1 <?xml version="1.0" encoding="UTF-8"?>
3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
20 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
22 Java JAXB binding classes are generated by running command line tool xjc:
23 xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
24 Note this also generates code for included schemas
26 <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">
27 <xs:complexType name="VAMSAS">
29 <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
30 <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
33 <xs:complexType name="mapListType">
36 developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
39 This effectively represents a java.util.MapList object
43 <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
45 <xs:documentation> a region from start to end inclusive</xs:documentation>
48 <xs:attribute name="start" type="xs:int" use="required"/>
49 <xs:attribute name="end" type="xs:int" use="required"/>
52 <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
54 <xs:documentation> a region from start to end inclusive</xs:documentation>
57 <xs:attribute name="start" type="xs:int" use="required"/>
58 <xs:attribute name="end" type="xs:int" use="required"/>
62 <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
64 <xs:documentation>number of dictionary symbol widths involved in each
65 mapped position on this sequence (for example, 3 for a dna sequence exon
66 region that is being mapped to a protein sequence). This is optional,
67 since the unit can be usually be inferred from the dictionary type of
68 each sequence involved in the mapping. </xs:documentation>
71 <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
73 <xs:documentation>number of dictionary symbol widths involved in each
74 mapped position on this sequence (for example, 3 for a dna sequence exon
75 region that is being mapped to a protein sequence). This is optional,
76 since the unit can be usually be inferred from the dictionary type of
77 each sequence involved in the mapping. </xs:documentation>
81 <xs:element name="Mapping">
85 Represent the jalview.datamodel.Mapping object - it also provides
86 a way of storing sequences that are mapped 'to' without adding them
87 to the sequence set (which will mean they are then added to the alignment too).
91 <xs:extension base="vamsas:mapListType">
93 <xs:choice minOccurs="0" maxOccurs="1">
94 <xs:element ref="vamsas:Sequence"/>
95 <xs:element name="dseqFor">
97 <xs:restriction base="xs:string">
99 <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
110 <xs:element name="AlcodonFrame">
113 <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
117 specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
118 Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
121 <xs:attribute name="pos1" type="xs:integer" use="optional"/>
122 <xs:attribute name="pos2" type="xs:integer" use="optional"/>
123 <xs:attribute name="pos3" type="xs:integer" use="optional"/>
126 <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
129 <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
132 a Mapping entry and an associated protein sequence
137 <xs:attribute name="dnasq" type="xs:string" use="required">
140 internal jalview id for the dnasq for this mapping.
151 <xs:element name="Sequence">
154 <xs:extension base="vamsas:SequenceType">
156 <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
159 <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
161 <xs:attribute name="source" type="xs:string"/>
162 <xs:attribute name="version" type="xs:string"/>
163 <xs:attribute name="accessionId" type="xs:string"/>
167 <xs:attribute name="dsseqid" type="xs:string" use="optional">
170 dataset sequence id for this sequence. Will be created as union of sequences.
178 <xs:element name="Annotation">
181 <xs:element ref="vamsas:annotationElement" minOccurs="0"
182 maxOccurs="unbounded" />
183 <xs:element name="label" type="xs:string" />
184 <xs:element name="description" type="xs:string"
186 <xs:element name="thresholdLine" minOccurs="0">
188 <xs:attribute name="label" type="xs:string" />
189 <xs:attribute name="value" type="xs:float" />
190 <xs:attribute name="colour" type="xs:int" />
193 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
195 <xs:attribute name="name" type="xs:string" />
196 <xs:attribute name="value" type="xs:string" />
200 <xs:attribute name="graph" type="xs:boolean" use="required" />
201 <xs:attribute name="graphType" type="xs:int" use="optional" />
202 <xs:attribute name="sequenceRef" type="xs:string"
204 <xs:attribute name="groupRef" type="xs:string"
206 <xs:attribute name="graphColour" type="xs:int"
208 <xs:attribute name="graphGroup" type="xs:int"
210 <xs:attribute name="graphHeight" type="xs:int" use="optional">
211 <xs:annotation><xs:documentation>height in pixels for the graph if this is a graph-type annotation.</xs:documentation></xs:annotation></xs:attribute>
212 <xs:attribute name="id" type="xs:string" use="optional" />
213 <xs:attribute name="scoreOnly" type="xs:boolean"
214 use="optional" default="false" />
215 <xs:attribute name="score" type="xs:double" use="optional" />
216 <xs:attribute name="visible" type="xs:boolean"
218 <xs:attribute name="centreColLabels" type="xs:boolean"
220 <xs:attribute name="scaleColLabels" type="xs:boolean"
222 <xs:attribute name="showAllColLabels" type="xs:boolean"
226 <xs:attribute name="autoCalculated" type="xs:boolean" use="optional" default="false">
227 <xs:annotation><xs:documentation>is an autocalculated annotation row</xs:documentation>
228 </xs:annotation></xs:attribute>
229 <xs:attribute name="belowAlignment" type="xs:boolean" use="optional" default="true">
230 <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>
231 <xs:attribute name="calcId" type="xs:string" use="optional">
232 <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>
236 <xs:element name="SequenceSet">
239 <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
240 <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
241 <xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
243 <xs:attribute name="key" type="xs:string"/>
244 <xs:attribute name="value" type="xs:string"/>
247 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
249 <xs:attribute name="gapChar" type="xs:string" use="required"/>
250 <xs:attribute name="datasetId" type="xs:string" use="optional">
253 reference to set where jalview will gather the dataset sequences for all sequences in the set.
259 <xs:element name="annotationElement">
262 <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
263 <xs:element name="description" type="xs:string" minOccurs="0"/>
264 <xs:element name="secondaryStructure" minOccurs="0">
266 <xs:restriction base="xs:string">
267 <xs:length value="1"/>
271 <xs:element name="value" type="xs:float" minOccurs="0"/>
273 <xs:attribute name="position" type="xs:int" use="required"/>
274 <xs:attribute name="colour" type="xs:int" use="optional"/>
277 <xs:complexType name="SequenceType">
279 <xs:element name="sequence" type="xs:string" minOccurs="0"/>
280 <xs:element name="name" type="xs:string" minOccurs="0"/>
282 <xs:attribute name="id" type="xs:string"/>
283 <xs:attribute name="description" type="xs:string"/>