<?xml version="1.0" encoding="UTF-8"?>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
-<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"/>
+<!-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors * * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file. -->
+<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="JSeq" maxOccurs="unbounded" minOccurs="0">
<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"
+ <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
</xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute
- name="alignwithAlignPanel" type="xs:boolean"
- use="optional" default="true">
+ <xs:attribute name="alignwithAlignPanel"
+ type="xs:boolean" use="optional" default="true">
<xs:annotation>
<xs:documentation>
Flag
</xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute
- name="colourwithAlignPanel" type="xs:boolean"
- use="optional" default="false">
+ <xs:attribute name="colourwithAlignPanel"
+ type="xs:boolean" use="optional" default="false">
<xs:annotation>
<xs:documentation>
Flag
</xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute
- name="colourByJmol" type="xs:boolean" use="optional"
- default="true">
+ <xs:attribute name="colourByJmol" type="xs:boolean"
+ use="optional" default="true">
<xs:annotation>
<xs:documentation>
Flag
use="optional">
<xs:annotation>
<xs:documentation>
- An identifier for the viewer type, currently either
- JMOL or CHIMERA
+ An
+ identifier
+ for
+ the
+ viewer
+ type,
+ currently
+ either
+ JMOL
+ or
+ CHIMERA
</xs:documentation>
</xs:annotation>
</xs:attribute>
</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:element name="rnaViewer" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Reference to a viewer showing RNA structure
+ for this sequence. Schema supports one viewer showing multiple
+ annotations for multiple sequences, though currently only one
+ annotation for one sequence (gapped or trimmed) is used
+ </xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="secondaryStructure" minOccurs="1"
+ maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:attribute name="title" type="xs:string" />
+ <xs:attribute name="annotationId" type="xs:string"
+ use="required">
+ <xs:annotation>
+ <xs:documentation>id attribute of Annotation in
+ vamsasModel for
+ the secondary structure annotation shown
+ in the viewer
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="gapped" type="xs:boolean">
+ <xs:annotation>
+ <xs:documentation>if true the RNA structure is shown with gaps, if false without
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="viewerState" type="xs:string">
+ <xs:annotation>
+ <xs:documentation>name of the project jar entry that holds
+ the VARNA viewer state for the structure
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attributeGroup ref="jv:swingwindow" />
+ <xs:attribute name="title" type="xs:string" />
+ <xs:attribute name="viewId" type="xs:string">
+ <xs:annotation>
+ <xs:documentation>An id unique to the RNA viewer panel
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="dividerLocation" type="xs:int">
+ <xs:annotation>
+ <xs:documentation>horizontal position of split pane divider
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="selectedRna" type="xs:int">
+ <xs:annotation>
+ <xs:documentation>Index of the selected structure in the
+ viewer panel
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ </xs:element>
</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="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:sequence>
<xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
<xs:element name="annotationColours" type="jv:AnnotationColourScheme"
minOccurs="0" maxOccurs="1" />
<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="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="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="normaliseSequenceLogo"
- type="xs:boolean" use="optional" default="false" />
- <xs:attribute name="id" type="xs:string"
- use="optional">
+ <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="normaliseSequenceLogo" 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
+ needs to be
+ unique for this
alignment)
</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
- <xs:element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ <xs:element name="Viewport" maxOccurs="unbounded"
+ minOccurs="0">
<xs:complexType>
<xs:sequence>
- <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
+ <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
minOccurs="0" maxOccurs="1">
</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 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="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="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="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="normaliseSequenceLogo"
