<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+ * 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/>.
+-->
<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:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
<xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
<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:ID" use="optional"/>
+ <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:annotation>
+ </xs:attribute>
</xs:extension>
<xs:attribute name="textCol1" type="xs:int"/>
<xs:attribute name="textCol2" type="xs:int"/>
<xs:attribute name="textColThreshold" type="xs:int"/>
+ <xs:attribute name="showUnconserved" type="xs:boolean" use="optional"/>
+ <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean" use="optional" default="true"/>
+ <xs:attribute name="showConsensusHistogram" type="xs:boolean" use="optional" default="true"/>
+ <xs:attribute name="showSequenceLogo" type="xs:boolean" use="optional" default="false"/>
+ <xs:attribute name="id" type="xs:string" use="optional"><xs:annotation>
+ <xs:documentation>
+ Optional sequence group ID (only needs to be unique for this alignment)
+ </xs:documentation>
+ </xs:annotation></xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="Viewport" maxOccurs="unbounded">
<xs: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="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:complexType>
+ <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:complexType>
git://source.jalview.org / jalview.git / blobdiff