*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours" xmlns:jv="www.jalview.org" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours" xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
<xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
+ <xs:import namespace="www.jalview.org/xml/wsparamset" schemaLocation="JalviewWsParamSet.xsd"/>
<xs:complexType name="JalviewModel">
<xs:sequence>
- <xs:element name="creationDate" type="xs:dateTime"/>
- <xs:element name="version" type="xs:string"/>
- <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>
+ <xs:element name="creationDate" type="xs:dateTime" />
+ <xs:element name="version" type="xs:string" />
+ <xs:element name="vamsasModel" type="vamsas:VAMSAS" />
<xs:sequence>
<xs:element name="JSeq" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element name="features" type="jv:feature" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="pdbids" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="features"
+ type="jv:feature" minOccurs="0" maxOccurs="unbounded" />
+ <xs:element name="pdbids" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
<xs:complexContent>
- <xs:extension base="jv:pdbentry">
+ <xs:extension
+ base="jv:pdbentry">
<xs:sequence>
- <xs:element name="structureState" minOccurs="0" maxOccurs="unbounded">
+ <xs:element
+ name="structureState" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
<xs:simpleContent>
- <xs:extension base="xs:string">
- <xs:attributeGroup ref="jv:swingwindow"/>
- <xs:attribute name="visible" type="xs:boolean"/>
- <xs:attribute name="viewId" type="xs:string" use="optional">
+ <xs:extension
+ base="xs:string">
+ <xs:attributeGroup
+ ref="jv:swingwindow" />
+ <xs:attribute
+ name="visible" type="xs:boolean" />
+ <xs:attribute
+ name="viewId" type="xs:string" use="optional">
<xs:annotation>
- <xs:documentation>additional identifier which properly disambiguates
- the structure view from any other view with the same attributes. This is not an ID,
- because it is possible to have many references to the same physical structure view
- from different sequences in an alignment. A structureState element citing the same
- viewId will appear for each instance.</xs:documentation>
+ <xs:documentation>
+ additional
+ identifier
+ which
+ properly
+ disambiguates
+ the
+ structure
+ view
+ from
+ any
+ other
+ view
+ with
+ the
+ same
+ attributes.
+ This
+ is
+ not
+ an
+ ID,
+ because
+ it
+ is
+ possible
+ to
+ have
+ many
+ references
+ to
+ the
+ same
+ physical
+ structure
+ view
+ from
+ different
+ sequences
+ in
+ an
+ alignment.
+ A
+ structureState
+ element
+ citing
+ the
+ same
+ viewId
+ will
+ appear
+ for
+ each
+ instance.
+ </xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="alignwithAlignPanel" type="xs:boolean" use="optional" default="true">
- <xs:annotation>
- <xs:documentation>
- Flag set if the alignment panel containing this JSeq should be included in those used to perform a structure superposition (since Jalview 2.7).
- </xs:documentation>
- </xs:annotation>
+ <xs:attribute
+ name="alignwithAlignPanel" type="xs:boolean"
+ use="optional" default="true">
+ <xs:annotation>
+ <xs:documentation>
+ Flag
+ set
+ if
+ the
+ alignment
+ panel
+ containing
+ this
+ JSeq
+ should
+ be
+ included
+ in
+ those
+ used
+ to
+ perform
+ a
+ structure
+ superposition
+ (since
+ Jalview
+ 2.7).
+ </xs:documentation>
+ </xs:annotation>
</xs:attribute>
- <xs:attribute name="colourwithAlignPanel" type="xs:boolean" use="optional" default="false">
- <xs:annotation>
- <xs:documentation>
- Flag set if the alignment panel containing this JSeq should be included in those used to colour its associated sequences in this structureState(since Jalview 2.7).
- </xs:documentation>
- </xs:annotation>
+ <xs:attribute
+ name="colourwithAlignPanel" type="xs:boolean"
+ use="optional" default="false">
+ <xs:annotation>
+ <xs:documentation>
+ Flag
+ set
+ if
+ the
+ alignment
+ panel
+ containing
+ this
+ JSeq
+ should
+ be
+ included
+ in
+ those
+ used
+ to
+ colour
+ its
+ associated
+ sequences
+ in
+ this
+ structureState(since
+ Jalview
+ 2.7).
