<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.
-->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours" xmlns:jv="www.jalview.org" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours" xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
<xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
+ <xs:import namespace="www.jalview.org/xml/wsparamset" schemaLocation="JalviewWsParamSet.xsd"/>
<xs:complexType name="JalviewModel">
<xs:sequence>
- <xs:element name="creationDate" type="xs:dateTime"/>
- <xs:element name="version" type="xs:string"/>
- <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>
+ <xs:element name="creationDate" type="xs:dateTime" />
+ <xs:element name="version" type="xs:string" />
+ <xs:element name="vamsasModel" type="vamsas:VAMSAS" />
<xs:sequence>
- <xs:element name="JSeq" maxOccurs="unbounded">
+ <xs: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" maxOccurs="unbounded">
+ <xs:element
+ name="structureState" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
<xs:simpleContent>
- <xs:extension base="xs:string">
- <xs:attribute name="visible" type="xs:boolean"/>
- <xs:attribute name="xpos" type="xs:int"/>
- <xs:attribute name="ypos" type="xs:int"/>
- <xs:attribute name="width" type="xs:int"/>
- <xs:attribute name="height" type="xs:int"/>
- <xs:attribute name="viewId" type="xs:string" use="optional">
+ <xs:extension
+ base="xs:string">
+ <xs:attributeGroup
+ ref="jv:swingwindow" />
+ <xs:attribute
+ name="visible" type="xs:boolean" />
+ <xs:attribute
+ name="viewId" type="xs:string" use="optional">
<xs:annotation>
- <xs:documentation>additional identifier which properly disambiguates
- the structure view from any other view with the same attributes. This is not an ID,
- because it is possible to have many references to the same physical structure view
- from different sequences in an alignment. A structureState element citing the same
- viewId will appear for each instance.</xs:documentation>
+ <xs:documentation>
+ additional
+ identifier
+ which
+ properly
+ disambiguates
+ the
+ structure
+ view
+ from
+ any
+ other
+ view
+ with
+ the
+ same
+ attributes.
+ This
+ is
+ not
+ an
+ ID,
+ because
+ it
+ is
+ possible
+ to
+ have
+ many
+ references
+ to
+ the
+ same
+ physical
+ structure
+ view
+ from
+ different
+ sequences
+ in
+ an
+ alignment.
+ A
+ structureState
+ element
+ citing
+ the
+ same
+ viewId
+ will
+ appear
+ for
+ each
+ instance.
+ </xs:documentation>
</xs:annotation>
</xs:attribute>
-
-
+ <xs:attribute
+ name="alignwithAlignPanel" type="xs:boolean"
+ use="optional" default="true">
+ <xs:annotation>
+ <xs:documentation>
+ Flag
+ set
+ if
+ the
+ alignment
+ panel
+ containing
+ this
+ JSeq
+ should
+ be
+ included
+ in
+ those
+ used
+ to
+ perform
+ a
+ structure
+ superposition
+ (since
+ Jalview
+ 2.7).
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute
+ name="colourwithAlignPanel" type="xs:boolean"
+ use="optional" default="false">
+ <xs:annotation>
+ <xs:documentation>
+ Flag
+ set
+ if
+ the
+ alignment
+ panel
+ containing
+ this
+ JSeq
+ should
+ be
+ included
+ in
+ those
+ used
+ to
+ colour
+ its
+ associated
+ sequences
+ in
+ this
+ structureState(since
+ Jalview
+ 2.7).
