<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ * 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 ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:element name="SequenceSet">
+ <xs:complexType name="mapListType">
+ <xs:annotation>
+ <xs:documentation>
+ developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+ </xs:documentation>
+ <xs:documentation>
+ This effectively represents a java.util.MapList object
+ </xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> a region from start to end inclusive</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="start" type="xs:int" use="required"/>
+ <xs:attribute name="end" type="xs:int" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> a region from start to end inclusive</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="start" type="xs:int" use="required"/>
+ <xs:attribute name="end" type="xs:int" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
+ <xs:annotation>
+ <xs:documentation>number of dictionary symbol widths involved in each
+ mapped position on this sequence (for example, 3 for a dna sequence exon
+ region that is being mapped to a protein sequence). This is optional,
+ since the unit can be usually be inferred from the dictionary type of
+ each sequence involved in the mapping. </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
+ <xs:annotation>
+ <xs:documentation>number of dictionary symbol widths involved in each
+ mapped position on this sequence (for example, 3 for a dna sequence exon
+ region that is being mapped to a protein sequence). This is optional,
+ since the unit can be usually be inferred from the dictionary type of
+ each sequence involved in the mapping. </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ <xs:element name="Mapping">
+ <xs:complexType>
+ <xs:annotation>
+ <xs:documentation>
+ Represent the jalview.datamodel.Mapping object - it also provides
+ a way of storing sequences that are mapped 'to' without adding them
+ to the sequence set (which will mean they are then added to the alignment too).
+ </xs:documentation>
+ </xs:annotation>
+ <xs:complexContent>
+ <xs:extension base="vamsas:mapListType">
+ <xs:sequence>
+ <xs:choice minOccurs="0" maxOccurs="1">
+ <xs:element ref="vamsas:Sequence"/>
+ <xs:element name="dseqFor">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:annotation>
+ <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
+ </xs:annotation>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:element>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="mappingType" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Biotype of the mapping e.g. CdsToPeptide</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="AlcodonFrame">
<xs:complexType>
<xs:sequence>
- <xs:element name="Sequence" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
- <xs:complexContent>
- <xs:extension base="vamsas:SequenceType">
- <xs:sequence>
- <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="source" type="xs:string"/>
- <xs:attribute name="version" type="xs:string"/>
- <xs:attribute name="accessionId" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:extension>
- </xs:complexContent>
+ <xs:annotation>
+ <xs:documentation>
+ specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
+ Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
+ </xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="pos1" type="xs:integer" use="optional"/>
+ <xs:attribute name="pos2" type="xs:integer" use="optional"/>
+ <xs:attribute name="pos3" type="xs:integer" use="optional"/>
</xs:complexType>
</xs:element>
- <xs:element name="Annotation" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
<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 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:complexType>
+ <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
+ <xs:annotation>
+ <xs:documentation>
+ a Mapping entry and an associated protein sequence
+ </xs:documentation>
+ </xs:annotation>
</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="dnasq" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation>
+ internal jalview id for the dnasq for this mapping.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:complexType>
+
</xs:element>
+
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="Sequence">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="vamsas:SequenceType">
+ <xs:sequence>
+ <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
+ </xs:sequence>
+ <xs:attribute name="source" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="accessionId" type="xs:string"/>
+ <xs:attribute name="locus" type="xs:boolean" default="false">
+ <xs:annotation>
+ <xs:documentation>
+ true for gene locus mapping, source=species, version=assembly, accession=chromosome
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="canonical" type="xs:boolean" default="false">
+ <xs:annotation>
+ <xs:documentation>
+ true for the representative accession for databases where multiple accessions map to the same entry (eg. Uniprot)
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="dsseqid" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ dataset sequence id for this sequence. Will be created as union of sequences.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="biotype" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ Biotype of the sequence (if known)
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <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 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: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="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">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="key" type="xs:string"/>
<xs:attribute name="value" type="xs:string"/>
</xs:complexType>
</xs:element>
+ <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="gapChar" type="xs:string" use="required"/>
+ <xs:attribute name="datasetId" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ reference to set where jalview will gather the dataset sequences for all sequences in the set.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="annotationElement">
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