+++ /dev/null
-<?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 name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
- </xs:sequence>
- </xs:complexType>
- <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:extension>
- </xs:complexContent>
- </xs:complexType>
- </xs:element>
- <xs:element name="AlcodonFrame">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <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="alcodMap" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <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="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: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: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">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
- <xs:element name="description" type="xs:string" minOccurs="0"/>
- <xs:element name="secondaryStructure" minOccurs="0">
- <xs:simpleType>
- <xs:restriction base="xs:string">
- <xs:length value="1"/>
- </xs:restriction>
- </xs:simpleType>
- </xs:element>
- <xs:element name="value" type="xs:float" minOccurs="0"/>
- </xs:sequence>
- <xs:attribute name="position" type="xs:int" use="required"/>
- <xs:attribute name="colour" type="xs:int" use="optional"/>
- </xs:complexType>
- </xs:element>
- <xs:complexType name="SequenceType">
- <xs:sequence>
- <xs:element name="sequence" type="xs:string" minOccurs="0"/>
- <xs:element name="name" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- <xs:attribute name="id" type="xs:string"/>
- <xs:attribute name="description" type="xs:string"/>
- </xs:complexType>
-</xs:schema>
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