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute
+ name="colourByJmol" type="xs:boolean" use="optional"
+ default="true">
+ <xs:annotation>
+ <xs:documentation>
+ Flag
+ set
+ if
+ the
+ structure
+ display
+ is
+ coloured
+ by
+ the
+ Jmol
+ state,
+ rather
+ than
+ by
+ one
+ or
+ more
+ linked
+ alignment
+ views.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+
</xs:extension>
</xs:simpleContent>
</xs:complexType>
</xs:complexContent>
</xs:complexType>
</xs:element>
- <xs:element name="hiddenSequences" type="xs:int" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="hiddenSequences"
+ type="xs:int" minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
- <xs:attribute name="colour" type="xs:int" use="optional"/>
- <xs:attribute name="start" type="xs:int" use="required"/>
- <xs:attribute name="end" type="xs:int" use="required"/>
- <xs:attribute name="id" type="xs:string" use="required"/>
- <xs:attribute name="hidden" type="xs:boolean"/>
+ <xs:attribute name="colour" type="xs:int"
+ use="optional" />
+ <xs:attribute name="start" type="xs:int"
+ use="required" />
+ <xs:attribute name="end" type="xs:int"
+ use="required" />
+ <xs:attribute name="id" type="xs:string"
+ use="required" />
+ <xs:attribute name="hidden" type="xs:boolean" />
</xs:complexType>
</xs:element>
- <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="JGroup" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
- <xs:sequence>
- <xs:element name="seq" type="xs:string" maxOccurs="unbounded"/>
+ <xs:sequence>
+ <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="pidThreshold" type="xs:int"/>
- <xs:attribute name="outlineColour" type="xs:int"/>
- <xs:attribute name="displayBoxes" type="xs:boolean"/>
- <xs:attribute name="displayText" type="xs:boolean"/>
- <xs:attribute name="colourText" type="xs:boolean"/>
- <xs:attribute name="textCol1" type="xs:int"/>
- <xs:attribute name="textCol2" type="xs:int"/>
- <xs:attribute name="textColThreshold" type="xs:int"/>
- <xs:attribute name="showUnconserved" type="xs:boolean" use="optional"/>
- <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean" use="optional" default="true"/>
- <xs:attribute name="showConsensusHistogram" type="xs:boolean" use="optional" default="true"/>
- <xs:attribute name="showSequenceLogo" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="id" type="xs:string" use="optional"><xs:annotation>
- <xs:documentation>
- Optional sequence group ID (only needs to be unique for this alignment)
- </xs:documentation>
- </xs:annotation></xs:attribute>
+ <xs:attribute name="start" type="xs:int" />
+ <xs:attribute name="end" type="xs:int" />
+ <xs:attribute name="name" type="xs:string" />
+ <xs:attribute name="colour" type="xs:string" />
+ <xs:attribute name="consThreshold"
+ type="xs:int" />
+ <xs:attribute name="pidThreshold" type="xs:int" />
+ <xs:attribute name="outlineColour"
+ type="xs:int" />
+ <xs:attribute name="displayBoxes"
+ type="xs:boolean" />
+ <xs:attribute name="displayText"
+ type="xs:boolean" />
+ <xs:attribute name="colourText"
+ type="xs:boolean" />
+ <xs:attribute name="textCol1" type="xs:int" />
+ <xs:attribute name="textCol2" type="xs:int" />
+ <xs:attribute name="textColThreshold"
+ type="xs:int" />
+ <xs:attribute name="showUnconserved"
+ type="xs:boolean" use="optional" />
+ <xs:attribute name="ignoreGapsinConsensus"
+ type="xs:boolean" use="optional" default="true" />
+ <xs:attribute name="showConsensusHistogram"
+ type="xs:boolean" use="optional" default="true" />
+ <xs:attribute name="showSequenceLogo"
+ type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="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
+ 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: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:complexType>
+ <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>
</xs:sequence>
- <xs:attribute name="conservationSelected" type="xs:boolean"/>
- <xs:attribute name="pidSelected" type="xs:boolean"/>
- <xs:attribute name="bgColour" type="xs:string"/>
- <xs:attribute name="consThreshold" type="xs:int"/>
- <xs:attribute name="pidThreshold" type="xs:int"/>
- <xs:attribute name="title" type="xs:string"/>
- <xs:attribute name="showFullId" type="xs:boolean"/>
- <xs:attribute name="rightAlignIds" type="xs:boolean"/>
- <xs:attribute name="showText" type="xs:boolean"/>
- <xs:attribute name="showColourText" type="xs:boolean"/>
- <xs:attribute name="showUnconserved" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="showBoxes" type="xs:boolean"/>
- <xs:attribute name="wrapAlignment" type="xs:boolean"/>
- <xs:attribute name="renderGaps" type="xs:boolean"/>