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute
+ name="colourByJmol" type="xs:boolean" use="optional"
+ default="true">
+ <xs:annotation>
+ <xs:documentation>
+ Flag
+ set
+ if
+ the
+ structure
+ display
+ is
+ coloured
+ by
+ the
+ Jmol
+ state,
+ rather
+ than
+ by
+ one
+ or
+ more
+ linked
+ alignment
+ views.
+ </xs:documentation>
+ </xs:annotation>
</xs:attribute>
- <xs:attribute name="colourByJmol" type="xs:boolean" use="optional" default="true">
- <xs:annotation><xs:documentation>
- Flag set if the structure display is coloured by the Jmol state, rather than by one or more linked alignment views.
- </xs:documentation></xs:annotation></xs:attribute>
-
+
</xs:extension>
- </xs:simpleContent>
+ </xs:simpleContent>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexContent>
</xs:complexType>
</xs:element>
- <xs:element name="hiddenSequences" type="xs:int" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="hiddenSequences"
+ type="xs:int" minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
- <xs:attribute name="colour" type="xs:int" use="optional"/>
- <xs:attribute name="start" type="xs:int" use="required"/>
- <xs:attribute name="end" type="xs:int" use="required"/>
- <xs:attribute name="id" type="xs:string" use="required"/>
- <xs:attribute name="hidden" type="xs:boolean"/>
+ <xs:attribute name="colour" type="xs:int"
+ use="optional" />
+ <xs:attribute name="start" type="xs:int"
+ use="required" />
+ <xs:attribute name="end" type="xs:int"
+ use="required" />
+ <xs:attribute name="id" type="xs:string"
+ use="required" />
+ <xs:attribute name="hidden" type="xs:boolean" />
</xs:complexType>
</xs:element>
- <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="JGroup" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element name="seq" type="xs:string" maxOccurs="unbounded"/>
+ <xs:element name="seq" type="xs:string"
+ maxOccurs="unbounded" />
</xs:sequence>
- <xs:attribute name="start" type="xs:int"/>
- <xs:attribute name="end" type="xs:int"/>
- <xs:attribute name="name" type="xs:string"/>
- <xs:attribute name="colour" type="xs:string"/>
- <xs:attribute name="consThreshold" type="xs:int"/>
- <xs:attribute name="pidThreshold" type="xs:int"/>
- <xs:attribute name="outlineColour" type="xs:int"/>
- <xs:attribute name="displayBoxes" type="xs:boolean"/>
- <xs:attribute name="displayText" type="xs:boolean"/>
- <xs:attribute name="colourText" type="xs:boolean"/>
- <xs:attribute name="textCol1" type="xs:int"/>
- <xs:attribute name="textCol2" type="xs:int"/>
- <xs:attribute name="textColThreshold" type="xs:int"/>
- <xs:attribute name="showUnconserved" type="xs:boolean" use="optional"/>
- <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean" use="optional" default="true"/>
- <xs:attribute name="showConsensusHistogram" type="xs:boolean" use="optional" default="true"/>
- <xs:attribute name="showSequenceLogo" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="id" type="xs:string" use="optional"><xs:annotation>
- <xs:documentation>
- Optional sequence group ID (only needs to be unique for this alignment)
- </xs:documentation>
- </xs:annotation></xs:attribute>
+ <xs:attribute name="start" type="xs:int" />
+ <xs:attribute name="end" type="xs:int" />
+ <xs:attribute name="name" type="xs:string" />
+ <xs:attribute name="colour" type="xs:string" />
+ <xs:attribute name="consThreshold"
+ type="xs:int" />
+ <xs:attribute name="pidThreshold" type="xs:int" />
+ <xs:attribute name="outlineColour"
+ type="xs:int" />
+ <xs:attribute name="displayBoxes"
+ type="xs:boolean" />
+ <xs:attribute name="displayText"
+ type="xs:boolean" />
+ <xs:attribute name="colourText"
+ type="xs:boolean" />
+ <xs:attribute name="textCol1" type="xs:int" />
+ <xs:attribute name="textCol2" type="xs:int" />
+ <xs:attribute name="textColThreshold"
+ type="xs:int" />
+ <xs:attribute name="showUnconserved"
+ type="xs:boolean" use="optional" />
+ <xs:attribute name="ignoreGapsinConsensus"
+ type="xs:boolean" use="optional" default="true" />
+ <xs:attribute name="showConsensusHistogram"
+ type="xs:boolean" use="optional" default="true" />
+ <xs:attribute name="showSequenceLogo"
+ type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="id" type="xs:string"
+ use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ Optional sequence group ID (only
+ needs to be unique for this