- 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="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="normaliseSequenceLogo" 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="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: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
+ synchronize
+ between stored and
instantiated views
</xs:documentation>
</xs:annotation>
use="optional">
<xs:annotation>
<xs:documentation>
- The viewport id of this viewport's (cdna/protein) coding complement, if any
+ The viewport id of this viewport's
+ (cdna/protein) coding complement, if any
</xs:documentation>
</xs:annotation>
</xs:attribute>
</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: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: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: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
+ visualization
+ settings to vamsas
document trees in jalview 2.4.1
</xs:documentation>
</xs:annotation>
<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: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
+ for graduated
+ feature
colour
</xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="threshold"
- type="xs:float" use="optional">
+ <xs:attribute name="threshold" type="xs:float"
+ use="optional">
<xs:annotation>
<xs:documentation>
threshold value for
</xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="threshstate"
- type="xs:int" use="optional">
+ <xs:attribute name="threshstate" type="xs:int"
+ use="optional">
<xs:annotation>
<xs:documentation>
threshold type for
</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: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>
<xs:sequence>
<xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
- <xs:attribute name="key" type="xs:string" use="required"/>
- <xs:attribute name="value" type="xs:string" use="required"/>
+ <xs:attribute name="key" type="xs:string" use="required" />
+ <xs:attribute name="value" type="xs:string" use="required" />
</xs:complexType>
</xs:element>
</xs:sequence>
- <xs:attribute name="begin" type="xs:int" use="required"/>
- <xs:attribute name="end" type="xs:int" use="required"/>
- <xs:attribute name="type" type="xs:string" use="required"/>
- <xs:attribute name="description" type="xs:string" use="optional"/>
- <xs:attribute name="status" type="xs:string" use="optional"/>
- <xs:attribute name="featureGroup" type="xs:string" use="optional"/>
- <xs:attribute name="score" type="xs:float" use="optional"/>
+ <xs:attribute name="begin" type="xs:int" use="required" />
+ <xs:attribute name="end" type="xs:int" use="required" />
+ <xs:attribute name="type" type="xs:string" use="required" />
+ <xs:attribute name="description" type="xs:string" use="optional" />
+ <xs:attribute name="status" type="xs:string" use="optional" />
+ <xs:attribute name="featureGroup" type="xs:string" use="optional" />
+ <xs:attribute name="score" type="xs:float" use="optional" />
</xs:complexType>
<xs:complexType name="pdbentry">
<xs:sequence minOccurs="0" maxOccurs="unbounded">
<xs:element name="property" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
- <xs:attribute name="name" type="xs:string" use="required"/>
- <xs:attribute name="value" type="xs:string" use="required"/>
+ <xs:attribute name="name" type="xs:string" use="required" />
+ <xs:attribute name="value" type="xs:string" use="required" />
</xs:complexType>
</xs:element>
</xs:sequence>
- <xs:attribute name="id" type="xs:string" use="required"/>
- <xs:attribute name="type" type="xs:string" use="optional"/>
- <xs:attribute name="file" type="xs:string"/>
+ <xs:attribute name="id" type="xs:string" use="required" />
+ <xs:attribute name="type" type="xs:string" use="optional" />
+ <xs:attribute name="file" type="xs:string" />
</xs:complexType>
- <!--
- <xs:complexType name="reportWindow">
- <xs:annotation>
- <xs:documentation>Generic type for windows containing mime-typed data associated with other jalview windows</xs:documentation>
- </xs:annotation>
- <xs:sequence>
- </xs:sequence>
- <xs:attribute name="id" type="xs:string" use="required"/>
- <xs:attribute name="type" type="xs:string" use="optional"/>
- <xs:attribute name="file" type="xs:string" use="optional"/>
+ <!-- <xs:complexType name="reportWindow"> <xs:annotation> <xs:documentation>Generic
+ type for windows containing mime-typed data associated with other jalview
+ windows</xs:documentation> </xs:annotation> <xs:sequence> </xs:sequence>
+ <xs:attribute name="id" type="xs:string" use="required"/> <xs:attribute name="type"
+ type="xs:string" use="optional"/> <xs:attribute name="file" type="xs:string"
+ use="optional"/> </xs:complexType> -->
+ <xs:attributeGroup name="swingwindow">
+ <xs:annotation>
+ <xs:documentation>
+ base attributes for windows displayed in Jalview
+ desktop.
