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:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
28 xmlns:vamsas="www.vamsas.ac.uk/jalview/version2"
29 targetNamespace="www.vamsas.ac.uk/jalview/version2"
30 elementFormDefault="qualified" attributeFormDefault="unqualified">
31 <xs:complexType name="VAMSAS">
33 <xs:element name="Tree" type="xs:string" minOccurs="0"
34 maxOccurs="unbounded" />
35 <xs:element ref="vamsas:SequenceSet" minOccurs="0"
36 maxOccurs="unbounded" />
39 <xs:complexType name="mapListType">
42 developed after mapRangeType from
43 http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
46 This effectively represents a java.util.MapList
51 <xs:element name="mapListFrom" minOccurs="0"
52 maxOccurs="unbounded">
54 <xs:documentation> a region from start to end inclusive
58 <xs:attribute name="start" type="xs:int"
60 <xs:attribute name="end" type="xs:int" use="required" />
63 <xs:element name="mapListTo" minOccurs="0"
64 maxOccurs="unbounded">
66 <xs:documentation> a region from start to end inclusive
70 <xs:attribute name="start" type="xs:int"
72 <xs:attribute name="end" type="xs:int" use="required" />
76 <xs:attribute name="mapFromUnit"
77 type="xs:positiveInteger" use="required">
79 <xs:documentation>number of dictionary symbol widths involved in
81 mapped position on this sequence (for example, 3 for a dna
83 region that is being mapped to a protein sequence).
85 since the unit can be usually be inferred from the
87 each sequence involved in the mapping.
91 <xs:attribute name="mapToUnit" type="xs:positiveInteger"
94 <xs:documentation>number of dictionary symbol widths involved in
96 mapped position on this sequence (for example, 3 for a dna
98 region that is being mapped to a protein sequence).
100 since the unit can be usually be inferred from the
102 each sequence involved in the mapping.
107 <xs:element name="Mapping">
111 Represent the jalview.datamodel.Mapping object -
113 a way of storing sequences that are mapped 'to'
115 to the sequence set (which will mean they are
116 then added to the alignment too).
120 <xs:extension base="vamsas:mapListType">
122 <xs:choice minOccurs="0" maxOccurs="1">
123 <xs:element ref="vamsas:Sequence" />
124 <xs:element name="dseqFor">
126 <xs:restriction base="xs:string">
128 <xs:documentation>The sequence whose dataset sequence is to
137 <xs:attribute name="mappingType" type="xs:string"
140 <xs:documentation>Biotype of the mapping e.g. CdsToPeptide
148 <xs:element name="AlcodonFrame">
151 <xs:element name="alcodon" minOccurs="0"
152 maxOccurs="unbounded">
156 specifies a series of aligned codons from an
157 associated DNA sequence alignment that when translated
158 correspond to columns of a peptide alignment.
160 either all pos1,2,3 attributes specified, or none at all
161 (indicating a gapped column with no translated peptide).
164 <xs:attribute name="pos1" type="xs:integer"
166 <xs:attribute name="pos2" type="xs:integer"
168 <xs:attribute name="pos3" type="xs:integer"
172 <xs:element name="alcodMap" minOccurs="0"
173 maxOccurs="unbounded">
176 <xs:element ref="vamsas:Mapping" maxOccurs="1"
180 a Mapping entry and an associated protein
186 <xs:attribute name="dnasq" type="xs:string"
190 internal jalview id for the dnasq for this
202 <xs:element name="Sequence">
205 <xs:extension base="vamsas:SequenceType">
207 <xs:element name="DBRef" minOccurs="0"
208 maxOccurs="unbounded">
211 <xs:element ref="vamsas:Mapping" minOccurs="0"
214 <xs:attribute name="source" type="xs:string" />
215 <xs:attribute name="version" type="xs:string" />
216 <xs:attribute name="accessionId" type="xs:string" />
217 <xs:attribute name="locus" type="xs:boolean"
221 true for gene locus mapping, source=species,
222 version=assembly, accession=chromosome
226 <xs:attribute name="canonical" type="xs:boolean"
230 true for the representative accession for
231 databases where multiple accessions map to the same entry
239 <xs:attribute name="dsseqid" type="xs:string"
243 dataset sequence id for this sequence. Will be
244 created as union of sequences.
248 <xs:attribute name="biotype" type="xs:string"
252 Biotype of the sequence (if known)
260 <xs:element name="Annotation">
263 <xs:element ref="vamsas:annotationElement" minOccurs="0"
264 maxOccurs="unbounded" />
265 <xs:element name="label" type="xs:string" />
266 <xs:element name="description" type="xs:string"
268 <xs:element name="thresholdLine" minOccurs="0">
270 <xs:attribute name="label" type="xs:string" />
271 <xs:attribute name="value" type="xs:float" />
272 <xs:attribute name="colour" type="xs:int" />
275 <xs:element name="contactmatrix"
276 type="vamsas:MapOnAMatrixType" maxOccurs="unbounded" minOccurs="0">
278 <xs:element name="property" type="vamsas:property"
279 minOccurs="0" maxOccurs="unbounded" />
281 <xs:attribute name="graph" type="xs:boolean"
283 <xs:attribute name="graphType" type="xs:int"
285 <xs:attribute name="sequenceRef" type="xs:string"
287 <xs:attribute name="groupRef" type="xs:string"
289 <xs:attribute name="graphColour" type="xs:int"
291 <xs:attribute name="graphGroup" type="xs:int"
293 <xs:attribute name="graphHeight" type="xs:int"
296 <xs:documentation>height in pixels for the graph if this is a
297 graph-type annotation.
