<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+
+ This program 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 2
+ of the License, or (at your option) any later version.
+
+ This program 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 this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+-->
+
<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="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="showConsensusProfile" 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"/>
+ <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="showConsensusProfile" 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>