+ </xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="width" type="xs:int" />
+ <xs:attribute name="height" type="xs:int" />
+ <xs:attribute name="xpos" type="xs:int" />
+ <xs:attribute name="ypos" type="xs:int" />
+ </xs:attributeGroup>
+ <xs:complexType name="AnnotationColourScheme">
+ <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="perSequence" type="xs:boolean" use="optional" />
+ <xs:attribute name="predefinedColours" type="xs:boolean"
+ use="optional" />
</xs:complexType>
- -->
- <xs:attributeGroup name="swingwindow">
- <xs:annotation>
- <xs:documentation>
- base attributes for windows displayed in Jalview desktop.
- </xs:documentation>
- </xs:annotation>
- <xs:attribute name="width" type="xs:int"/>
- <xs:attribute name="height" type="xs:int"/>
- <xs:attribute name="xpos" type="xs:int"/>
- <xs:attribute name="ypos" type="xs:int"/>
- </xs:attributeGroup>
- <xs:complexType name="AnnotationColourScheme">
- <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="perSequence" type="xs:boolean" use="optional" />
- <xs:attribute name="predefinedColours" type="xs:boolean"
- use="optional" />
- </xs:complexType>
-
+
</xs:schema>
-#Wed Jun 10 11:15:53 BST 2015
+#Wed Jun 17 15:04:02 BST 2015
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.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor
jalview.schemabinding.version2.AlcodonFrame=jalview.schemabinding.version2.descriptors.AlcodonFrameDescriptor
jalview.schemabinding.version2.AnnotationElement=jalview.schemabinding.version2.descriptors.AnnotationElementDescriptor
+jalview.schemabinding.version2.SecondaryStructure=jalview.schemabinding.version2.descriptors.SecondaryStructureDescriptor
jalview.schemabinding.version2.SequenceSet=jalview.schemabinding.version2.descriptors.SequenceSetDescriptor
jalview.schemabinding.version2.Viewport=jalview.schemabinding.version2.descriptors.ViewportDescriptor
+jalview.schemabinding.version2.RnaViewer=jalview.schemabinding.version2.descriptors.RnaViewerDescriptor
jalview.schemabinding.version2.MapListType=jalview.schemabinding.version2.descriptors.MapListTypeDescriptor
jalview.schemabinding.version2.Property=jalview.schemabinding.version2.descriptors.PropertyDescriptor
jalview.schemabinding.version2.UserColourScheme=jalview.schemabinding.version2.descriptors.UserColourSchemeDescriptor
*/
private java.util.Vector _hiddenSequencesList;
+ /**
+ * Reference to a viewer showing RNA structure
+ * for this sequence. Schema supports one viewer showing
+ * multiple
+ * annotations for multiple sequences, though currently only
+ * one
+ * annotation for one sequence (gapped or trimmed) is used
+ *
+ */
+ private java.util.Vector _rnaViewerList;
+
//----------------/
//- Constructors -/
this._featuresList = new java.util.Vector();
this._pdbidsList = new java.util.Vector();
this._hiddenSequencesList = new java.util.Vector();
+ this._rnaViewerList = new java.util.Vector();
}
}
/**
+ *
+ *
+ * @param vRnaViewer
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addRnaViewer(
+ final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+ throws java.lang.IndexOutOfBoundsException {
+ this._rnaViewerList.addElement(vRnaViewer);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vRnaViewer
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addRnaViewer(
+ final int index,
+ final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+ throws java.lang.IndexOutOfBoundsException {
+ this._rnaViewerList.add(index, vRnaViewer);
+ }
+
+ /**
*/
public void deleteColour(
) {
}
/**
+ * Method enumerateRnaViewer.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.RnaViewer elements
+ */
+ public java.util.Enumeration enumerateRnaViewer(
+ ) {
+ return this._rnaViewerList.elements();
+ }
+
+ /**
* Returns the value of field 'colour'.