301 <xs:attribute name="id" type="xs:string" use="optional" />
302 <xs:attribute name="scoreOnly" type="xs:boolean"
303 use="optional" default="false" />
304 <xs:attribute name="score" type="xs:double"
306 <xs:attribute name="visible" type="xs:boolean"
308 <xs:attribute name="centreColLabels" type="xs:boolean"
310 <xs:attribute name="scaleColLabels" type="xs:boolean"
312 <xs:attribute name="showAllColLabels" type="xs:boolean"
316 <xs:attribute name="autoCalculated" type="xs:boolean"
317 use="optional" default="false">
319 <xs:documentation>is an autocalculated annotation row
323 <xs:attribute name="belowAlignment" type="xs:boolean"
324 use="optional" default="true">
326 <xs:documentation>is to be shown below the alignment - introduced
327 in Jalview 2.8 for visualizing T-COFFEE alignment scores
331 <xs:attribute name="calcId" type="xs:string"
334 <xs:documentation>Optional string identifier used to group sets of
335 annotation produced by a particular calculation. Values are opaque
336 strings but have semantic meaning to Jalview's renderer, data
337 importer and calculation system.
343 <xs:element name="SequenceSet">
346 <xs:element ref="vamsas:Sequence" minOccurs="0"
347 maxOccurs="unbounded" />
348 <xs:element ref="vamsas:Annotation" minOccurs="0"
349 maxOccurs="unbounded" />
350 <xs:element name="sequenceSetProperties" minOccurs="0"
351 maxOccurs="unbounded">
353 <xs:attribute name="key" type="xs:string" />
354 <xs:attribute name="value" type="xs:string" />
357 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0"
358 maxOccurs="unbounded" />
359 <xs:element name="Matrices" type="vamsas:MatrixType"
360 minOccurs="0" maxOccurs="unbounded">
362 <xs:documentation>Matrices referred to by this set of sequences.
367 <xs:attribute name="gapChar" type="xs:string"
369 <xs:attribute name="datasetId" type="xs:string"
373 reference to set where jalview will gather the
374 dataset sequences for all sequences in the set.
380 <xs:element name="annotationElement">
383 <xs:element name="displayCharacter" type="xs:string"
385 <xs:element name="description" type="xs:string"
387 <xs:element name="secondaryStructure" minOccurs="0">
389 <xs:restriction base="xs:string">
390 <xs:length value="1" />
394 <xs:element name="value" type="xs:float" minOccurs="0" />
396 <xs:attribute name="position" type="xs:int"
398 <xs:attribute name="colour" type="xs:int" use="optional" />
401 <xs:complexType name="SequenceType">
403 <xs:element name="sequence" type="xs:string" minOccurs="0" />
404 <xs:element name="name" type="xs:string" minOccurs="0" />
406 <xs:attribute name="id" type="xs:string" />
407 <xs:attribute name="description" type="xs:string" />
409 <xs:complexType name="MatrixType">
411 <xs:documentation>Represents matrix data imported to Jalview, and the
412 results of any derived calculations (independent of a particular
418 <xs:element name="elements" type="xs:string" minOccurs="1"
421 <xs:documentation>serialised representation of matrix as one or
422 more sets of comma separated values
426 <xs:element name="groups" type="xs:string" minOccurs="0"
427 maxOccurs="unbounded">
429 <xs:documentation>Comma separated series of longs formed from
430 bitsets defining partitions on the rows/columns of the matrix
434 <xs:element name="newick" type="xs:string" minOccurs="0"
435 maxOccurs="unbounded">
437 <xs:documentation>tree computed for this</xs:documentation>
440 <xs:element name="property" type="vamsas:property"
441 minOccurs="0" maxOccurs="unbounded" />
444 <xs:attribute name="type" type="xs:string" use="required" />
445 <xs:attribute name="rows" type="xs:integer"
447 <xs:attribute name="cols" type="xs:integer"
449 <xs:attribute name="treeMethod" type="xs:string"
451 <xs:attribute name="cutHeight" type="xs:double"
453 <xs:attribute name="id" type="xs:string" use="required" />
456 <xs:complexType name="MapOnAMatrixType">
458 <xs:documentation>Defines a mapping from the local frame to a matrix
459 and its associated data specified by MatrixType
463 <xs:element name="property" type="vamsas:property"
464 minOccurs="0" maxOccurs="unbounded" />
465 <xs:element name="mapping" type="vamsas:mapListType"
466 minOccurs="0" maxOccurs="1">
468 <xs:documentation>mapping from the matrix row and column positions
470 associated reference frame
476 <xs:attribute name="matrix" type="xs:string"
480 <xs:documentation>reference to the matrix type this Map refers to
484 <xs:attribute name="id" type="xs:string" use="optional" />
486 <xs:complexType name="property">
487 <xs:attribute name="name" type="xs:string" />
488 <xs:attribute name="value" type="xs:string" />