From cb16a5e1595755bf28fdf82f4cc17bbd48638902 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 5 Apr 2019 08:08:35 +0100 Subject: [PATCH] JAL-3204 update to uniprot schema --- schemas/uniprot.xsd | 56 ++++++-- src/jalview/xml/binding/uniprot/CitationType.java | 2 +- src/jalview/xml/binding/uniprot/CofactorType.java | 2 +- src/jalview/xml/binding/uniprot/CommentType.java | 63 ++++++++- .../xml/binding/uniprot/ConsortiumType.java | 2 +- .../xml/binding/uniprot/DbReferenceType.java | 2 +- src/jalview/xml/binding/uniprot/Entry.java | 2 +- src/jalview/xml/binding/uniprot/EventType.java | 2 +- src/jalview/xml/binding/uniprot/EvidenceType.java | 2 +- .../xml/binding/uniprot/EvidencedStringType.java | 2 +- src/jalview/xml/binding/uniprot/FeatureType.java | 2 +- .../xml/binding/uniprot/GeneLocationType.java | 2 +- src/jalview/xml/binding/uniprot/GeneNameType.java | 2 +- src/jalview/xml/binding/uniprot/GeneType.java | 2 +- .../xml/binding/uniprot/ImportedFromType.java | 2 +- .../xml/binding/uniprot/InteractantType.java | 2 +- src/jalview/xml/binding/uniprot/IsoformType.java | 2 +- src/jalview/xml/binding/uniprot/KeywordType.java | 2 +- src/jalview/xml/binding/uniprot/LocationType.java | 2 +- src/jalview/xml/binding/uniprot/MoleculeType.java | 2 +- src/jalview/xml/binding/uniprot/NameListType.java | 2 +- src/jalview/xml/binding/uniprot/ObjectFactory.java | 18 ++- .../xml/binding/uniprot/OrganismNameType.java | 2 +- src/jalview/xml/binding/uniprot/OrganismType.java | 2 +- src/jalview/xml/binding/uniprot/PersonType.java | 2 +- .../binding/uniprot/PhysiologicalReactionType.java | 140 ++++++++++++++++++++ src/jalview/xml/binding/uniprot/PositionType.java | 2 +- src/jalview/xml/binding/uniprot/PropertyType.java | 2 +- .../xml/binding/uniprot/ProteinExistenceType.java | 2 +- src/jalview/xml/binding/uniprot/ProteinType.java | 2 +- src/jalview/xml/binding/uniprot/ReactionType.java | 139 +++++++++++++++++++ src/jalview/xml/binding/uniprot/ReferenceType.java | 2 +- src/jalview/xml/binding/uniprot/SequenceType.java | 2 +- .../xml/binding/uniprot/SourceDataType.java | 2 +- src/jalview/xml/binding/uniprot/SourceType.java | 2 +- src/jalview/xml/binding/uniprot/StatusType.java | 2 +- .../binding/uniprot/SubcellularLocationType.java | 2 +- src/jalview/xml/binding/uniprot/Uniprot.java | 2 +- src/jalview/xml/binding/uniprot/package-info.java | 2 +- 39 files changed, 440 insertions(+), 44 deletions(-) create mode 100644 src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java create mode 100644 src/jalview/xml/binding/uniprot/ReactionType.java diff --git a/schemas/uniprot.xsd b/schemas/uniprot.xsd index 1744d37..ce30fe5 100644 --- a/schemas/uniprot.xsd +++ b/schemas/uniprot.xsd @@ -1,23 +1,26 @@ + - + + @@ -489,6 +492,14 @@ + Used in 'catalytic activity' annotations. + + + + + + + Used in 'cofactor' annotations. @@ -714,6 +725,35 @@ + + + Describes a chemical reaction. + + + + + + + + + + + Describes a physiological reaction. + + + + + + + + + + + + + + + Describes a cofactor. @@ -1074,4 +1114,4 @@ - + \ No newline at end of file diff --git a/src/jalview/xml/binding/uniprot/CitationType.java b/src/jalview/xml/binding/uniprot/CitationType.java index cc5f14e..07adace 100644 --- a/src/jalview/xml/binding/uniprot/CitationType.java +++ b/src/jalview/xml/binding/uniprot/CitationType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/CofactorType.java b/src/jalview/xml/binding/uniprot/CofactorType.java index 9b91dc4..a0d1dfa 100644 --- a/src/jalview/xml/binding/uniprot/CofactorType.java +++ b/src/jalview/xml/binding/uniprot/CofactorType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/CommentType.java b/src/jalview/xml/binding/uniprot/CommentType.java index b0bbf77..9cc5164 100644 --- a/src/jalview/xml/binding/uniprot/CommentType.java +++ b/src/jalview/xml/binding/uniprot/CommentType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // @@ -35,6 +35,10 @@ import javax.xml.bind.annotation.XmlType; * <choice minOccurs="0"> * <group