biojava-core - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT org.biojava biojava-structure - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT org.biojava biojava-structure-gui - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 6b1de229a0..a86a7fb13b 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index bf6f64246e..8b3522352b 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT compile org.biojava biojava-core - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 21f5b5ec84..4ee0ee2e3f 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT biojava-structure biojava-structure @@ -44,13 +44,13 @@ org.biojava biojava-alignment - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT compile org.biojava biojava-core - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index e28fae4370..61bcb2369f 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 8dd7dd399d..86cf1004f9 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index 8e4b8ae2a1..1b079ca711 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 8.0.0.JAXB-SNAPSHOT + 7.0.3-SNAPSHOT biojava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the @@ -33,7 +33,7 @@ - 17 + 11 UTF-8 UTF-8 From f0320f5b024b7aedb0ddca1f9aa32080e4c28d36 Mon Sep 17 00:00:00 2001 From: Gary Murphy Date: Thu, 4 Jan 2024 07:45:22 -0600 Subject: [PATCH 3/3] Removed explicit versioning for JAX-B API and runtime, except for the dependencyManagement section in the POM. Reran unit tests with no errors. --- biojava-aa-prop/pom.xml | 3 --- biojava-core/pom.xml | 3 --- biojava-modfinder/pom.xml | 3 --- biojava-protein-disorder/pom.xml | 3 --- biojava-structure/pom.xml | 3 --- 5 files changed, 15 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 48c9e35962..908f2d28c2 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -107,13 +107,10 @@ jakarta.xml.bind jakarta.xml.bind-api - 4.0.0 org.glassfish.jaxb jaxb-runtime - 4.0.3 - runtime \ No newline at end of file diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index c0b3c2ca47..fb44bbadd3 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -76,13 +76,10 @@ jakarta.xml.bind jakarta.xml.bind-api - 4.0.0 org.glassfish.jaxb jaxb-runtime - 4.0.3 - runtime \ No newline at end of file diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 44e2e50e4a..ff8771babc 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -56,13 +56,10 @@ jakarta.xml.bind jakarta.xml.bind-api - 4.0.0 org.glassfish.jaxb jaxb-runtime - 4.0.3 - runtime diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index a86a7fb13b..c86173990f 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -87,13 +87,10 @@ jakarta.xml.bind jakarta.xml.bind-api - 4.0.0 org.glassfish.jaxb jaxb-runtime - 4.0.3 - runtime diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 4ee0ee2e3f..bd779d4ba0 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -70,13 +70,10 @@ jakarta.xml.bind jakarta.xml.bind-api - 4.0.0 org.glassfish.jaxb jaxb-runtime - 4.0.3 - runtime