From a3af95d79b82dad26b033d8bae458d4bffe9a95c Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 8 Nov 2019 09:32:22 +0000 Subject: [PATCH] JAL-3081 schema and binding class changes to save annotation sort order --- schemas/jalview.xsd | 4 +- src/jalview/xml/binding/jalview/JalviewModel.java | 206 +++++++++++++-------- 2 files changed, 134 insertions(+), 76 deletions(-) diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index 07dee98..777afa3 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -11,7 +11,7 @@ GNU General Public License along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> @@ -418,6 +418,8 @@ + + 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: 2019.11.07 at 02:47:42 PM GMT // @@ -187,6 +187,8 @@ import javax.xml.datatype.XMLGregorianCalendar; * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showAutocalcAbove" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="sortAnnotationsBy" type="{http://www.w3.org/2001/XMLSchema}string" /> * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> @@ -292,8 +294,8 @@ import javax.xml.datatype.XMLGregorianCalendar; * </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}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" /> @@ -3106,8 +3108,8 @@ public class JalviewModel { * </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}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" /> @@ -3162,14 +3164,6 @@ public class JalviewModel { 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") @@ -3178,6 +3172,14 @@ public class JalviewModel { 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. @@ -3526,195 +3528,195 @@ public class JalviewModel { } /** - * Gets the value of the width property. + * Gets the value of the includeGaps property. * * @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 - * {@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 - * {@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 - * {@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 - * {@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 - * {@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 - * {@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 - * {@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 - * {@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 - * {@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 - * {@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 - * {@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 - * {@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 - * {@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 - * {@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 - * {@link Boolean } + * {@link Integer } * */ - public void setDenominateByShortestLength(Boolean value) { - this.denominateByShortestLength = value; + public void setYpos(Integer value) { + this.ypos = value; } @@ -4787,6 +4789,8 @@ public class JalviewModel { * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showAutocalcAbove" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="sortAnnotationsBy" type="{http://www.w3.org/2001/XMLSchema}string" /> * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> @@ -4869,6 +4873,10 @@ public class JalviewModel { protected Boolean followSelection; @XmlAttribute(name = "showAnnotation") protected Boolean showAnnotation; + @XmlAttribute(name = "showAutocalcAbove") + protected Boolean showAutocalcAbove; + @XmlAttribute(name = "sortAnnotationsBy") + protected String sortAnnotationsBy; @XmlAttribute(name = "centreColumnLabels") protected Boolean centreColumnLabels; @XmlAttribute(name = "showGroupConservation") @@ -5498,6 +5506,54 @@ public class JalviewModel { } /** + * Gets the value of the showAutocalcAbove property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowAutocalcAbove() { + return showAutocalcAbove; + } + + /** + * Sets the value of the showAutocalcAbove property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowAutocalcAbove(Boolean value) { + this.showAutocalcAbove = value; + } + + /** + * Gets the value of the sortAnnotationsBy property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getSortAnnotationsBy() { + return sortAnnotationsBy; + } + + /** + * Sets the value of the sortAnnotationsBy property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setSortAnnotationsBy(String value) { + this.sortAnnotationsBy = value; + } + + /** * Gets the value of the centreColumnLabels property. * * @return -- 1.7.10.2