ref="{http://uniprot.org/uniprot}bpcCommentGroup"/> * <sequence> + * <element name="reaction" type="{http://uniprot.org/uniprot}reactionType"/> + * <element name="physiologicalReaction" type="{http://uniprot.org/uniprot}physiologicalReactionType" maxOccurs="2" minOccurs="0"/> + * </sequence> + * <sequence> * <element name="cofactor" type="{http://uniprot.org/uniprot}cofactorType" maxOccurs="unbounded"/> * </sequence> * <sequence> @@ -176,6 +180,8 @@ import javax.xml.bind.annotation.XmlType; "phDependence", "redoxPotential", "temperatureDependence", + "reaction", + "physiologicalReaction", "cofactor", "subcellularLocation", "conflict", @@ -197,6 +203,8 @@ public class CommentType { protected CommentType.PhDependence phDependence; protected CommentType.RedoxPotential redoxPotential; protected CommentType.TemperatureDependence temperatureDependence; + protected ReactionType reaction; + protected List physiologicalReaction; protected List cofactor; protected List subcellularLocation; protected CommentType.Conflict conflict; @@ -370,6 +378,59 @@ public class CommentType { } /** + * Gets the value of the reaction property. + * + * @return + * possible object is + * {@link ReactionType } + * + */ + public ReactionType getReaction() { + return reaction; + } + + /** + * Sets the value of the reaction property. + * + * @param value + * allowed object is + * {@link ReactionType } + * + */ + public void setReaction(ReactionType value) { + this.reaction = value; + } + + /** + * Gets the value of the physiologicalReaction property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the physiologicalReaction property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getPhysiologicalReaction().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link PhysiologicalReactionType } + * + * + */ + public List getPhysiologicalReaction() { + if (physiologicalReaction == null) { + physiologicalReaction = new ArrayList(); + } + return this.physiologicalReaction; + } + + /** * Gets the value of the cofactor property. * *

diff --git a/src/jalview/xml/binding/uniprot/ConsortiumType.java b/src/jalview/xml/binding/uniprot/ConsortiumType.java index c74c1e7..b2c4fdd 100644 --- a/src/jalview/xml/binding/uniprot/ConsortiumType.java +++ b/src/jalview/xml/binding/uniprot/ConsortiumType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/DbReferenceType.java b/src/jalview/xml/binding/uniprot/DbReferenceType.java index 184ee40..ea6f728 100644 --- a/src/jalview/xml/binding/uniprot/DbReferenceType.java +++ b/src/jalview/xml/binding/uniprot/DbReferenceType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/Entry.java b/src/jalview/xml/binding/uniprot/Entry.java index 1ca91bc..dc211e8 100644 --- a/src/jalview/xml/binding/uniprot/Entry.java +++ b/src/jalview/xml/binding/uniprot/Entry.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/EventType.java b/src/jalview/xml/binding/uniprot/EventType.java index 3b5b8a0..0c3de0e 100644 --- a/src/jalview/xml/binding/uniprot/EventType.java +++ b/src/jalview/xml/binding/uniprot/EventType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/EvidenceType.java b/src/jalview/xml/binding/uniprot/EvidenceType.java index 77a7561..484d42d 100644 --- a/src/jalview/xml/binding/uniprot/EvidenceType.java +++ b/src/jalview/xml/binding/uniprot/EvidenceType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/EvidencedStringType.java b/src/jalview/xml/binding/uniprot/EvidencedStringType.java index 4c1fa7b..ad22872 100644 --- a/src/jalview/xml/binding/uniprot/EvidencedStringType.java +++ b/src/jalview/xml/binding/uniprot/EvidencedStringType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/FeatureType.java b/src/jalview/xml/binding/uniprot/FeatureType.java index 0ef367c..e951659 100644 --- a/src/jalview/xml/binding/uniprot/FeatureType.java +++ b/src/jalview/xml/binding/uniprot/FeatureType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/GeneLocationType.java b/src/jalview/xml/binding/uniprot/GeneLocationType.java index 5a2ebcf..3e3da7b 100644 --- a/src/jalview/xml/binding/uniprot/GeneLocationType.java +++ b/src/jalview/xml/binding/uniprot/GeneLocationType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/GeneNameType.java b/src/jalview/xml/binding/uniprot/GeneNameType.java index 1716731..bd93a7c 100644 --- a/src/jalview/xml/binding/uniprot/GeneNameType.java +++ b/src/jalview/xml/binding/uniprot/GeneNameType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/GeneType.java b/src/jalview/xml/binding/uniprot/GeneType.java index b466644..7440d6b 100644 --- a/src/jalview/xml/binding/uniprot/GeneType.java +++ b/src/jalview/xml/binding/uniprot/GeneType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/ImportedFromType.java b/src/jalview/xml/binding/uniprot/ImportedFromType.java index 92fa6f4..80cdfe5 100644 --- a/src/jalview/xml/binding/uniprot/ImportedFromType.java +++ b/src/jalview/xml/binding/uniprot/ImportedFromType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/InteractantType.java b/src/jalview/xml/binding/uniprot/InteractantType.java index 66ba19d..2ba310e 100644 --- a/src/jalview/xml/binding/uniprot/InteractantType.java +++ b/src/jalview/xml/binding/uniprot/InteractantType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/IsoformType.java b/src/jalview/xml/binding/uniprot/IsoformType.java index 35a085a..9d218cf 100644 --- a/src/jalview/xml/binding/uniprot/IsoformType.java +++ b/src/jalview/xml/binding/uniprot/IsoformType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/KeywordType.java b/src/jalview/xml/binding/uniprot/KeywordType.java index 5b7e0f7..21590e4 100644 --- a/src/jalview/xml/binding/uniprot/KeywordType.java +++ b/src/jalview/xml/binding/uniprot/KeywordType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/LocationType.java b/src/jalview/xml/binding/uniprot/LocationType.java index 749871a..35d5f87 100644 --- a/src/jalview/xml/binding/uniprot/LocationType.java +++ b/src/jalview/xml/binding/uniprot/LocationType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/MoleculeType.java b/src/jalview/xml/binding/uniprot/MoleculeType.java index 0392a4b..197e899 100644 --- a/src/jalview/xml/binding/uniprot/MoleculeType.java +++ b/src/jalview/xml/binding/uniprot/MoleculeType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/NameListType.java b/src/jalview/xml/binding/uniprot/NameListType.java index 70d5e2f..3567be6 100644 --- a/src/jalview/xml/binding/uniprot/NameListType.java +++ b/src/jalview/xml/binding/uniprot/NameListType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/ObjectFactory.java b/src/jalview/xml/binding/uniprot/ObjectFactory.java index 20cba73..67c3d83 100644 --- a/src/jalview/xml/binding/uniprot/ObjectFactory.java +++ b/src/jalview/xml/binding/uniprot/ObjectFactory.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // @@ -233,6 +233,14 @@ public class ObjectFactory { } /** + * Create an instance of {@link PhysiologicalReactionType } + * + */ + public PhysiologicalReactionType createPhysiologicalReactionType() { + return new PhysiologicalReactionType(); + } + + /** * Create an instance of {@link CofactorType } * */ @@ -289,6 +297,14 @@ public class ObjectFactory { } /** + * Create an instance of {@link ReactionType } + * + */ + public ReactionType createReactionType() { + return new ReactionType(); + } + + /** * Create an instance of {@link SourceType } * */ diff --git a/src/jalview/xml/binding/uniprot/OrganismNameType.java b/src/jalview/xml/binding/uniprot/OrganismNameType.java index a658e36..fc0ba68 100644 --- a/src/jalview/xml/binding/uniprot/OrganismNameType.java +++ b/src/jalview/xml/binding/uniprot/OrganismNameType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/OrganismType.java b/src/jalview/xml/binding/uniprot/OrganismType.java index feabacd..d75b9b1 100644 --- a/src/jalview/xml/binding/uniprot/OrganismType.java +++ b/src/jalview/xml/binding/uniprot/OrganismType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/PersonType.java b/src/jalview/xml/binding/uniprot/PersonType.java index 2a3e8bd..6328682 100644 --- a/src/jalview/xml/binding/uniprot/PersonType.java +++ b/src/jalview/xml/binding/uniprot/PersonType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java new file mode 100644 index 0000000..8dbf704 --- /dev/null +++ b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java @@ -0,0 +1,140 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2019.04.05 at 08:01:44 AM BST +// + + +package jalview.xml.binding.uniprot; + +import java.util.ArrayList; +import java.util.List; +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 javax.xml.bind.annotation.XmlType; + + +/** + * Describes a physiological reaction. + * + *

Java class for physiologicalReactionType complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="physiologicalReactionType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+ *       </sequence>
+ *       <attribute name="direction" use="required">
+ *         <simpleType>
+ *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *             <enumeration value="left-to-right"/>
+ *             <enumeration value="right-to-left"/>
+ *           </restriction>
+ *         </simpleType>
+ *       </attribute>
+ *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "physiologicalReactionType", propOrder = { + "dbReference" +}) +public class PhysiologicalReactionType { + + @XmlElement(required = true) + protected DbReferenceType dbReference; + @XmlAttribute(name = "direction", required = true) + protected String direction; + @XmlAttribute(name = "evidence") + protected List evidence; + + /** + * Gets the value of the dbReference property. + * + * @return + * possible object is + * {@link DbReferenceType } + * + */ + public DbReferenceType getDbReference() { + return dbReference; + } + + /** + * Sets the value of the dbReference property. + * + * @param value + * allowed object is + * {@link DbReferenceType } + * + */ + public void setDbReference(DbReferenceType value) { + this.dbReference = value; + } + + /** + * Gets the value of the direction property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDirection() { + return direction; + } + + /** + * Sets the value of the direction property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDirection(String value) { + this.direction = value; + } + + /** + * Gets the value of the evidence property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the evidence property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getEvidence().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Integer } + * + * + */ + public List getEvidence() { + if (evidence == null) { + evidence = new ArrayList(); + } + return this.evidence; + } + +} diff --git a/src/jalview/xml/binding/uniprot/PositionType.java b/src/jalview/xml/binding/uniprot/PositionType.java index 92d8906..a850dbb 100644 --- a/src/jalview/xml/binding/uniprot/PositionType.java +++ b/src/jalview/xml/binding/uniprot/PositionType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/PropertyType.java b/src/jalview/xml/binding/uniprot/PropertyType.java index a9299f4..977e428 100644 --- a/src/jalview/xml/binding/uniprot/PropertyType.java +++ b/src/jalview/xml/binding/uniprot/PropertyType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java index 315f62d..fb12cd6 100644 --- a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java +++ b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/ProteinType.java b/src/jalview/xml/binding/uniprot/ProteinType.java index dd5a8be..defaff2 100644 --- a/src/jalview/xml/binding/uniprot/ProteinType.java +++ b/src/jalview/xml/binding/uniprot/ProteinType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/ReactionType.java b/src/jalview/xml/binding/uniprot/ReactionType.java new file mode 100644 index 0000000..800f518 --- /dev/null +++ b/src/jalview/xml/binding/uniprot/ReactionType.java @@ -0,0 +1,139 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2019.04.05 at 08:01:44 AM BST +// + + +package jalview.xml.binding.uniprot; + +import java.util.ArrayList; +import java.util.List; +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 javax.xml.bind.annotation.XmlType; + + +/** + * Describes a chemical reaction. + * + *