+ alignment)
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="Viewport" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element name="AnnotationColours" minOccurs="0">
+ <xs:element name="AnnotationColours"
+ minOccurs="0">
<xs:complexType>
- <xs:attribute name="aboveThreshold" type="xs:int"/>
- <xs:attribute name="annotation" type="xs:string"/>
- <xs:attribute name="minColour" type="xs:int"/>
- <xs:attribute name="maxColour" type="xs:int"/>
- <xs:attribute name="colourScheme" type="xs:string"/>
- <xs:attribute name="threshold" type="xs:float"/>
+ <xs:attribute name="aboveThreshold"
+ type="xs:int" />
+ <xs:attribute name="annotation"
+ type="xs:string" />
+ <xs:attribute name="minColour"
+ type="xs:int" />
+ <xs:attribute name="maxColour"
+ type="xs:int" />
+ <xs:attribute name="colourScheme"
+ type="xs:string" />
+ <xs:attribute name="threshold"
+ type="xs:float" />
</xs:complexType>
</xs:element>
- <xs:element name="hiddenColumns" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="hiddenColumns"
+ minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
- <xs:attribute name="start" type="xs:int"/>
- <xs:attribute name="end" type="xs:int"/>
+ <xs:attribute name="start"
+ type="xs:int" />
+ <xs:attribute name="end"
+ type="xs:int" />
</xs:complexType>
</xs:element>
+ <xs:element name="calcIdParam"
+
+ minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="jvws:WebServiceParameterSet">
+ <xs:attribute name="calcId" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation>handle for the calculation which uses this parameter set</xs:documentation></xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="needsUpdate" type="xs:boolean" use="optional" default="false">
+ <xs:annotation><xs:documentation>should the calculation be performed immediately after loading in order to refresh results</xs:documentation></xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="autoUpdate" type="xs:boolean" use="required">
+ <xs:annotation><xs:documentation>should the calculation be automatically performed on edits</xs:documentation></xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
</xs:sequence>
- <xs:attributeGroup ref="jv:swingwindow"/>
- <xs:attribute name="conservationSelected" type="xs:boolean"/>
- <xs:attribute name="pidSelected" type="xs:boolean"/>
- <xs:attribute name="bgColour" type="xs:string"/>
- <xs:attribute name="consThreshold" type="xs:int"/>
- <xs:attribute name="pidThreshold" type="xs:int"/>
- <xs:attribute name="title" type="xs:string"/>
- <xs:attribute name="showFullId" type="xs:boolean"/>
- <xs:attribute name="rightAlignIds" type="xs:boolean"/>
- <xs:attribute name="showText" type="xs:boolean"/>
- <xs:attribute name="showColourText" type="xs:boolean"/>
- <xs:attribute name="showUnconserved" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="showBoxes" type="xs:boolean"/>
- <xs:attribute name="wrapAlignment" type="xs:boolean"/>
- <xs:attribute name="renderGaps" type="xs:boolean"/>
- <xs:attribute name="showSequenceFeatures" type="xs:boolean"/>
- <xs:attribute name="showNPfeatureTooltip" type="xs:boolean" use="optional"/>
- <xs:attribute name="showDbRefTooltip" type="xs:boolean" use="optional"/>
- <xs:attribute name="followHighlight" type="xs:boolean" use="optional" default="true"/>
- <xs:attribute name="followSelection" type="xs:boolean" use="optional" default="true"/>
- <xs:attribute name="showAnnotation" type="xs:boolean"/>
- <xs:attribute name="centreColumnLabels" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="showGroupConservation" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="showGroupConsensus" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="showConsensusHistogram" type="xs:boolean" use="optional" default="true"/>
- <xs:attribute name="showSequenceLogo" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean" use="optional" default="true"/>
-
- <xs:attribute name="startRes" type="xs:int"/>
- <xs:attribute name="startSeq" type="xs:int"/>
- <xs:attribute name="fontName" type="xs:string"/>
- <xs:attribute name="fontSize" type="xs:int"/>
- <xs:attribute name="fontStyle" type="xs:int"/>
- <xs:attribute name="viewName" type="xs:string"/>
- <xs:attribute name="sequenceSetId" type="xs:string"/>
- <xs:attribute name="gatheredViews" type="xs:boolean"/>
- <xs:attribute name="textCol1" type="xs:int"/>
