<?xml version="1.0" encoding="UTF-8"?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 ($$Version-Rel$$)
+ * 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: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"
</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: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>
</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">
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="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="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: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:complexType>
</xs:element>
<xs:element name="UserColours" minOccurs="0"
<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>
git://source.jalview.org / jalview.git / blobdiff