<?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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 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:element name="structureState" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:simpleContent>
- <xs:extension base="xs:string">
+ <xs:extension base="xs:string">
+ <xs:attributeGroup ref="jv:swingwindow"/>
<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:annotation>
<xs:documentation>additional identifier which properly disambiguates
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:simpleContent>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
+ <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="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:documentation>
</xs:annotation>
</xs:attribute>
- </xs:complexType>
+ </xs:complexType>
</xs:element>
<xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
</xs:element>
<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: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>
- </xs:complexType>
+ <xs:sequence minOccurs="0">
+ <xs:element name="title" type="xs:string"/>
+ <xs:element name="newick" type="xs:string"/>
+ </xs:sequence>
+ <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: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:schema>
git://source.jalview.org / jalview.git / blobdiff