- <xs:attribute name="textCol2" type="xs:int"/>
- <xs:attribute name="textColThreshold" type="xs:int"/>
- <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:attributeGroup ref="jv:swingwindow" />
+ <xs:attribute name="conservationSelected"
+ type="xs:boolean" />
+ <xs:attribute name="pidSelected"
+ type="xs:boolean" />
+ <xs:attribute name="bgColour" type="xs:string" />
+ <xs:attribute name="consThreshold"
+ type="xs:int" />
+ <xs:attribute name="pidThreshold" type="xs:int" />
+ <xs:attribute name="title" type="xs:string" />
+ <xs:attribute name="showFullId"
+ type="xs:boolean" />
+ <xs:attribute name="rightAlignIds"
+ type="xs:boolean" />
+ <xs:attribute name="showText" type="xs:boolean" />
+ <xs:attribute name="showColourText"
+ type="xs:boolean" />
+ <xs:attribute name="showUnconserved"
+ type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="showBoxes"
+ type="xs:boolean" />
+ <xs:attribute name="wrapAlignment"
+ type="xs:boolean" />
+ <xs:attribute name="renderGaps"
+ type="xs:boolean" />
+ <xs:attribute name="showSequenceFeatures"
+ type="xs:boolean" />
+ <xs:attribute name="showNPfeatureTooltip"
+ type="xs:boolean" use="optional" />
+ <xs:attribute name="showDbRefTooltip"
+ type="xs:boolean" use="optional" />
+ <xs:attribute name="followHighlight"
+ type="xs:boolean" use="optional" default="true" />
+ <xs:attribute name="followSelection"
+ type="xs:boolean" use="optional" default="true" />
+ <xs:attribute name="showAnnotation"
+ type="xs:boolean" />
+ <xs:attribute name="centreColumnLabels"
+ type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="showGroupConservation"
+ type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="showGroupConsensus"
+ type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="showConsensusHistogram"
+ type="xs:boolean" use="optional" default="true" />
+ <xs:attribute name="showSequenceLogo"
+ type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="ignoreGapsinConsensus"
+ type="xs:boolean" use="optional" default="true" />
+
+ <xs:attribute name="startRes" type="xs:int" />
+ <xs:attribute name="startSeq" type="xs:int" />
+ <xs:attribute name="fontName" type="xs:string" />
+ <xs:attribute name="fontSize" type="xs:int" />
+ <xs:attribute name="fontStyle" type="xs:int" />
+ <xs:attribute name="viewName" type="xs:string" />
+ <xs:attribute name="sequenceSetId"
+ type="xs:string" />
+ <xs:attribute name="gatheredViews"
+ type="xs:boolean" />
+ <xs:attribute name="textCol1" type="xs:int" />
+ <xs:attribute name="textCol2" type="xs:int" />
+ <xs:attribute name="textColThreshold"
+ type="xs:int" />
+ <xs:attribute name="id" type="xs:ID"
+ use="optional">
<xs:annotation>
<xs:documentation>
- unique id used by jalview to synchronize between stored and instantiated views
+ unique id used by jalview to
+ synchronize between stored and
+ instantiated views
</xs:documentation>
</xs:annotation>
</xs:attribute>
- </xs:complexType>
+ </xs:complexType>
</xs:element>
- <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="UserColours" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
+ <xs:element name="UserColourScheme"
+ type="jalview:JalviewUserColours" />
</xs:sequence>
- <xs:attribute name="id" type="xs:string"/>
+ <xs:attribute name="id" type="xs:string" />
</xs:complexType>
</xs:element>
- <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="tree" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
- <xs:sequence minOccurs="0">
- <xs:element name="title" type="xs:string"/>
- <xs:element name="newick" type="xs:string"/>
- </xs:sequence>
- <xs:attribute name="fontName" type="xs:string"/>
- <xs:attribute name="fontSize" type="xs:int"/>
- <xs:attribute name="fontStyle" type="xs:int"/>
- <xs:attribute name="threshold" type="xs:float"/>
- <xs:attribute name="showBootstrap" type="xs:boolean"/>
- <xs:attribute name="showDistances" type="xs:boolean"/>
- <xs:attribute name="markUnlinked" type="xs:boolean"/>
- <xs:attribute name="fitToWindow" type="xs:boolean"/>
- <xs:attribute name="currentTree" type="xs:boolean"/>
- <xs:attribute name="id" type="xs:ID" use="optional">
- <xs:annotation><xs:documentation>Tree ID added for binding tree visualization settings to vamsas document trees in jalview 2.4.1</xs:documentation></xs:annotation>
- </xs:attribute>
- <xs:attributeGroup ref="jv:swingwindow"/>
- </xs:complexType>
+ <xs:sequence minOccurs="0">