*
* @return the value of field 'Colour'.
}
/**
+ * Method getRnaViewer.
+ *
+ * @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.RnaViewer at the given index
+ */
+ public jalview.schemabinding.version2.RnaViewer getRnaViewer(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._rnaViewerList.size()) {
+ throw new IndexOutOfBoundsException("getRnaViewer: Index value '" + index + "' not in range [0.." + (this._rnaViewerList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList.get(index);
+ }
+
+ /**
+ * Method getRnaViewer.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.RnaViewer[] getRnaViewer(
+ ) {
+ jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0];
+ return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList.toArray(array);
+ }
+
+ /**
+ * Method getRnaViewerCount.
+ *
+ * @return the size of this collection
+ */
+ public int getRnaViewerCount(
+ ) {
+ return this._rnaViewerList.size();
+ }
+
+ /**
* Returns the value of field 'start'.
*
* @return the value of field 'Start'.
}
/**
+ */
+ public void removeAllRnaViewer(
+ ) {
+ this._rnaViewerList.clear();
+ }
+
+ /**
* Method removeFeatures.
*
* @param vFeatures
}
/**
+ * Method removeRnaViewer.
+ *
+ * @param vRnaViewer
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeRnaViewer(
+ final jalview.schemabinding.version2.RnaViewer vRnaViewer) {
+ boolean removed = _rnaViewerList.remove(vRnaViewer);
+ return removed;
+ }
+
+ /**
+ * Method removeRnaViewerAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt(
+ final int index) {
+ java.lang.Object obj = this._rnaViewerList.remove(index);
+ return (jalview.schemabinding.version2.RnaViewer) obj;
+ }
+
+ /**
* Sets the value of field 'colour'.
*
* @param colour the value of field 'colour'.
}
/**
+ *
+ *
+ * @param index
+ * @param vRnaViewer
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setRnaViewer(
+ final int index,
+ final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._rnaViewerList.size()) {
+ throw new IndexOutOfBoundsException("setRnaViewer: Index value '" + index + "' not in range [0.." + (this._rnaViewerList.size() - 1) + "]");
+ }
+
+ this._rnaViewerList.set(index, vRnaViewer);
+ }
+
+ /**
+ *
+ *
+ * @param vRnaViewerArray
+ */
+ public void setRnaViewer(
+ final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray) {
+ //-- copy array
+ _rnaViewerList.clear();
+
+ for (int i = 0; i < vRnaViewerArray.length; i++) {
+ this._rnaViewerList.add(vRnaViewerArray[i]);
+ }
+ }
+
+ /**
* Sets the value of field 'start'.
*
* @param start the value of field 'start'.
--- /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;
+
+/**
+ * Reference to a viewer showing RNA structure
+ * for this sequence. Schema supports one viewer showing multiple
+ * annotations for multiple sequences, though currently only one
+ * annotation for one sequence (gapped or trimmed) is used
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class RnaViewer implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * An id unique to the RNA viewer panel
+ *
+ */
+ private java.lang.String _viewId;
+
+ /**
+ * horizontal position of split pane divider
+ *
+ */
+ private int _dividerLocation;
+
+ /**
+ * keeps track of state for field: _dividerLocation
+ */
+ private boolean _has_dividerLocation;
+
+ /**
+ * Index of the selected structure in the
+ * viewer panel
+ *
+ */
+ private int _selectedRna;
+
+ /**
+ * keeps track of state for field: _selectedRna
+ */
+ private boolean _has_selectedRna;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _secondaryStructureList.
