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JAL-3251 added optional attributes Sequence.biotype, Mapping.mappingType
feature/JAL-3187viewstyleFlags
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 7 Jun 2019 13:03:58 +0000
(14:03 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 7 Jun 2019 13:03:58 +0000
(14:03 +0100)
26 files changed:
schemas/vamsas.xsd
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src/jalview/xml/binding/jalview/AlcodonFrame.java
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src/jalview/xml/binding/jalview/Annotation.java
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src/jalview/xml/binding/jalview/AnnotationColourScheme.java
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src/jalview/xml/binding/jalview/AnnotationElement.java
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src/jalview/xml/binding/jalview/DoubleMatrix.java
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src/jalview/xml/binding/jalview/DoubleVector.java
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src/jalview/xml/binding/jalview/Feature.java
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src/jalview/xml/binding/jalview/FeatureMatcher.java
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src/jalview/xml/binding/jalview/FeatureMatcherSet.java
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src/jalview/xml/binding/jalview/FilterBy.java
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src/jalview/xml/binding/jalview/JalviewModel.java
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src/jalview/xml/binding/jalview/JalviewUserColours.java
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src/jalview/xml/binding/jalview/MapListType.java
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src/jalview/xml/binding/jalview/Mapping.java
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src/jalview/xml/binding/jalview/NoValueColour.java
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src/jalview/xml/binding/jalview/ObjectFactory.java
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src/jalview/xml/binding/jalview/PcaDataType.java
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src/jalview/xml/binding/jalview/Pdbentry.java
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src/jalview/xml/binding/jalview/Sequence.java
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src/jalview/xml/binding/jalview/SequenceSet.java
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src/jalview/xml/binding/jalview/SequenceType.java
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src/jalview/xml/binding/jalview/ThresholdType.java
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src/jalview/xml/binding/jalview/VAMSAS.java
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src/jalview/xml/binding/jalview/WebServiceParameterSet.java
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src/jalview/xml/binding/jalview/package-info.java
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diff --git
a/schemas/vamsas.xsd
b/schemas/vamsas.xsd
index
22b7aac
..
72ac603
100755
(executable)
--- a/
schemas/vamsas.xsd
+++ b/
schemas/vamsas.xsd
@@
-103,6
+103,11
@@
</xs:element>
</xs:choice>
</xs:sequence>
</xs:element>
</xs:choice>
</xs:sequence>
+ <xs:attribute name="mappingType" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Biotype of the mapping e.g. CdsToPeptide</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:extension>
</xs:complexContent>
</xs:complexType>
@@
-171,6
+176,13
@@
</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:documentation>
</xs:annotation>
</xs:attribute>
+ <xs:attribute name="biotype" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ Biotype of the sequence (if known)
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:extension>
</xs:complexContent>
</xs:complexType>
diff --git
a/src/jalview/xml/binding/jalview/AlcodonFrame.java
b/src/jalview/xml/binding/jalview/AlcodonFrame.java
index
112247e
..
4b0fc8d
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/Annotation.java
b/src/jalview/xml/binding/jalview/Annotation.java
index
5cc23eb
..
1f34d54
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
index
25ad072
..
da30801
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/AnnotationElement.java
b/src/jalview/xml/binding/jalview/AnnotationElement.java
index
ac45865
..
ce52188
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/DoubleMatrix.java
b/src/jalview/xml/binding/jalview/DoubleMatrix.java
index
308125d
..
d264908
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/DoubleVector.java
b/src/jalview/xml/binding/jalview/DoubleVector.java
index
b627a52
..
139378d
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/Feature.java
b/src/jalview/xml/binding/jalview/Feature.java
index
b870a50
..
615b21e
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/FeatureMatcher.java
b/src/jalview/xml/binding/jalview/FeatureMatcher.java
index
cb42c91
..
004739f
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
index
e3dd183
..
e1c64e6
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/FilterBy.java
b/src/jalview/xml/binding/jalview/FilterBy.java
index
24349cc
..
2bf548c
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/JalviewModel.java
b/src/jalview/xml/binding/jalview/JalviewModel.java
index
346d74d
..