+ <xs:element name="title" type="xs:string" />
+ <xs:element name="newick" type="xs:string" />
+ </xs:sequence>
+ <xs:attribute name="fontName" type="xs:string" />
+ <xs:attribute name="fontSize" type="xs:int" />
+ <xs:attribute name="fontStyle" type="xs:int" />
+ <xs:attribute name="threshold" type="xs:float" />
+ <xs:attribute name="showBootstrap"
+ type="xs:boolean" />
+ <xs:attribute name="showDistances"
+ type="xs:boolean" />
+ <xs:attribute name="markUnlinked"
+ type="xs:boolean" />
+ <xs:attribute name="fitToWindow"
+ type="xs:boolean" />
+ <xs:attribute name="currentTree"
+ type="xs:boolean" />
+ <xs:attribute name="id" type="xs:ID"
+ use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ Tree ID added for binding tree
+ visualization settings to vamsas
+ document trees in jalview 2.4.1
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attributeGroup ref="jv:swingwindow" />
+ </xs:complexType>
</xs:element>
<xs:element name="FeatureSettings" minOccurs="0">
<xs:complexType>
<xs:sequence>
- <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="setting" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
- <xs:attribute name="type" type="xs:string" use="required"/>
- <xs:attribute name="colour" type="xs:int" use="required"/>
- <xs:attribute name="display" type="xs:boolean" use="required"/>
- <xs:attribute name="order" type="xs:float" use="optional"/>
- <xs:attribute name="mincolour" type="xs:int" use="optional">
- <xs:annotation><xs:documentation>Optional minimum colour for graduated feature colour</xs:documentation>
- </xs:annotation></xs:attribute>
- <xs:attribute name="threshold" type="xs:float" use="optional">
- <xs:annotation><xs:documentation>threshold value for graduated feature colour</xs:documentation>
- </xs:annotation></xs:attribute>
- <xs:attribute name="threshstate" type="xs:int" use="optional">
- <xs:annotation><xs:documentation>threshold type for graduated feature colour</xs:documentation>
- </xs:annotation></xs:attribute>
- <xs:attribute name="max" type="xs:float" use="optional"/>
- <xs:attribute name="min" type="xs:float" use="optional"/>
- <xs:attribute name="colourByLabel" type="xs:boolean" use="optional"/>
- <xs:attribute name="autoScale" type="xs:boolean" use="optional"/>
- </xs:complexType>
+ <xs:attribute name="type"
+ type="xs:string" use="required" />
+ <xs:attribute name="colour"
+ type="xs:int" use="required" />
+ <xs:attribute name="display"
+ type="xs:boolean" use="required" />
+ <xs:attribute name="order"
+ type="xs:float" use="optional" />
+ <xs:attribute name="mincolour"
+ type="xs:int" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ Optional minimum colour
+ for graduated feature
+ colour
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="threshold"
+ type="xs:float" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ threshold value for
+ graduated feature colour
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="threshstate"
+ type="xs:int" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ threshold type for
+ graduated feature colour
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="max"
+ type="xs:float" use="optional" />
+ <xs:attribute name="min"
+ type="xs:float" use="optional" />
+ <xs:attribute name="colourByLabel"
+ type="xs:boolean" use="optional" />
+ <xs:attribute name="autoScale"
+ type="xs:boolean" use="optional" />
+ </xs:complexType>
</xs:element>
- <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="group" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
- <xs:attribute name="name" type="xs:string" use="required"/>
- <xs:attribute name="display" type="xs:boolean" use="required"/>
+ <xs:attribute name="name"
+ type="xs:string" use="required" />
+ <xs:attribute name="display"
+ type="xs:boolean" use="required" />
</xs:complexType>
</xs:element>
</xs:sequence>
-#Thu May 24 20:06:46 BST 2012
+#Fri Jul 06 18:02:04 BST 2012
jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor
jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor
+jalview.schemabinding.version2.CalcIdParam=jalview.schemabinding.version2.descriptors.CalcIdParamDescriptor
jalview.schemabinding.version2.Tree=jalview.schemabinding.version2.descriptors.TreeDescriptor
jalview.schemabinding.version2.JalviewModel=jalview.schemabinding.version2.descriptors.JalviewModelDescriptor