+ */
+ private java.util.Vector _secondaryStructureList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public RnaViewer() {
+ super();
+ this._secondaryStructureList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vSecondaryStructure
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSecondaryStructure(
+ final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+ throws java.lang.IndexOutOfBoundsException {
+ this._secondaryStructureList.addElement(vSecondaryStructure);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSecondaryStructure
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSecondaryStructure(
+ final int index,
+ final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+ throws java.lang.IndexOutOfBoundsException {
+ this._secondaryStructureList.add(index, vSecondaryStructure);
+ }
+
+ /**
+ */
+ public void deleteDividerLocation(
+ ) {
+ this._has_dividerLocation= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deleteSelectedRna(
+ ) {
+ this._has_selectedRna= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Method enumerateSecondaryStructure.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.SecondaryStructure elements
+ */
+ public java.util.Enumeration enumerateSecondaryStructure(
+ ) {
+ return this._secondaryStructureList.elements();
+ }
+
+ /**
+ * Returns the value of field 'dividerLocation'. The field
+ * 'dividerLocation' has the following description: horizontal
+ * position of split pane divider
+ *
+ *
+ * @return the value of field 'DividerLocation'.
+ */
+ public int getDividerLocation(
+ ) {
+ return this._dividerLocation;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight(
+ ) {
+ return this._height;
+ }
+
+ /**
+ * Method getSecondaryStructure.
+ *
+ * @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.SecondaryStructure at the
+ * given index
+ */
+ public jalview.schemabinding.version2.SecondaryStructure getSecondaryStructure(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._secondaryStructureList.size()) {
+ throw new IndexOutOfBoundsException("getSecondaryStructure: Index value '" + index + "' not in range [0.." + (this._secondaryStructureList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.SecondaryStructure) _secondaryStructureList.get(index);
+ }
+
+ /**
+ * Method getSecondaryStructure.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.SecondaryStructure[] getSecondaryStructure(
+ ) {
+ jalview.schemabinding.version2.SecondaryStructure[] array = new jalview.schemabinding.version2.SecondaryStructure[0];
+ return (jalview.schemabinding.version2.SecondaryStructure[]) this._secondaryStructureList.toArray(array);
+ }
+
+ /**
+ * Method getSecondaryStructureCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSecondaryStructureCount(
+ ) {
+ return this._secondaryStructureList.size();
+ }
+
+ /**
+ * Returns the value of field 'selectedRna'. The field
+ * 'selectedRna' has the following description: Index of the
+ * selected structure in the
+ * viewer panel
+ *
+ *
+ * @return the value of field 'SelectedRna'.
+ */
+ public int getSelectedRna(
+ ) {
+ return this._selectedRna;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle(
+ ) {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'viewId'. The field 'viewId' has
+ * the following description: An id unique to the RNA viewer
+ * panel
+ *
+ *
+ * @return the value of field 'ViewId'.
+ */
+ public java.lang.String getViewId(
+ ) {
+ return this._viewId;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth(
+ ) {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos(
+ ) {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos(
+ ) {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasDividerLocation.
+ *
+ * @return true if at least one DividerLocation has been added
+ */
+ public boolean hasDividerLocation(
+ ) {
+ return this._has_dividerLocation;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasSelectedRna.
+ *
+ * @return true if at least one SelectedRna has been added
+ */
+ public boolean hasSelectedRna(
+ ) {
+ return this._has_selectedRna;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth(
+ ) {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos(
+ ) {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos(
+ ) {
+ return this._has_ypos;
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ */
+ public void removeAllSecondaryStructure(
+ ) {
+ this._secondaryStructureList.clear();
+ }
+
+ /**
+ * Method removeSecondaryStructure.
+ *
+ * @param vSecondaryStructure
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSecondaryStructure(
+ final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure) {
+ boolean removed = _secondaryStructureList.remove(vSecondaryStructure);
+ return removed;
+ }
+
+ /**
+ * Method removeSecondaryStructureAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.SecondaryStructure removeSecondaryStructureAt(
+ final int index) {
+ java.lang.Object obj = this._secondaryStructureList.remove(index);
+ return (jalview.schemabinding.version2.SecondaryStructure) obj;
+ }
+
+ /**
+ * Sets the value of field 'dividerLocation'. The field
+ * 'dividerLocation' has the following description: horizontal
+ * position of split pane divider
+ *
+ *
+ * @param dividerLocation the value of field 'dividerLocation'.