Java class for reactionType complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="reactionType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="text" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded"/>
+ *       </sequence>
+ *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "reactionType", propOrder = { + "text", + "dbReference" +}) +public class ReactionType { + + @XmlElement(required = true) + protected String text; + @XmlElement(required = true) + protected List dbReference; + @XmlAttribute(name = "evidence") + protected List evidence; + + /** + * Gets the value of the text property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getText() { + return text; + } + + /** + * Sets the value of the text property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setText(String value) { + this.text = value; + } + + /** + * Gets the value of the dbReference property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the dbReference property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getDbReference().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link DbReferenceType } + * + * + */ + public List getDbReference() { + if (dbReference == null) { + dbReference = new ArrayList(); + } + return this.dbReference; + } + + /** + * Gets the value of the evidence property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the evidence property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getEvidence().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Integer } + * + * + */ + public List getEvidence() { + if (evidence == null) { + evidence = new ArrayList(); + } + return this.evidence; + } + +} diff --git a/src/jalview/xml/binding/uniprot/ReferenceType.java b/src/jalview/xml/binding/uniprot/ReferenceType.java index 33e6251..75fb044 100644 --- a/src/jalview/xml/binding/uniprot/ReferenceType.java +++ b/src/jalview/xml/binding/uniprot/ReferenceType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/SequenceType.java b/src/jalview/xml/binding/uniprot/SequenceType.java index f0b110b..8c10faf 100644 --- a/src/jalview/xml/binding/uniprot/SequenceType.java +++ b/src/jalview/xml/binding/uniprot/SequenceType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/SourceDataType.java b/src/jalview/xml/binding/uniprot/SourceDataType.java index 03cace3..c3838ec 100644 --- a/src/jalview/xml/binding/uniprot/SourceDataType.java +++ b/src/jalview/xml/binding/uniprot/SourceDataType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/SourceType.java b/src/jalview/xml/binding/uniprot/SourceType.java index 44edbba..2814911 100644 --- a/src/jalview/xml/binding/uniprot/SourceType.java +++ b/src/jalview/xml/binding/uniprot/SourceType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/StatusType.java b/src/jalview/xml/binding/uniprot/StatusType.java index 29fb34e..3f956c3 100644 --- a/src/jalview/xml/binding/uniprot/StatusType.java +++ b/src/jalview/xml/binding/uniprot/StatusType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java index 29848d7..b9ff7d3 100644 --- a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java +++ b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/Uniprot.java b/src/jalview/xml/binding/uniprot/Uniprot.java index 4e2cdb0..5751e61 100644 --- a/src/jalview/xml/binding/uniprot/Uniprot.java +++ b/src/jalview/xml/binding/uniprot/Uniprot.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // diff --git a/src/jalview/xml/binding/uniprot/package-info.java b/src/jalview/xml/binding/uniprot/package-info.java index 9741acc..71f7eaa 100644 --- a/src/jalview/xml/binding/uniprot/package-info.java +++ b/src/jalview/xml/binding/uniprot/package-info.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.13 at 10:18:53 AM BST +// Generated on: 2019.04.05 at 08:01:44 AM BST // @javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) -- 1.7.10.2