jalview.schemabinding.version2.SequenceType=jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor
jalview.schemabinding.version2.DBRef=jalview.schemabinding.version2.descriptors.DBRefDescriptor
jalview.schemabinding.version2.AlcodMap=jalview.schemabinding.version2.descriptors.AlcodMapDescriptor
jalview.schemabinding.version2.Annotation=jalview.schemabinding.version2.descriptors.AnnotationDescriptor
+jalview.schemabinding.version2.Wsparameters=jalview.schemabinding.version2.descriptors.WsparametersDescriptor
jalview.schemabinding.version2.JSeq=jalview.schemabinding.version2.descriptors.JSeqDescriptor
jalview.schemabinding.version2.Sequence=jalview.schemabinding.version2.descriptors.SequenceDescriptor
jalview.schemabinding.version2.WebServiceParameterSet=jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor
jalview.schemabinding.version2.Colour=jalview.schemabinding.version2.descriptors.ColourDescriptor
jalview.schemabinding.version2.MapListFrom=jalview.schemabinding.version2.descriptors.MapListFromDescriptor
jalview.schemabinding.version2.PdbentryItem=jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor
-jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor
jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor
-jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor
-jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor
+jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor
jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor
+jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor
+jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor
jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor
jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor
-jalview.schemabinding.version2.DseqFor=jalview.schemabinding.version2.descriptors.DseqForDescriptor
jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor
+jalview.schemabinding.version2.DseqFor=jalview.schemabinding.version2.descriptors.DseqForDescriptor
jalview.schemabinding.version2.VAMSAS=jalview.schemabinding.version2.descriptors.VAMSASDescriptor
jalview.schemabinding.version2.MappingChoiceItem=jalview.schemabinding.version2.descriptors.MappingChoiceItemDescriptor
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class CalcIdParam.
+ *
+ * @version $Revision$ $Date$
+ */
+public class CalcIdParam extends WebServiceParameterSet
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * handle for the calculation which uses this parameter set
+ */
+ private java.lang.String _calcId;
+
+ /**
+ * should the calculation be performed immediately after
+ * loading in order to refresh results
+ */
+ private boolean _needsUpdate = false;
+
+ /**
+ * keeps track of state for field: _needsUpdate
+ */
+ private boolean _has_needsUpdate;
+
+ /**
+ * should the calculation be automatically performed on edits
+ */
+ private boolean _autoUpdate;
+
+ /**
+ * keeps track of state for field: _autoUpdate
+ */
+ private boolean _has_autoUpdate;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public CalcIdParam() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteAutoUpdate(
+ ) {
+ this._has_autoUpdate= false;
+ }
+
+ /**
+ */
+ public void deleteNeedsUpdate(
+ ) {
+ this._has_needsUpdate= false;
+ }
+
+ /**
+ * Returns the value of field 'autoUpdate'. The field
+ * 'autoUpdate' has the following description: should the
+ * calculation be automatically performed on edits
+ *
+ * @return the value of field 'AutoUpdate'.
+ */
+ public boolean getAutoUpdate(
+ ) {
+ return this._autoUpdate;
+ }
+
+ /**
+ * Returns the value of field 'calcId'. The field 'calcId' has
+ * the following description: handle for the calculation which
+ * uses this parameter set
+ *
+ * @return the value of field 'CalcId'.
+ */
+ public java.lang.String getCalcId(
+ ) {
+ return this._calcId;
+ }
+
+ /**
+ * Returns the value of field 'needsUpdate'. The field
+ * 'needsUpdate' has the following description: should the
+ * calculation be performed immediately after loading in order
+ * to refresh results
+ *
+ * @return the value of field 'NeedsUpdate'.
+ */
+ public boolean getNeedsUpdate(
+ ) {
+ return this._needsUpdate;
+ }
+
+ /**
+ * Method hasAutoUpdate.
+ *
+ * @return true if at least one AutoUpdate has been added
+ */
+ public boolean hasAutoUpdate(
+ ) {
+ return this._has_autoUpdate;
+ }
+
+ /**
+ * Method hasNeedsUpdate.
