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extend XML model for graduated feature colours, group associated manual/auto annotati...
[jalview.git] / schemas / jalview.xsd
diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 72c1270..99a4e10 100755 (executable)
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,4 +1,23 @@
 <?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"/>
@@ -74,7 +93,14 @@
                                                <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">
@@ -107,12 +133,23 @@
                                                <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"/>
@@ -178,7 +215,20 @@
                                                                        <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>