- <xs:attribute name="showSequenceFeatures" type="xs:boolean"/>
- <xs:attribute name="showNPfeatureTooltip" type="xs:boolean" use="optional"/>
- <xs:attribute name="showDbRefTooltip" type="xs:boolean" use="optional"/>
- <xs:attribute name="followHighlight" type="xs:boolean" use="optional" default="true"/>
- <xs:attribute name="followSelection" type="xs:boolean" use="optional" default="true"/>
- <xs:attribute name="showAnnotation" type="xs:boolean"/>
- <xs:attribute name="centreColumnLabels" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="showGroupConservation" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="showGroupConsensus" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="showConsensusHistogram" type="xs:boolean" use="optional" default="true"/>
- <xs:attribute name="showSequenceLogo" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean" use="optional" default="true"/>
-
- <xs:attribute name="xpos" type="xs:int"/>
- <xs:attribute name="ypos" type="xs:int"/>
- <xs:attribute name="width" type="xs:int"/>
- <xs:attribute name="height" type="xs:int"/>
- <xs:attribute name="startRes" type="xs:int"/>
- <xs:attribute name="startSeq" type="xs:int"/>
- <xs:attribute name="fontName" type="xs:string"/>
- <xs:attribute name="fontSize" type="xs:int"/>
- <xs:attribute name="fontStyle" type="xs:int"/>
- <xs:attribute name="viewName" type="xs:string"/>
- <xs:attribute name="sequenceSetId" type="xs:string"/>
- <xs:attribute name="gatheredViews" type="xs:boolean"/>
- <xs:attribute name="textCol1" type="xs:int"/>
- <xs:attribute name="textCol2" type="xs:int"/>
- <xs:attribute name="textColThreshold" type="xs:int"/>
- <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:attributeGroup ref="jv:swingwindow" />
+ <xs:attribute name="conservationSelected"
+ type="xs:boolean" />
+ <xs:attribute name="pidSelected"
+ type="xs:boolean" />
+ <xs:attribute name="bgColour" type="xs:string" />
+ <xs:attribute name="consThreshold"
+ type="xs:int" />
+ <xs:attribute name="pidThreshold" type="xs:int" />
+ <xs:attribute name="title" type="xs:string" />
+ <xs:attribute name="showFullId"
+ type="xs:boolean" />
+ <xs:attribute name="rightAlignIds"
+ type="xs:boolean" />
+ <xs:attribute name="showText" type="xs:boolean" />
+ <xs:attribute name="showColourText"
+ type="xs:boolean" />
+ <xs:attribute name="showUnconserved"
+ type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="showBoxes"
+ type="xs:boolean" />
+ <xs:attribute name="wrapAlignment"
+ type="xs:boolean" />
+ <xs:attribute name="renderGaps"
+ type="xs:boolean" />
+ <xs:attribute name="showSequenceFeatures"
+ type="xs:boolean" />
+ <xs:attribute name="showNPfeatureTooltip"
+ type="xs:boolean" use="optional" />
+ <xs:attribute name="showDbRefTooltip"
+ type="xs:boolean" use="optional" />
+ <xs:attribute name="followHighlight"
+ type="xs:boolean" use="optional" default="true" />
+ <xs:attribute name="followSelection"
+ type="xs:boolean" use="optional" default="true" />
+ <xs:attribute name="showAnnotation"
+ type="xs:boolean" />
+ <xs:attribute name="centreColumnLabels"
+ type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="showGroupConservation"
+ type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="showGroupConsensus"
+ type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="showConsensusHistogram"
+ type="xs:boolean" use="optional" default="true" />
+ <xs:attribute name="showSequenceLogo"
+ type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="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="textCol1" type="xs:int" />
+ <xs:attribute name="textCol2" type="xs:int" />
+ <xs:attribute name="textColThreshold"
+ type="xs:int" />
+ <xs:attribute name="id" type="xs:ID"
+ use="optional">
<xs:annotation>
<xs:documentation>
- unique id used by jalview to synchronize between stored and instantiated views
+ unique id used by jalview to
+ synchronize between stored and
+ instantiated views
</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
- <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="UserColours" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
+ <xs:element name="UserColourScheme"
+ type="jalview:JalviewUserColours" />
</xs:sequence>
- <xs:attribute name="id" type="xs:string"/>
+ <xs:attribute name="id" type="xs:string" />
</xs:complexType>
</xs:element>
- <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="tree" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
<xs:sequence minOccurs="0">
- <xs:element name="title" type="xs:string"/>
- <xs:element name="newick" type="xs:string"/>
+ <xs:element name="title" type="xs:string" />