+ *
+ * @return true if at least one NeedsUpdate has been added
+ */
+ public boolean hasNeedsUpdate(
+ ) {
+ return this._has_needsUpdate;
+ }
+
+ /**
+ * Returns the value of field 'autoUpdate'. The field
+ * 'autoUpdate' has the following description: should the
+ * calculation be automatically performed on edits
+ *
+ * @return the value of field 'AutoUpdate'.
+ */
+ public boolean isAutoUpdate(
+ ) {
+ return this._autoUpdate;
+ }
+
+ /**
+ * Returns the value of field 'needsUpdate'. The field
+ * 'needsUpdate' has the following description: should the
+ * calculation be performed immediately after loading in order
+ * to refresh results
+ *
+ * @return the value of field 'NeedsUpdate'.
+ */
+ public boolean isNeedsUpdate(
+ ) {
+ return this._needsUpdate;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'autoUpdate'. The field 'autoUpdate'
+ * has the following description: should the calculation be
+ * automatically performed on edits
+ *
+ * @param autoUpdate the value of field 'autoUpdate'.
+ */
+ public void setAutoUpdate(
+ final boolean autoUpdate) {
+ this._autoUpdate = autoUpdate;
+ this._has_autoUpdate = true;
+ }
+
+ /**
+ * Sets the value of field 'calcId'. The field 'calcId' has the
+ * following description: handle for the calculation which uses
+ * this parameter set
+ *
+ * @param calcId the value of field 'calcId'.
+ */
+ public void setCalcId(
+ final java.lang.String calcId) {
+ this._calcId = calcId;
+ }
+
+ /**
+ * Sets the value of field 'needsUpdate'. The field
+ * 'needsUpdate' has the following description: should the
+ * calculation be performed immediately after loading in order
+ * to refresh results
+ *
+ * @param needsUpdate the value of field 'needsUpdate'.
+ */
+ public void setNeedsUpdate(
+ final boolean needsUpdate) {
+ this._needsUpdate = needsUpdate;
+ this._has_needsUpdate = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.CalcIdParam
+ */
+ public static jalview.schemabinding.version2.CalcIdParam unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.CalcIdParam) Unmarshaller.unmarshal(jalview.schemabinding.version2.CalcIdParam.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- *******************************************************************************/
/*
* This class was automatically generated with
* <a href="http://www.castor.org">Castor 1.1</a>, using an XML
private boolean _has_textColThreshold;
/**
- * unique id used by jalview to synchronize between stored and
- * instantiated views
+ * unique id used by jalview to
+ * synchronize between stored and
+ * instantiated views
*
*/
private java.lang.String _id;
*/
private java.util.Vector _hiddenColumnsList;
+ /**
+ * Field _calcIdParamList.
+ */
+ private java.util.Vector _calcIdParamList;
+
//----------------/
//- Constructors -/
public Viewport() {
super();
this._hiddenColumnsList = new java.util.Vector();
+ this._calcIdParamList = new java.util.Vector();
}
/**
*
*
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException {
+ this._calcIdParamList.addElement(vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addCalcIdParam(
+ final int index,
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException {
+ this._calcIdParamList.add(index, vCalcIdParam);
+ }
+
+ /**
+ *
+ *
* @param vHiddenColumns
* @throws java.lang.IndexOutOfBoundsException if the index
* given is outside the bounds of the collection
}
/**
+ * Method enumerateCalcIdParam.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.CalcIdParam elements
+ */
+ public java.util.Enumeration enumerateCalcIdParam(
+ ) {
+ return this._calcIdParamList.elements();
+ }
+
+ /**
* Method enumerateHiddenColumns.
*
* @return an Enumeration over all
}
/**
+ * Method getCalcIdParam.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the
+ * jalview.schemabinding.version2.CalcIdParam at the given index
+ */
+ public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._calcIdParamList.size()) {
+ throw new IndexOutOfBoundsException("getCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList.get(index);
+ }
+
+ /**
+ * Method getCalcIdParam.Returns the contents of the collection
+ * in an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam(
+ ) {
+ jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
+ return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList.toArray(array);
+ }
+
+ /**
+ * Method getCalcIdParamCount.
+ *
+ * @return the size of this collection
+ */
+ public int getCalcIdParamCount(
+ ) {
+ return this._calcIdParamList.size();
+ }
+
+ /**
* Returns the value of field 'centreColumnLabels'.
