JAL-3469 add "Number=." fields (all values) to all alleles in VCF record
[jalview.git] / schemas / vamsas.xsd
1 <?xml version="1.0" encoding="UTF-8"?>
2 <!--
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19 -->
20 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
21 <!-- 
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
25 -->
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">
28                 <xs:sequence>
29                         <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
30                         <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
31                 </xs:sequence>
32         </xs:complexType>
33         <xs:complexType name="mapListType">
34                 <xs:annotation>
35                         <xs:documentation> 
36                                 developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
37                         </xs:documentation>
38                         <xs:documentation>
39                                 This effectively represents a java.util.MapList object
40                         </xs:documentation>
41                 </xs:annotation>
42                 <xs:sequence>
43                         <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
44                                 <xs:annotation>
45                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
46                                 </xs:annotation>
47                                 <xs:complexType>
48                                         <xs:attribute name="start" type="xs:int" use="required"/>
49                                         <xs:attribute name="end" type="xs:int" use="required"/>
50                                 </xs:complexType>
51                         </xs:element>                                   
52                         <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
53                                 <xs:annotation>
54                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
55                                 </xs:annotation>
56                                 <xs:complexType>
57                                         <xs:attribute name="start" type="xs:int" use="required"/>
58                                         <xs:attribute name="end" type="xs:int" use="required"/>
59                                 </xs:complexType>
60                         </xs:element>                                   
61                 </xs:sequence>
62                 <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
63                         <xs:annotation>
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>
69                         </xs:annotation>
70                 </xs:attribute>
71                 <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
72                         <xs:annotation>
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>
78                         </xs:annotation>
79                 </xs:attribute>
80         </xs:complexType>
81         <xs:element name="Mapping">
82                 <xs:complexType>
83                         <xs:annotation>
84                                 <xs:documentation>
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).
88                                 </xs:documentation>
89                         </xs:annotation>
90                         <xs:complexContent>
91                                 <xs:extension base="vamsas:mapListType">
92                                         <xs:sequence>
93                                                 <xs:choice minOccurs="0" maxOccurs="1">
94                                                         <xs:element ref="vamsas:Sequence"/>
95                                                         <xs:element name="dseqFor">
96                                                                 <xs:simpleType>
97                                                                         <xs:restriction base="xs:string">
98                                                                                 <xs:annotation>
99                                                                                         <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
100                                                                                 </xs:annotation>
101                                                                         </xs:restriction>
102                                                                 </xs:simpleType>
103                                                         </xs:element>
104                                                 </xs:choice>
105                                         </xs:sequence>
106                                         <xs:attribute name="mappingType" type="xs:string" use="optional">
107                                                 <xs:annotation>
108                                                         <xs:documentation>Biotype of the mapping e.g. CdsToPeptide</xs:documentation>
109                                                 </xs:annotation>
110                                         </xs:attribute>
111                                 </xs:extension>
112                         </xs:complexContent>    
113                 </xs:complexType>
114         </xs:element>
115         <xs:element name="AlcodonFrame">
116                 <xs:complexType>
117                         <xs:sequence>
118                                 <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
119                                         <xs:complexType>
120                                                 <xs:annotation>
121                                                         <xs:documentation>
122                                                                 specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
123                                                                 Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
124                                                         </xs:documentation>
125                                                 </xs:annotation>
126                                                 <xs:attribute name="pos1" type="xs:integer" use="optional"/>
127                                                 <xs:attribute name="pos2" type="xs:integer" use="optional"/>
128                                                 <xs:attribute name="pos3" type="xs:integer" use="optional"/>
129                                         </xs:complexType>
130                                 </xs:element>
131                                 <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
132                                         <xs:complexType>
133                                                 <xs:sequence>
134                                                         <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
135                                                                 <xs:annotation>
136                                                                         <xs:documentation>
137                                                                                 a Mapping entry and an associated protein sequence
138                                                                         </xs:documentation>
139                                                                 </xs:annotation>
140                                                         </xs:element>
141                                                 </xs:sequence>
142                                                 <xs:attribute name="dnasq" type="xs:string" use="required">
143                                                         <xs:annotation>
144                                                                 <xs:documentation>
145                                                                         internal jalview id for the dnasq for this mapping.
146                                                                 </xs:documentation>
147                                                         </xs:annotation>
148                                                 </xs:attribute>
149                                         </xs:complexType>
150                                         
151                                 </xs:element>
152                                 
153                         </xs:sequence>
154                 </xs:complexType>
155         </xs:element>
156         <xs:element name="Sequence">
157                 <xs:complexType>
158                         <xs:complexContent>
159                                 <xs:extension base="vamsas:SequenceType">
160                                         <xs:sequence>
161                                                 <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
162                                                         <xs:complexType>
163                                                                 <xs:sequence>
164                                                                         <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
165                                                                 </xs:sequence>                                                                                                  
166                                                                 <xs:attribute name="source" type="xs:string"/>
167                                                                 <xs:attribute name="version" type="xs:string"/>
168                                                                 <xs:attribute name="accessionId" type="xs:string"/>
169                                                                 <xs:attribute name="locus" type="xs:boolean" default="false">
170                                                                         <xs:annotation>
171                                                                                 <xs:documentation>
172                                                                                         true for gene locus mapping, source=species, version=assembly, accession=chromosome
173                                                                                 </xs:documentation>
174                                                                         </xs:annotation>
175                                                                 </xs:attribute>
176                                                         </xs:complexType>
177                                                 </xs:element>
178                                         </xs:sequence>
179                                         <xs:attribute name="dsseqid" type="xs:string" use="optional">
180                                                 <xs:annotation>
181                                                         <xs:documentation>
182                                                                 dataset sequence id for this sequence. Will be created as union of sequences.
