From 17625a5cfc226dc98fe65fedaa8678a6bdfdbaf1 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 7 Jun 2019 14:03:58 +0100 Subject: [PATCH] JAL-3251 added optional attributes Sequence.biotype, Mapping.mappingType Conflicts: src/jalview/xml/binding/jalview/AlcodonFrame.java src/jalview/xml/binding/jalview/Annotation.java src/jalview/xml/binding/jalview/AnnotationColourScheme.java src/jalview/xml/binding/jalview/AnnotationElement.java src/jalview/xml/binding/jalview/DoubleMatrix.java src/jalview/xml/binding/jalview/DoubleVector.java src/jalview/xml/binding/jalview/Feature.java src/jalview/xml/binding/jalview/FeatureMatcher.java src/jalview/xml/binding/jalview/FeatureMatcherSet.java src/jalview/xml/binding/jalview/FilterBy.java src/jalview/xml/binding/jalview/JalviewModel.java src/jalview/xml/binding/jalview/JalviewUserColours.java src/jalview/xml/binding/jalview/MapListType.java src/jalview/xml/binding/jalview/Mapping.java src/jalview/xml/binding/jalview/NoValueColour.java src/jalview/xml/binding/jalview/ObjectFactory.java src/jalview/xml/binding/jalview/PcaDataType.java src/jalview/xml/binding/jalview/Pdbentry.java src/jalview/xml/binding/jalview/Sequence.java src/jalview/xml/binding/jalview/SequenceSet.java src/jalview/xml/binding/jalview/SequenceType.java src/jalview/xml/binding/jalview/ThresholdType.java src/jalview/xml/binding/jalview/VAMSAS.java src/jalview/xml/binding/jalview/WebServiceParameterSet.java src/jalview/xml/binding/jalview/package-info.java --- schemas/vamsas.xsd | 12 ++++++++ src/jalview/xml/binding/jalview/AlcodonFrame.java | 2 +- src/jalview/xml/binding/jalview/Annotation.java | 2 +- .../binding/jalview/AnnotationColourScheme.java | 2 +- .../xml/binding/jalview/AnnotationElement.java | 2 +- src/jalview/xml/binding/jalview/DoubleMatrix.java | 2 +- src/jalview/xml/binding/jalview/DoubleVector.java | 2 +- src/jalview/xml/binding/jalview/Feature.java | 2 +- .../xml/binding/jalview/FeatureMatcher.java | 2 +- .../xml/binding/jalview/FeatureMatcherSet.java | 2 +- src/jalview/xml/binding/jalview/FilterBy.java | 2 +- src/jalview/xml/binding/jalview/JalviewModel.java | 2 +- .../xml/binding/jalview/JalviewUserColours.java | 2 +- src/jalview/xml/binding/jalview/MapListType.java | 2 +- src/jalview/xml/binding/jalview/Mapping.java | 30 +++++++++++++++++++- src/jalview/xml/binding/jalview/NoValueColour.java | 2 +- src/jalview/xml/binding/jalview/ObjectFactory.java | 2 +- src/jalview/xml/binding/jalview/PcaDataType.java | 2 +- src/jalview/xml/binding/jalview/Pdbentry.java | 2 +- src/jalview/xml/binding/jalview/Sequence.java | 29 ++++++++++++++++++- src/jalview/xml/binding/jalview/SequenceSet.java | 2 +- src/jalview/xml/binding/jalview/SequenceType.java | 2 +- src/jalview/xml/binding/jalview/ThresholdType.java | 2 +- src/jalview/xml/binding/jalview/VAMSAS.java | 2 +- .../binding/jalview/WebServiceParameterSet.java | 2 +- src/jalview/xml/binding/jalview/package-info.java | 2 +- 26 files changed, 92 insertions(+), 25 deletions(-) diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index 2ef0c15..20c19dd 100755 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -103,6 +103,11 @@ + + + Biotype of the mapping e.g. CdsToPeptide + + @@ -178,6 +183,13 @@ + + + + Biotype of the sequence (if known) + + + diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index 83f1ee2..3e84f59 100644 --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java index 0dbcad0..3149d77 100644 --- a/src/jalview/xml/binding/jalview/Annotation.java +++ b/src/jalview/xml/binding/jalview/Annotation.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java index 44affa2..3e6bacd 100644 --- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java +++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java index de408d2..0d36902 100644 --- a/src/jalview/xml/binding/jalview/AnnotationElement.java +++ b/src/jalview/xml/binding/jalview/AnnotationElement.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java index b4c07bc..fb88b73 100644 --- a/src/jalview/xml/binding/jalview/DoubleMatrix.java +++ b/src/jalview/xml/binding/jalview/DoubleMatrix.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java index e2592ab..997982e 100644 --- a/src/jalview/xml/binding/jalview/DoubleVector.java +++ b/src/jalview/xml/binding/jalview/DoubleVector.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java index 9001ee2..294c28c 100644 --- a/src/jalview/xml/binding/jalview/Feature.java +++ b/src/jalview/xml/binding/jalview/Feature.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java index 0daf56a..1225838 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcher.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcher.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java index bf69d5b..56d511b 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java index 5684acf..0e52dc7 100644 --- a/src/jalview/xml/binding/jalview/FilterBy.java +++ b/src/jalview/xml/binding/jalview/FilterBy.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java index ed57edc..dd47f48 100644 --- a/src/jalview/xml/binding/jalview/JalviewModel.java +++ b/src/jalview/xml/binding/jalview/JalviewModel.