+ <xs:element name="newick" type="xs:string" />
</xs:sequence>
- <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:attribute name="fontName" type="xs:string"/>
- <xs:attribute name="fontSize" type="xs:int"/>
- <xs:attribute name="fontStyle" type="xs:int"/>
- <xs:attribute name="threshold" type="xs:float"/>
- <xs:attribute name="showBootstrap" type="xs:boolean"/>
- <xs:attribute name="showDistances" type="xs:boolean"/>
- <xs:attribute name="markUnlinked" type="xs:boolean"/>
- <xs:attribute name="fitToWindow" type="xs:boolean"/>
- <xs:attribute name="currentTree" type="xs:boolean"/>
- <xs:attribute name="id" type="xs:ID" use="optional">
- <xs:annotation><xs:documentation>Tree ID added for binding tree visualization settings to vamsas document trees in jalview 2.4.1</xs:documentation></xs:annotation>
+ <xs:attribute name="fontName" type="xs:string" />
+ <xs:attribute name="fontSize" type="xs:int" />
+ <xs:attribute name="fontStyle" type="xs:int" />
+ <xs:attribute name="threshold" type="xs:float" />
+ <xs:attribute name="showBootstrap"
+ type="xs:boolean" />
+ <xs:attribute name="showDistances"
+ type="xs:boolean" />
+ <xs:attribute name="markUnlinked"
+ type="xs:boolean" />
+ <xs:attribute name="fitToWindow"
+ type="xs:boolean" />
+ <xs:attribute name="currentTree"
+ type="xs:boolean" />
+ <xs:attribute name="id" type="xs:ID"
+ use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ Tree ID added for binding tree
+ visualization settings to vamsas
+ document trees in jalview 2.4.1
+ </xs:documentation>
+ </xs:annotation>
</xs:attribute>
+ <xs:attributeGroup ref="jv:swingwindow" />
</xs:complexType>
</xs:element>
<xs:element name="FeatureSettings" minOccurs="0">
<xs:complexType>
<xs:sequence>
- <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="setting" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
- <xs:attribute name="type" type="xs:string" use="required"/>
- <xs:attribute name="colour" type="xs:int" use="required"/>
- <xs:attribute name="display" type="xs:boolean" use="required"/>
- <xs:attribute name="order" type="xs:float" use="optional"/>
- <xs:attribute name="mincolour" type="xs:int" use="optional">
- <xs:annotation><xs:documentation>Optional minimum colour for graduated feature colour</xs:documentation>
- </xs:annotation></xs:attribute>
- <xs:attribute name="threshold" type="xs:float" use="optional">
- <xs:annotation><xs:documentation>threshold value for graduated feature colour</xs:documentation>
- </xs:annotation></xs:attribute>
- <xs:attribute name="threshstate" type="xs:int" use="optional">
- <xs:annotation><xs:documentation>threshold type for graduated feature colour</xs:documentation>
- </xs:annotation></xs:attribute>
- <xs:attribute name="max" type="xs:float" use="optional"/>
- <xs:attribute name="min" type="xs:float" use="optional"/>
- <xs:attribute name="colourByLabel" type="xs:boolean" use="optional"/>
- <xs:attribute name="autoScale" type="xs:boolean" use="optional"/>
- </xs:complexType>
+ <xs:attribute name="type"
+ type="xs:string" use="required" />
+ <xs:attribute name="colour"
+ type="xs:int" use="required" />
+ <xs:attribute name="display"
+ type="xs:boolean" use="required" />
+ <xs:attribute name="order"
+ type="xs:float" use="optional" />
+ <xs:attribute name="mincolour"
+ type="xs:int" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ Optional minimum colour
+ for graduated feature
+ colour
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="threshold"
+ type="xs:float" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ threshold value for
+ graduated feature colour
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="threshstate"
+ type="xs:int" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ threshold type for
+ graduated feature colour
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="max"
+ type="xs:float" use="optional" />
+ <xs:attribute name="min"
+ type="xs:float" use="optional" />
+ <xs:attribute name="colourByLabel"
+ type="xs:boolean" use="optional" />
+ <xs:attribute name="autoScale"
+ type="xs:boolean" use="optional" />
+ </xs:complexType>
</xs:element>
- <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="group" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
- <xs:attribute name="name" type="xs:string" use="required"/>
- <xs:attribute name="display" type="xs:boolean" use="required"/>
+ <xs:attribute name="name"
+ type="xs:string" use="required" />
+ <xs:attribute name="display"
+ type="xs:boolean" use="required" />
</xs:complexType>
</xs:element>
</xs:sequence>
<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>
+ -->
+ <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>