183                                                         </xs:documentation>
184                                                 </xs:annotation>
185                                         </xs:attribute>
186                                         <xs:attribute name="biotype" type="xs:string" use="optional">
187                                                 <xs:annotation>
188                                                         <xs:documentation>
189                                                                 Biotype of the sequence (if known)
190                                                         </xs:documentation>
191                                                 </xs:annotation>
192                                         </xs:attribute>
193                                 </xs:extension>
194                         </xs:complexContent>
195                 </xs:complexType>
196         </xs:element>
197         <xs:element name="Annotation">
198                 <xs:complexType>
199                         <xs:sequence>
200                                 <xs:element ref="vamsas:annotationElement" minOccurs="0"
201                                         maxOccurs="unbounded" />
202                                 <xs:element name="label" type="xs:string" />
203                                 <xs:element name="description" type="xs:string"
204                                         minOccurs="0" />
205                                 <xs:element name="thresholdLine" minOccurs="0">
206                                         <xs:complexType>
207                                                 <xs:attribute name="label" type="xs:string" />
208                                                 <xs:attribute name="value" type="xs:float" />
209                                                 <xs:attribute name="colour" type="xs:int" />
210                                         </xs:complexType>
211                                 </xs:element>
212                                 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
213                                         <xs:complexType>
214                                                 <xs:attribute name="name" type="xs:string" />
215                                                 <xs:attribute name="value" type="xs:string" />
216                                         </xs:complexType>
217                                 </xs:element>
218                         </xs:sequence>
219                         <xs:attribute name="graph" type="xs:boolean" use="required" />
220                         <xs:attribute name="graphType" type="xs:int" use="optional" />
221                         <xs:attribute name="sequenceRef" type="xs:string"
222                                 use="optional" />
223                         <xs:attribute name="groupRef" type="xs:string"
224                                 use="optional" />
225                         <xs:attribute name="graphColour" type="xs:int"
226                                 use="optional" />
227                         <xs:attribute name="graphGroup" type="xs:int"
228                                 use="optional" />
229                         <xs:attribute name="graphHeight" type="xs:int" use="optional">
230                         <xs:annotation><xs:documentation>height in pixels for the graph if this is a graph-type annotation.</xs:documentation></xs:annotation></xs:attribute>
231                         <xs:attribute name="id" type="xs:string" use="optional" />
232                         <xs:attribute name="scoreOnly" type="xs:boolean"
233                                 use="optional" default="false" />
234                         <xs:attribute name="score" type="xs:double" use="optional" />
235                         <xs:attribute name="visible" type="xs:boolean"
236                                 use="optional" />
237                         <xs:attribute name="centreColLabels" type="xs:boolean"
238                                 use="optional" />
239                         <xs:attribute name="scaleColLabels" type="xs:boolean"
240                                 use="optional" />
241                         <xs:attribute name="showAllColLabels" type="xs:boolean"
242                                 use="optional" />
243
244
245                         <xs:attribute name="autoCalculated" type="xs:boolean" use="optional" default="false">
246                         <xs:annotation><xs:documentation>is an autocalculated annotation row</xs:documentation>
247                         </xs:annotation></xs:attribute>
248                         <xs:attribute name="belowAlignment" type="xs:boolean" use="optional" default="true">
249                         <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>
250                         <xs:attribute name="calcId" type="xs:string" use="optional">
251                         <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>
252                         </xs:attribute>
253                 </xs:complexType>
254         </xs:element>   
255         <xs:element name="SequenceSet">
256                 <xs:complexType>
257                         <xs:sequence>
258                                 <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
259                                 <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
260                                 <xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
261                                         <xs:complexType>
262                                                 <xs:attribute name="key" type="xs:string"/>
263                                                 <xs:attribute name="value" type="xs:string"/>
264                                         </xs:complexType>
265                                 </xs:element>
266                                 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
267                         </xs:sequence>
268                         <xs:attribute name="gapChar" type="xs:string" use="required"/>
269                         <xs:attribute name="datasetId" type="xs:string" use="optional">
270                                 <xs:annotation>
271                                         <xs:documentation>
272                                                 reference to set where jalview will gather the dataset sequences for all sequences in the set. 
273                                         </xs:documentation>
274                                 </xs:annotation>
275                         </xs:attribute>
276                 </xs:complexType>
277         </xs:element>
278         <xs:element name="annotationElement">
279                 <xs:complexType>
280                         <xs:sequence>
281                                 <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
282                                 <xs:element name="description" type="xs:string" minOccurs="0"/>
283                                 <xs:element name="secondaryStructure" minOccurs="0">
284                                         <xs:simpleType>
285                                                 <xs:restriction base="xs:string">
286                                                         <xs:length value="1"/>
287                                                 </xs:restriction>
288                                         </xs:simpleType>
289                                 </xs:element>
290                                 <xs:element name="value" type="xs:float" minOccurs="0"/>
291                         </xs:sequence>
292                         <xs:attribute name="position" type="xs:int" use="required"/>
293                         <xs:attribute name="colour" type="xs:int" use="optional"/>
294                 </xs:complexType>
295         </xs:element>
296         <xs:complexType name="SequenceType">
297                 <xs:sequence>
298                         <xs:element name="sequence" type="xs:string" minOccurs="0"/>
299                         <xs:element name="name" type="xs:string" minOccurs="0"/>
300                 </xs:sequence>
301                 <xs:attribute name="id" type="xs:string"/>
302                 <xs:attribute name="description" type="xs:string"/>
303         </xs:complexType>
304 </xs:schema>