+ */
+ public void setDividerLocation(
+ final int dividerLocation) {
+ this._dividerLocation = dividerLocation;
+ this._has_dividerLocation = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height the value of field 'height'.
+ */
+ public void setHeight(
+ final int height) {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSecondaryStructure
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSecondaryStructure(
+ final int index,
+ final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._secondaryStructureList.size()) {
+ throw new IndexOutOfBoundsException("setSecondaryStructure: Index value '" + index + "' not in range [0.." + (this._secondaryStructureList.size() - 1) + "]");
+ }
+
+ this._secondaryStructureList.set(index, vSecondaryStructure);
+ }
+
+ /**
+ *
+ *
+ * @param vSecondaryStructureArray
+ */
+ public void setSecondaryStructure(
+ final jalview.schemabinding.version2.SecondaryStructure[] vSecondaryStructureArray) {
+ //-- copy array
+ _secondaryStructureList.clear();
+
+ for (int i = 0; i < vSecondaryStructureArray.length; i++) {
+ this._secondaryStructureList.add(vSecondaryStructureArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'selectedRna'. The field
+ * 'selectedRna' has the following description: Index of the
+ * selected structure in the
+ * viewer panel
+ *
+ *
+ * @param selectedRna the value of field 'selectedRna'.
+ */
+ public void setSelectedRna(
+ final int selectedRna) {
+ this._selectedRna = selectedRna;
+ this._has_selectedRna = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title the value of field 'title'.
+ */
+ public void setTitle(
+ final java.lang.String title) {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'viewId'. The field 'viewId' has the
+ * following description: An id unique to the RNA viewer panel
+ *
+ *
+ * @param viewId the value of field 'viewId'.
+ */
+ public void setViewId(
+ final java.lang.String viewId) {
+ this._viewId = viewId;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width the value of field 'width'.
+ */
+ public void setWidth(
+ final int width) {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos the value of field 'xpos'.
+ */
+ public void setXpos(
+ final int xpos) {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos the value of field 'ypos'.
+ */
+ public void setYpos(
+ final int ypos) {
+ this._ypos = ypos;
+ this._has_ypos = 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.RnaViewer
+ */
+ public static jalview.schemabinding.version2.RnaViewer unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.RnaViewer) Unmarshaller.unmarshal(jalview.schemabinding.version2.RnaViewer.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);
+ }
+
+}
--- /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 SecondaryStructure.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SecondaryStructure implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * id attribute of Annotation in
+ * vamsasModel for
+ * the secondary structure annotation shown
+ * in the viewer
+ *
+ */
+ private java.lang.String _annotationId;
+
+ /**
+ * if true the RNA structure is shown with gaps, if false
+ * without
+ *
+ */
+ private boolean _gapped;
+
+ /**
+ * keeps track of state for field: _gapped
+ */
+ private boolean _has_gapped;
+
+ /**
+ * name of the project jar entry that holds
+ * the VARNA viewer state for the structure
+ *
+ */
+ private java.lang.String _viewerState;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SecondaryStructure() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteGapped(
+ ) {
+ this._has_gapped= false;
+ }
+
+ /**
+ * Returns the value of field 'annotationId'. The field
+ * 'annotationId' has the following description: id attribute
+ * of Annotation in
+ * vamsasModel for
+ * the secondary structure annotation shown
+ * in the viewer
+ *
+ *
+ * @return the value of field 'AnnotationId'.
+ */
+ public java.lang.String getAnnotationId(
+ ) {
+ return this._annotationId;
+ }
+
+ /**
+ * Returns the value of field 'gapped'. The field 'gapped' has
+ * the following description: if true the RNA structure is
+ * shown with gaps, if false without
+ *
+ *
+ * @return the value of field 'Gapped'.
