<?xml version="1.0" encoding="UTF-8"?>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 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.
+<!-- * 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. -->
+<!--
+ Java JAXB binding classes are generated by running command line tool xjc:
+ xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
+ Note this also generates code for included schemas
-->
-<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: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:element name="JalviewModel" type="jv:JalviewModel" />
<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:sequence>
- <xs:element name="JSeq" maxOccurs="unbounded">
+ <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
</xs:documentation>
</xs:annotation>
</xs:attribute>
+ <xs:attribute name="type" type="xs:string"
+ use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ An
+ identifier
+ for
+ the
+ viewer
+ type,
+ currently
+ either
+ JMOL
+ or
+ CHIMERA
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:extension>
</xs:simpleContent>
</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:attribute name="viewreference" type="xs:boolean" use="optional"/>
</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:element name="annotationColours" type="jv:AnnotationColourScheme"
+ minOccurs="0" maxOccurs="1" />
</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="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">
+ <xs:element name="Viewport" maxOccurs="unbounded"
+ minOccurs="0">
<xs:complexType>
<xs:sequence>
- <xs:element name="AnnotationColours"
- minOccurs="0">
+ <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
+ minOccurs="0" maxOccurs="1">
+ </xs:element>
+ <xs:element name="hiddenColumns" minOccurs="0"
+ maxOccurs="unbounded">
<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="perSequence"
- type="xs:boolean"
- use="optional" />
- <xs:attribute name="predefinedColours"
- type="xs:boolean"
- use="optional" />
+ <xs:attribute name="start" type="xs:int" />
+ <xs:attribute name="end" type="xs:int" />
</xs:complexType>
</xs:element>
- <xs:element name="hiddenColumns"
- minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="calcIdParam" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
- <xs:attribute name="start"
- type="xs:int" />
- <xs:attribute name="end"
- type="xs:int" />
+ <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: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="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="scaleProteinAsCdna" type="xs:boolean" use="optional" default="true" />
<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>
</xs:attribute>
+ <xs:attribute name="complementId" type="xs:string"
+ use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ The viewport id of this viewport's
+ (cdna/protein) coding complement, if any
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="showComplementFeatures" type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="showComplementFeaturesOnTop" type="xs:boolean" use="optional" default="false" />
</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:attribute>
<xs:attributeGroup ref="jv:swingwindow" />
+ <xs:attribute name="linkToAllViews" use="optional" default="false" type="xs:boolean" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="PcaViewer" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="sequencePoint" minOccurs="1" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:attribute name="sequenceRef" type="xs:string" />
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="axis" minOccurs="3" maxOccurs="3">
+ <xs:annotation>
+ <xs:documentation>
+ endpoints of X, Y and Z axes in that order
+ </xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="seqPointMin">
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="seqPointMax">
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="pcaData" type="jv:PcaDataType" />
+ </xs:sequence>
+ <xs:attribute name="title" type="xs:string" />
+ <xs:attribute name="scoreModelName" type="xs:string" />
+ <xs:attribute name="xDim" type="xs:int" />
+ <xs:attribute name="yDim" type="xs:int" />
+ <xs:attribute name="zDim" type="xs:int" />
+ <xs:attribute name="bgColour" type="xs:int" />
+ <xs:attribute name="scaleFactor" type="xs:float" />
+ <xs:attribute name="showLabels" type="xs:boolean" />
+ <xs:attribute name="linkToAllViews" type="xs:boolean" />
+ <xs:attributeGroup ref="jv:SimilarityParams" />
+ <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:sequence>
+ <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
+ <xs:annotation>
+ <xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
+ <xs:annotation>
+ <xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <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="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
+ <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="key2" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <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="SimilarityParams">
+ <xs:annotation>
+ <xs:documentation>
+ parameters that condition a similarity score calculation
+ </xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="includeGaps" type="xs:boolean" />
+ <xs:attribute name="matchGaps" type="xs:boolean" />
+ <xs:attribute name="includeGappedColumns" type="xs:boolean" />
+ <xs:attribute name="denominateByShortestLength" type="xs:boolean" />
+ </xs:attributeGroup>
+ <xs:attributeGroup name="position">
+ <xs:attribute name="xPos" type="xs:float" />
+ <xs:attribute name="yPos" type="xs:float" />
+ <xs:attribute name="zPos" type="xs:float" />
+ </xs:attributeGroup>
+ <xs:complexType name="PcaDataType">
+ <xs:annotation>
+ <xs:documentation>
+ The results of a PCA calculation
+ </xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="pairwiseMatrix" type="jv:DoubleMatrix" />
+ <xs:element name="tridiagonalMatrix" type="jv:DoubleMatrix" />
+ <xs:element name="eigenMatrix" type="jv:DoubleMatrix" />
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="DoubleVector">
+ <xs:sequence>
+ <xs:element name="v" type="xs:double" minOccurs="0" maxOccurs="unbounded" />
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="DoubleMatrix">
+ <xs:sequence>
+ <xs:element name="row" type="jv:DoubleVector" minOccurs="0" maxOccurs="unbounded" />
+ <xs:element name="D" minOccurs="0" type="jv:DoubleVector" />
+ <xs:element name="E" minOccurs="0" type="jv:DoubleVector" />
+ </xs:sequence>
+ <xs:attribute name="rows" type="xs:int" />
+ <xs:attribute name="columns" type="xs:int" />
</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:schema>
git://source.jalview.org / jalview.git / blobdiff