b0fc2b8
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
@@
-294,8
+294,8
@@
import javax.xml.datatype.XMLGregorianCalendar;
* </element>
* <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
* </sequence>
* </element>
* <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
* </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
* <attGroup ref="{www.jalview.org}SimilarityParams"/>
* <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
* <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
* <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
@@
-3108,8
+3108,8
@@
public class JalviewModel {
* </element>
* <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
* </sequence>
* </element>
* <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
* </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
* <attGroup ref="{www.jalview.org}SimilarityParams"/>
* <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
* <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
* <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
@@
-3164,14
+3164,6
@@
public class JalviewModel {
protected Boolean showLabels;
@XmlAttribute(name = "linkToAllViews")
protected Boolean linkToAllViews;
protected Boolean showLabels;
@XmlAttribute(name = "linkToAllViews")
protected Boolean linkToAllViews;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
@XmlAttribute(name = "includeGaps")
protected Boolean includeGaps;
@XmlAttribute(name = "matchGaps")
@XmlAttribute(name = "includeGaps")
protected Boolean includeGaps;
@XmlAttribute(name = "matchGaps")
@@
-3180,6
+3172,14
@@
public class JalviewModel {
protected Boolean includeGappedColumns;
@XmlAttribute(name = "denominateByShortestLength")
protected Boolean denominateByShortestLength;
protected Boolean includeGappedColumns;
@XmlAttribute(name = "denominateByShortestLength")
protected Boolean denominateByShortestLength;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
/**
* Gets the value of the sequencePoint property.
/**
* Gets the value of the sequencePoint property.
@@
-3528,195
+3528,195
@@
public class JalviewModel {
}
/**
}
/**
- * Gets the value of the width property.
+ * Gets the value of the includeGaps property.
*
* @return
* possible object is
*
* @return
* possible object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
*
*/
- public Integer getWidth() {
- return width;
+ public Boolean isIncludeGaps() {
+ return includeGaps;
}
/**
}
/**
- * Sets the value of the width property.
+ * Sets the value of the includeGaps property.
*
* @param value
* allowed object is
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
*
*/
- public void setWidth(Integer value) {
- this.width = value;
+ public void setIncludeGaps(Boolean value) {
+ this.includeGaps = value;
}
/**
}
/**
- * Gets the value of the height property.
+ * Gets the value of the matchGaps property.
*
* @return
* possible object is
*
* @return
* possible object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
*
*/
- public Integer getHeight() {
- return height;
+ public Boolean isMatchGaps() {
+ return matchGaps;
}
/**
}
/**
- * Sets the value of the height property.
+ * Sets the value of the matchGaps property.
*
* @param value
* allowed object is
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
*
*/
- public void setHeight(Integer value) {
- this.height = value;
+ public void setMatchGaps(Boolean value) {
+ this.matchGaps = value;
}
/**
}
/**
- * Gets the value of the xpos property.
+ * Gets the value of the includeGappedColumns property.
*
* @return
* possible object is
*
* @return
* possible object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
*
*/
- public Integer getXpos() {
- return xpos;
+ public Boolean isIncludeGappedColumns() {
+ return includeGappedColumns;
}
/**
}
/**
- * Sets the value of the xpos property.
+ * Sets the value of the includeGappedColumns property.
*
* @param value
* allowed object is
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
*
*/
- public void setXpos(Integer value) {
- this.xpos = value;
+ public void setIncludeGappedColumns(Boolean value) {
+ this.includeGappedColumns = value;
}
/**
}
/**
- * Gets the value of the ypos property.
+ * Gets the value of the denominateByShortestLength property.
*
* @return
* possible object is
*
* @return
* possible object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
*
*/
- public Integer getYpos() {
- return ypos;
+ public Boolean isDenominateByShortestLength() {
+ return denominateByShortestLength;
}
/**
}
/**
- * Sets the value of the ypos property.
+ * Sets the value of the denominateByShortestLength property.
*
* @param value
* allowed object is
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
*
*/
- public void setYpos(Integer value) {
- this.ypos = value;
+ public void setDenominateByShortestLength(Boolean value) {
+ this.denominateByShortestLength = value;
}
/**
}
/**
- * Gets the value of the includeGaps property.
+ * Gets the value of the width property.
*
* @return
* possible object is
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
*
*/
- public Boolean isIncludeGaps() {
- return includeGaps;
+ public Integer getWidth() {
+ return width;
}
/**
}
/**
- * Sets the value of the includeGaps property.
+ * Sets the value of the width property.
*
* @param value
* allowed object is
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
*
*/
- public void setIncludeGaps(Boolean value) {
- this.includeGaps = value;
+ public void setWidth(Integer value) {
+ this.width = value;
}
/**
}
/**
- * Gets the value of the matchGaps property.
+ * Gets the value of the height property.
*
* @return
* possible object is
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
*
*/
- public Boolean isMatchGaps() {
- return matchGaps;
+ public Integer getHeight() {
+ return height;
}
/**
}
/**
- * Sets the value of the matchGaps property.
+ * Sets the value of the height property.
*
* @param value
* allowed object is
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
*
*/
- public void setMatchGaps(Boolean value) {
- this.matchGaps = value;
+ public void setHeight(Integer value) {
+ this.height = value;
}
/**
}
/**
- * Gets the value of the includeGappedColumns property.
