<?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 ($$Version-Rel$$)
+ * 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.
-->
-
<!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
+<!--
+ Java JAXB binding classes are generated by running command line tool xjc:
+ xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
+ Note this also generates code for included schemas
+-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:complexType name="VAMSAS">
<xs:sequence>
<xs:element name="Annotation">
<xs:complexType>
<xs:sequence>
- <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="label" type="xs:string"/>
- <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element ref="vamsas:annotationElement" minOccurs="0"
+ maxOccurs="unbounded" />
+ <xs:element name="label" type="xs:string" />
+ <xs:element name="description" type="xs:string"
+ minOccurs="0" />
<xs:element name="thresholdLine" minOccurs="0">
<xs:complexType>
- <xs:attribute name="label" type="xs:string"/>
- <xs:attribute name="value" type="xs:float"/>
- <xs:attribute name="colour" type="xs:int"/>
+ <xs:attribute name="label" type="xs:string" />
+ <xs:attribute name="value" type="xs:float" />
+ <xs:attribute name="colour" type="xs:int" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:attribute name="name" type="xs:string" />
+ <xs:attribute name="value" type="xs:string" />
</xs:complexType>
</xs:element>
</xs:sequence>
- <xs:attribute name="graph" type="xs:boolean" use="required"/>
- <xs:attribute name="graphType" type="xs:int" use="optional"/>
- <xs:attribute name="sequenceRef" type="xs:string" use="optional"/>
- <xs:attribute name="graphColour" type="xs:int" use="optional"/>
- <xs:attribute name="graphGroup" type="xs:int" use="optional"/>
- <xs:attribute name="id" type="xs:string" use="optional"/>
- <xs:attribute name="scoreOnly" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="score" type="xs:double" use="optional"/>
- <xs:attribute name="visible" type="xs:boolean" use="optional"/>
+ <xs:attribute name="graph" type="xs:boolean" use="required" />
+ <xs:attribute name="graphType" type="xs:int" use="optional" />
+ <xs:attribute name="sequenceRef" type="xs:string"
+ use="optional" />
+ <xs:attribute name="groupRef" type="xs:string"
+ use="optional" />
+ <xs:attribute name="graphColour" type="xs:int"
+ use="optional" />
+ <xs:attribute name="graphGroup" type="xs:int"
+ use="optional" />
+ <xs:attribute name="graphHeight" type="xs:int" use="optional">
+ <xs:annotation><xs:documentation>height in pixels for the graph if this is a graph-type annotation.</xs:documentation></xs:annotation></xs:attribute>
+ <xs:attribute name="id" type="xs:string" use="optional" />
+ <xs:attribute name="scoreOnly" type="xs:boolean"
+ use="optional" default="false" />
+ <xs:attribute name="score" type="xs:double" use="optional" />
+ <xs:attribute name="visible" type="xs:boolean"
+ use="optional" />
+ <xs:attribute name="centreColLabels" type="xs:boolean"
+ use="optional" />
+ <xs:attribute name="scaleColLabels" type="xs:boolean"
+ use="optional" />
+ <xs:attribute name="showAllColLabels" type="xs:boolean"
+ use="optional" />
+
+
+ <xs:attribute name="autoCalculated" type="xs:boolean" use="optional" default="false">
+ <xs:annotation><xs:documentation>is an autocalculated annotation row</xs:documentation>
+ </xs:annotation></xs:attribute>
+ <xs:attribute name="belowAlignment" type="xs:boolean" use="optional" default="true">
+ <xs:annotation><xs:documentation>is to be shown below the alignment - introduced in Jalview 2.8 for visualizing T-COFFEE alignment scores</xs:documentation></xs:annotation></xs:attribute>
+ <xs:attribute name="calcId" type="xs:string" use="optional">
+ <xs:annotation><xs:documentation>Optional string identifier used to group sets of annotation produced by a particular calculation. Values are opaque strings but have semantic meaning to Jalview's renderer, data importer and calculation system.</xs:documentation></xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="SequenceSet">
git://source.jalview.org / jalview.git / blobdiff