+ */
+ public boolean getGapped(
+ ) {
+ return this._gapped;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle(
+ ) {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'viewerState'. The field
+ * 'viewerState' has the following description: name of the
+ * project jar entry that holds
+ * the VARNA viewer state for the structure
+ *
+ *
+ * @return the value of field 'ViewerState'.
+ */
+ public java.lang.String getViewerState(
+ ) {
+ return this._viewerState;
+ }
+
+ /**
+ * Method hasGapped.
+ *
+ * @return true if at least one Gapped has been added
+ */
+ public boolean hasGapped(
+ ) {
+ return this._has_gapped;
+ }
+
+ /**
+ * Returns the value of field 'gapped'. The field 'gapped' has
+ * the following description: if true the RNA structure is
+ * shown with gaps, if false without
+ *
+ *
+ * @return the value of field 'Gapped'.
+ */
+ public boolean isGapped(
+ ) {
+ return this._gapped;
+ }
+
+ /**
+ * 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 'annotationId'. The field
+ * 'annotationId' has the following description: id attribute
+ * of Annotation in
+ * vamsasModel for
+ * the secondary structure annotation shown
+ * in the viewer
+ *
+ *
+ * @param annotationId the value of field 'annotationId'.
+ */
+ public void setAnnotationId(
+ final java.lang.String annotationId) {
+ this._annotationId = annotationId;
+ }
+
+ /**
+ * Sets the value of field 'gapped'. The field 'gapped' has the
+ * following description: if true the RNA structure is shown
+ * with gaps, if false without
+ *
+ *
+ * @param gapped the value of field 'gapped'.
+ */
+ public void setGapped(
+ final boolean gapped) {
+ this._gapped = gapped;
+ this._has_gapped = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title the value of field 'title'.
+ */
+ public void setTitle(
+ final java.lang.String title) {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'viewerState'. The field
+ * 'viewerState' has the following description: name of the
+ * project jar entry that holds
+ * the VARNA viewer state for the structure
+ *
+ *
+ * @param viewerState the value of field 'viewerState'.
+ */
+ public void setViewerState(
+ final java.lang.String viewerState) {
+ this._viewerState = viewerState;
+ }
+
+ /**
+ * 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.SecondaryStructure
+ */
+ public static jalview.schemabinding.version2.SecondaryStructure unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.SecondaryStructure) Unmarshaller.unmarshal(jalview.schemabinding.version2.SecondaryStructure.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);
+ }
+
+}
typeValidator.setMaxInclusive(2147483647);
}
desc.setValidator(fieldValidator);
+ //-- _rnaViewerList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.RnaViewer.class, "_rnaViewerList", "rnaViewer", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ JSeq target = (JSeq) object;
+ return target.getRnaViewer();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ JSeq target = (JSeq) object;
+ target.addRnaViewer( (jalview.schemabinding.version2.RnaViewer) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
+ try {
+ JSeq target = (JSeq) object;
+ target.removeAllRnaViewer();
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return new jalview.schemabinding.version2.RnaViewer();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _rnaViewerList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
}
--- /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.RnaViewer;
+
+/**
+ * Class RnaViewerDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class RnaViewerDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+ //--------------------------/
+ //- 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 RnaViewerDescriptor() {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "rnaViewer";
+ _elementDefinition = true;
+
+ //-- set grouping compositor
+ setCompositorAsSequence();
+ 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
+
+ //-- _title
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", 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
+ {
+ RnaViewer target = (RnaViewer) object;
+ return target.getTitle();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RnaViewer target = (RnaViewer) object;
+ target.setTitle( (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.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _title
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- 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);
+ //-- _viewId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewId", "viewId", 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
+ {
+ RnaViewer target = (RnaViewer) object;
+ return target.getViewId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RnaViewer target = (RnaViewer) object;
+ target.setViewId( (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.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _viewId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- 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);
+ //-- _dividerLocation
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_dividerLocation", "dividerLocation", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ if (!target.hasDividerLocation()) { return null; }
+ return new java.lang.Integer(target.getDividerLocation());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RnaViewer target = (RnaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteDividerLocation();
+ return;
+ }
+ target.setDividerLocation( ((java.lang.Integer) value).intValue());
+ } 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: _dividerLocation
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _selectedRna
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_selectedRna", "selectedRna", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ if (!target.hasSelectedRna()) { return null; }
+ return new java.lang.Integer(target.getSelectedRna());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RnaViewer target = (RnaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteSelectedRna();
+ return;
+ }