+ * Gets the value of the xpos property.
*
* @return
* possible object is
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
*
*/
- public Boolean isIncludeGappedColumns() {
- return includeGappedColumns;
+ public Integer getXpos() {
+ return xpos;
}
/**
}
/**
- * Sets the value of the includeGappedColumns property.
+ * Sets the value of the xpos property.
*
* @param value
* allowed object is
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
*
*/
- public void setIncludeGappedColumns(Boolean value) {
- this.includeGappedColumns = value;
+ public void setXpos(Integer value) {
+ this.xpos = value;
}
/**
}
/**
- * Gets the value of the denominateByShortestLength property.
+ * Gets the value of the ypos property.
*
* @return
* possible object is
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
*
*/
- public Boolean isDenominateByShortestLength() {
- return denominateByShortestLength;
+ public Integer getYpos() {
+ return ypos;
}
/**
}
/**
- * Sets the value of the denominateByShortestLength property.
+ * Sets the value of the ypos property.
*
* @param value
* allowed object is
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
*
*/
- public void setDenominateByShortestLength(Boolean value) {
- this.denominateByShortestLength = value;
+ public void setYpos(Integer value) {
+ this.ypos = value;
}
}
diff --git
a/src/jalview/xml/binding/jalview/JalviewUserColours.java
b/src/jalview/xml/binding/jalview/JalviewUserColours.java
index
5362365
..
b1b45da
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/MapListType.java
b/src/jalview/xml/binding/jalview/MapListType.java
index
9771383
..
b2ff435
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/Mapping.java
b/src/jalview/xml/binding/jalview/Mapping.java
index
611c450
..
08550f3
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 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.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;
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>
* </element>
* </choice>
* </sequence>
+ * <attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" />
* </extension>
* </complexContent>
* </complexType>
* </extension>
* </complexContent>
* </complexType>
@@
-61,6
+63,8
@@
public class Mapping
@XmlElement(name = "Sequence")
protected Sequence sequence;
protected String dseqFor;
@XmlElement(name = "Sequence")
protected Sequence sequence;
protected String dseqFor;
+ @XmlAttribute(name = "mappingType")
+ protected String mappingType;
/**
* Gets the value of the sequence property.
/**
* Gets the value of the sequence property.
@@
-110,4
+114,28
@@
public class Mapping
this.dseqFor = value;
}
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
0e9159c
..
b11e574
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/ObjectFactory.java
b/src/jalview/xml/binding/jalview/ObjectFactory.java
index
df3ee93
..
6e31dfe
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/PcaDataType.java
b/src/jalview/xml/binding/jalview/PcaDataType.java
index
2db832a
..
f7c8654
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/Pdbentry.java
b/src/jalview/xml/binding/jalview/Pdbentry.java
index
a013503
..
3d31e8d
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/Sequence.java
b/src/jalview/xml/binding/jalview/Sequence.java
index
2f1aada
..
d228d6d
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
@@
-44,6
+44,7
@@
import javax.xml.bind.annotation.XmlType;
* </element>
* </sequence>
* <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
* </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>
* </extension>
* </complexContent>
* </complexType>
@@
-64,6
+65,8
@@
public class Sequence
protected List<Sequence.DBRef> dbRef;
@XmlAttribute(name = "dsseqid")
protected String dsseqid;
protected List<Sequence.DBRef> dbRef;
@XmlAttribute(name = "dsseqid")
protected String dsseqid;
+ @XmlAttribute(name = "biotype")
+ protected String biotype;
/**
* Gets the value of the dbRef property.
/**
* Gets the value of the dbRef property.
@@
-118,6
+121,30
@@
public class Sequence
this.dsseqid = value;
}
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;
+ }
+
/**
* <p>Java class for anonymous complex type.
/**
* <p>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
00eb15e
..
6053e27
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/SequenceType.java
b/src/jalview/xml/binding/jalview/SequenceType.java
index
97176a8
..
305b5a1
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/ThresholdType.java
b/src/jalview/xml/binding/jalview/ThresholdType.java
index
704b020
..
89aa050
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/VAMSAS.java
b/src/jalview/xml/binding/jalview/VAMSAS.java
index
25f2d97
..
e1a6f68
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
index
2bfd3e0
..
acafd21
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
//
diff --git
a/src/jalview/xml/binding/jalview/package-info.java
b/src/jalview/xml/binding/jalview/package-info.java
index
e7464ad
..
c759814
100644
(file)
--- 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 01:41:05 PM BST
+// Generated on: 2019.06.07 at 02:01:32 PM BST
//
@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
//
@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)