1 <?xml version="1.0" encoding="UTF-8"?>
3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
20 <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">
21 <xs:complexType name="VAMSAS">
23 <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
24 <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
27 <xs:complexType name="mapListType">
30 developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
33 This effectively represents a java.util.MapList object
37 <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
39 <xs:documentation> a region from start to end inclusive</xs:documentation>
42 <xs:attribute name="start" type="xs:int" use="required"/>
43 <xs:attribute name="end" type="xs:int" use="required"/>
46 <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
48 <xs:documentation> a region from start to end inclusive</xs:documentation>
51 <xs:attribute name="start" type="xs:int" use="required"/>
52 <xs:attribute name="end" type="xs:int" use="required"/>
56 <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
58 <xs:documentation>number of dictionary symbol widths involved in each
59 mapped position on this sequence (for example, 3 for a dna sequence exon
60 region that is being mapped to a protein sequence). This is optional,
61 since the unit can be usually be inferred from the dictionary type of
62 each sequence involved in the mapping. </xs:documentation>
65 <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
67 <xs:documentation>number of dictionary symbol widths involved in each
68 mapped position on this sequence (for example, 3 for a dna sequence exon
69 region that is being mapped to a protein sequence). This is optional,
70 since the unit can be usually be inferred from the dictionary type of
71 each sequence involved in the mapping. </xs:documentation>
75 <xs:element name="Mapping">
79 Represent the jalview.datamodel.Mapping object - it also provides
80 a way of storing sequences that are mapped 'to' without adding them
81 to the sequence set (which will mean they are then added to the alignment too).
85 <xs:extension base="vamsas:mapListType">
87 <xs:choice minOccurs="0" maxOccurs="1">
88 <xs:element ref="vamsas:Sequence"/>
89 <xs:element name="dseqFor">
91 <xs:restriction base="xs:string">
93 <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
104 <xs:element name="AlcodonFrame">
107 <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
111 specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
112 Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
115 <xs:attribute name="pos1" type="xs:integer" use="optional"/>
116 <xs:attribute name="pos2" type="xs:integer" use="optional"/>
117 <xs:attribute name="pos3" type="xs:integer" use="optional"/>
120 <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
123 <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
126 a Mapping entry and an associated protein sequence
131 <xs:attribute name="dnasq" type="xs:string" use="required">
134 internal jalview id for the dnasq for this mapping.
145 <xs:element name="Sequence">
148 <xs:extension base="vamsas:SequenceType">
150 <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
153 <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
155 <xs:attribute name="source" type="xs:string"/>
156 <xs:attribute name="version" type="xs:string"/>
157 <xs:attribute name="accessionId" type="xs:string"/>
161 <xs:attribute name="dsseqid" type="xs:string" use="optional">
164 dataset sequence id for this sequence. Will be created as union of sequences.
172 <xs:element name="Annotation">
175 <xs:element ref="vamsas:annotationElement" minOccurs="0"
176 maxOccurs="unbounded" />
177 <xs:element name="label" type="xs:string" />
178 <xs:element name="description" type="xs:string"
180 <xs:element name="thresholdLine" minOccurs="0">
182 <xs:attribute name="label" type="xs:string" />
183 <xs:attribute name="value" type="xs:float" />
184 <xs:attribute name="colour" type="xs:int" />
188 <xs:attribute name="graph" type="xs:boolean" use="required" />
189 <xs:attribute name="graphType" type="xs:int" use="optional" />
190 <xs:attribute name="sequenceRef" type="xs:string"
192 <xs:attribute name="groupRef" type="xs:string"
194 <xs:attribute name="graphColour" type="xs:int"
196 <xs:attribute name="graphGroup" type="xs:int"
198 <xs:attribute name="graphHeight" type="xs:int" use="optional">
199 <xs:annotation><xs:documentation>height in pixels for the graph if this is a graph-type annotation.</xs:documentation></xs:annotation></xs:attribute>
200 <xs:attribute name="id" type="xs:string" use="optional" />
201 <xs:attribute name="scoreOnly" type="xs:boolean"
202 use="optional" default="false" />
203 <xs:attribute name="score" type="xs:double" use="optional" />
204 <xs:attribute name="visible" type="xs:boolean"
206 <xs:attribute name="centreColLabels" type="xs:boolean"
208 <xs:attribute name="scaleColLabels" type="xs:boolean"
210 <xs:attribute name="showAllColLabels" type="xs:boolean"
214 <xs:attribute name="autoCalculated" type="xs:boolean" use="optional" default="false">
215 <xs:annotation><xs:documentation>is an autocalculated annotation row</xs:documentation>
216 </xs:annotation></xs:attribute>
219 <xs:element name="SequenceSet">
222 <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
223 <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
224 <xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
226 <xs:attribute name="key" type="xs:string"/>
227 <xs:attribute name="value" type="xs:string"/>
230 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
232 <xs:attribute name="gapChar" type="xs:string" use="required"/>
233 <xs:attribute name="datasetId" type="xs:string" use="optional">
236 reference to set where jalview will gather the dataset sequences for all sequences in the set.
242 <xs:element name="annotationElement">
245 <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
246 <xs:element name="description" type="xs:string" minOccurs="0"/>
247 <xs:element name="secondaryStructure" minOccurs="0">
249 <xs:restriction base="xs:string">
250 <xs:length value="1"/>
254 <xs:element name="value" type="xs:float" minOccurs="0"/>
256 <xs:attribute name="position" type="xs:int" use="required"/>
257 <xs:attribute name="colour" type="xs:int" use="optional"/>
260 <xs:complexType name="SequenceType">
262 <xs:element name="sequence" type="xs:string" minOccurs="0"/>
263 <xs:element name="name" type="xs:string" minOccurs="0"/>
265 <xs:attribute name="id" type="xs:string"/>
266 <xs:attribute name="description" type="xs:string"/>