*
* @return the value of field 'CentreColumnLabels'.
/**
* Returns the value of field 'id'. The field 'id' has the
* following description: unique id used by jalview to
- * synchronize between stored and instantiated views
+ * synchronize between stored and
+ * instantiated views
*
*
* @return the value of field 'Id'.
/**
*/
+ public void removeAllCalcIdParam(
+ ) {
+ this._calcIdParamList.clear();
+ }
+
+ /**
+ */
public void removeAllHiddenColumns(
) {
this._hiddenColumnsList.clear();
}
/**
+ * Method removeCalcIdParam.
+ *
+ * @param vCalcIdParam
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) {
+ boolean removed = _calcIdParamList.remove(vCalcIdParam);
+ return removed;
+ }
+
+ /**
+ * Method removeCalcIdParamAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
+ final int index) {
+ java.lang.Object obj = this._calcIdParamList.remove(index);
+ return (jalview.schemabinding.version2.CalcIdParam) obj;
+ }
+
+ /**
* Method removeHiddenColumns.
*
* @param vHiddenColumns
}
/**
+ *
+ *
+ * @param index
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setCalcIdParam(
+ final int index,
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._calcIdParamList.size()) {
+ throw new IndexOutOfBoundsException("setCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
+ }
+
+ this._calcIdParamList.set(index, vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param vCalcIdParamArray
+ */
+ public void setCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) {
+ //-- copy array
+ _calcIdParamList.clear();
+
+ for (int i = 0; i < vCalcIdParamArray.length; i++) {
+ this._calcIdParamList.add(vCalcIdParamArray[i]);
+ }
+ }
+
+ /**
* Sets the value of field 'centreColumnLabels'.
*
* @param centreColumnLabels the value of field
/**
* Sets the value of field 'id'. The field 'id' has the
* following description: unique id used by jalview to
- * synchronize between stored and instantiated views
+ * synchronize between stored and
+ * instantiated views
*
*
* @param id the value of field 'id'.
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.CalcIdParam;
+
+/**
+ * Class CalcIdParamDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class CalcIdParamDescriptor extends jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public CalcIdParamDescriptor() {
+ super();
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "calcIdParam";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ //-- initialize attribute descriptors
+
+ //-- _calcId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_calcId", "calcId", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ CalcIdParam target = (CalcIdParam) object;
+ return target.getCalcId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ CalcIdParam target = (CalcIdParam) object;
+ target.setCalcId( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _calcId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ //-- _needsUpdate
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_needsUpdate", "needsUpdate", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ CalcIdParam target = (CalcIdParam) object;
+ if (!target.hasNeedsUpdate()) { return null; }
+ return (target.getNeedsUpdate() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ CalcIdParam target = (CalcIdParam) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteNeedsUpdate();
+ return;
+ }
+ target.setNeedsUpdate( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _needsUpdate
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _autoUpdate
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoUpdate", "autoUpdate", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ CalcIdParam target = (CalcIdParam) object;
+ if (!target.hasAutoUpdate()) { return null; }
+ return (target.getAutoUpdate() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ CalcIdParam target = (CalcIdParam) object;
+ // ignore null values for non optional primitives
+ if (value == null) { return; }
+
+ target.setAutoUpdate( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _autoUpdate
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode(
+ ) {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no
+ * identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(
+ ) {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass(
+ ) {
+ return jalview.schemabinding.version2.CalcIdParam.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix(
+ ) {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and
+ * unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI(
+ ) {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator(
+ ) {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName(
+ ) {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that
+ * of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition(
+ ) {
+ return _elementDefinition;
+ }
+
+}
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- *******************************************************************************/
/*
* This class was automatically generated with
* <a href="http://www.castor.org">Castor 1.1</a>, using an XML
{ //-- local scope
}
desc.setValidator(fieldValidator);
+ //-- _calcIdParamList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.CalcIdParam.class, "_calcIdParamList", "calcIdParam", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getCalcIdParam();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ target.addCalcIdParam( (jalview.schemabinding.version2.CalcIdParam) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
+ try {
+ Viewport target = (Viewport) object;
+ target.removeAllCalcIdParam();
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return new jalview.schemabinding.version2.CalcIdParam();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _calcIdParamList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
}
git://source.jalview.org / jalview.git / commitdiff