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java index 701647c..7369c8b 100644 --- a/src/jalview/xml/binding/jalview/JalviewUserColours.java +++ b/src/jalview/xml/binding/jalview/JalviewUserColours.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java index 3d7b5eb..3d505b3 100644 --- a/src/jalview/xml/binding/jalview/MapListType.java +++ b/src/jalview/xml/binding/jalview/MapListType.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java index 3cbebc0..344d15f 100644 --- a/src/jalview/xml/binding/jalview/Mapping.java +++ b/src/jalview/xml/binding/jalview/Mapping.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // @@ -10,6 +10,7 @@ package jalview.xml.binding.jalview; 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.XmlRootElement; import javax.xml.bind.annotation.XmlType; @@ -41,6 +42,7 @@ import javax.xml.bind.annotation.XmlType; * </element> * </choice> * </sequence> + * <attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" /> * </extension> * </complexContent> * </complexType> @@ -61,6 +63,8 @@ public class Mapping @XmlElement(name = "Sequence") protected Sequence sequence; protected String dseqFor; + @XmlAttribute(name = "mappingType") + protected String mappingType; /** * Gets the value of the sequence property. @@ -110,4 +114,28 @@ public class Mapping this.dseqFor = value; } + /** + * Gets the value of the mappingType property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getMappingType() { + return mappingType; + } + + /** + * Sets the value of the mappingType property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setMappingType(String value) { + this.mappingType = value; + } + } diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java index 15fc45d..e13c4c5 100644 --- a/src/jalview/xml/binding/jalview/NoValueColour.java +++ b/src/jalview/xml/binding/jalview/NoValueColour.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java index 6858f07..5063042 100644 --- a/src/jalview/xml/binding/jalview/ObjectFactory.java +++ b/src/jalview/xml/binding/jalview/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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java index e8c7cf2..92d89a3 100644 --- a/src/jalview/xml/binding/jalview/PcaDataType.java +++ b/src/jalview/xml/binding/jalview/PcaDataType.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java index 843ea6c..9f0bf91 100644 --- a/src/jalview/xml/binding/jalview/Pdbentry.java +++ b/src/jalview/xml/binding/jalview/Pdbentry.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java index 4442017..8da342c 100644 --- a/src/jalview/xml/binding/jalview/Sequence.java +++ b/src/jalview/xml/binding/jalview/Sequence.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: 2019.02.06 at 10:59:19 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // @@ -45,6 +45,7 @@ import javax.xml.bind.annotation.XmlType; * </element> * </sequence> * <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /> * </extension> * </complexContent> * </complexType> @@ -65,6 +66,8 @@ public class Sequence protected List dbRef; @XmlAttribute(name = "dsseqid") protected String dsseqid; + @XmlAttribute(name = "biotype") + protected String biotype; /** * Gets the value of the dbRef property. @@ -119,6 +122,30 @@ public class Sequence this.dsseqid = value; } + /** + * Gets the value of the biotype property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getBiotype() { + return biotype; + } + + /** + * Sets the value of the biotype property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setBiotype(String value) { + this.biotype = value; + } + /** *

Java class for anonymous complex type. diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java index 0fc7771..d187631 100644 --- a/src/jalview/xml/binding/jalview/SequenceSet.java +++ b/src/jalview/xml/binding/jalview/SequenceSet.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java index 07b8c24..46f5fa6 100644 --- a/src/jalview/xml/binding/jalview/SequenceType.java +++ b/src/jalview/xml/binding/jalview/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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java index e8b7e28..d48a44a 100644 --- a/src/jalview/xml/binding/jalview/ThresholdType.java +++ b/src/jalview/xml/binding/jalview/ThresholdType.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java index 1f68de9..b7fbdee 100644 --- a/src/jalview/xml/binding/jalview/VAMSAS.java +++ b/src/jalview/xml/binding/jalview/VAMSAS.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java index c884556..f27ae98 100644 --- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java +++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java index bd6dc77..f39e4c2 100644 --- a/src/jalview/xml/binding/jalview/package-info.java +++ b/src/jalview/xml/binding/jalview/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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.07 at 02:14:40 PM BST // @javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) -- 1.7.10.2