+ target.setSelectedRna( ((java.lang.Integer) value).intValue());
+ } 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: _selectedRna
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _width
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ if (!target.hasWidth()) { return null; }
+ return new java.lang.Integer(target.getWidth());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RnaViewer target = (RnaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteWidth();
+ return;
+ }
+ target.setWidth( ((java.lang.Integer) value).intValue());
+ } 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: _width
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _height
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ if (!target.hasHeight()) { return null; }
+ return new java.lang.Integer(target.getHeight());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RnaViewer target = (RnaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteHeight();
+ return;
+ }
+ target.setHeight( ((java.lang.Integer) value).intValue());
+ } 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: _height
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _xpos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ if (!target.hasXpos()) { return null; }
+ return new java.lang.Integer(target.getXpos());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RnaViewer target = (RnaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteXpos();
+ return;
+ }
+ target.setXpos( ((java.lang.Integer) value).intValue());
+ } 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: _xpos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _ypos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ if (!target.hasYpos()) { return null; }
+ return new java.lang.Integer(target.getYpos());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RnaViewer target = (RnaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteYpos();
+ return;
+ }
+ target.setYpos( ((java.lang.Integer) value).intValue());
+ } 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: _ypos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
+ //-- _secondaryStructureList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SecondaryStructure.class, "_secondaryStructureList", "secondaryStructure", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RnaViewer target = (RnaViewer) object;
+ return target.getSecondaryStructure();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RnaViewer target = (RnaViewer) object;
+ target.addSecondaryStructure( (jalview.schemabinding.version2.SecondaryStructure) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
+ try {
+ RnaViewer target = (RnaViewer) object;
+ target.removeAllSecondaryStructure();
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return new jalview.schemabinding.version2.SecondaryStructure();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _secondaryStructureList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ }
+
+
+ //-----------/
+ //- 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.RnaViewer.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;
+ }
+
+}
--- /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.SecondaryStructure;
+
+/**
+ * Class SecondaryStructureDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SecondaryStructureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+ //--------------------------/
+ //- 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 SecondaryStructureDescriptor() {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "secondaryStructure";
+ _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
+
+ //-- _title
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", 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
+ {
+ SecondaryStructure target = (SecondaryStructure) object;
+ return target.getTitle();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ SecondaryStructure target = (SecondaryStructure) object;
+ target.setTitle( (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.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _title
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- 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);
+ //-- _annotationId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotationId", "annotationId", 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
+ {
+ SecondaryStructure target = (SecondaryStructure) object;
+ return target.getAnnotationId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ SecondaryStructure target = (SecondaryStructure) object;
+ target.setAnnotationId( (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: _annotationId
+ 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);
+ //-- _gapped
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gapped", "gapped", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ SecondaryStructure target = (SecondaryStructure) object;
+ if (!target.hasGapped()) { return null; }
+ return (target.getGapped() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ SecondaryStructure target = (SecondaryStructure) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteGapped();
+ return;
+ }
+ target.setGapped( ((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: _gapped
+ 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);
+ //-- _viewerState
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewerState", "viewerState", 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
+ {
+ SecondaryStructure target = (SecondaryStructure) object;
+ return target.getViewerState();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ SecondaryStructure target = (SecondaryStructure) object;
+ target.setViewerState( (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.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _viewerState
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- 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);
+ //-- 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.SecondaryStructure.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;
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff