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"
27 xmlns:vamsas="www.vamsas.ac.uk/jalview/version2"
28 targetNamespace="www.vamsas.ac.uk/jalview/version2"
29 elementFormDefault="qualified" attributeFormDefault="unqualified">
30 <xs:complexType name="VAMSAS">
32 <xs:element name="Tree" type="xs:string" minOccurs="0"
33 maxOccurs="unbounded" />
34 <xs:element ref="vamsas:SequenceSet" minOccurs="0"
35 maxOccurs="unbounded" />
38 <xs:complexType name="mapListType">
41 developed after mapRangeType from
42 http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
45 This effectively represents a java.util.MapList
50 <xs:element name="mapListFrom" minOccurs="0"
51 maxOccurs="unbounded">
53 <xs:documentation> a region from start to end inclusive
57 <xs:attribute name="start" type="xs:int"
59 <xs:attribute name="end" type="xs:int" use="required" />
62 <xs:element name="mapListTo" minOccurs="0"
63 maxOccurs="unbounded">
65 <xs:documentation> a region from start to end inclusive
69 <xs:attribute name="start" type="xs:int"
71 <xs:attribute name="end" type="xs:int" use="required" />
75 <xs:attribute name="mapFromUnit"
76 type="xs:positiveInteger" use="required">
78 <xs:documentation>number of dictionary symbol widths involved in
80 mapped position on this sequence (for example, 3 for a dna
82 region that is being mapped to a protein sequence).
84 since the unit can be usually be inferred from the
86 each sequence involved in the mapping.
90 <xs:attribute name="mapToUnit" type="xs:positiveInteger"
93 <xs:documentation>number of dictionary symbol widths involved in
95 mapped position on this sequence (for example, 3 for a dna
97 region that is being mapped to a protein sequence).
99 since the unit can be usually be inferred from the
101 each sequence involved in the mapping.
106 <xs:element name="Mapping">
110 Represent the jalview.datamodel.Mapping object -
112 a way of storing sequences that are mapped 'to'
114 to the sequence set (which will mean they are
115 then added to the alignment too).
119 <xs:extension base="vamsas:mapListType">
121 <xs:choice minOccurs="0" maxOccurs="1">
122 <xs:element ref="vamsas:Sequence" />
123 <xs:element name="dseqFor">
125 <xs:restriction base="xs:string">
127 <xs:documentation>The sequence whose dataset sequence is to
136 <xs:attribute name="mappingType" type="xs:string"
139 <xs:documentation>Biotype of the mapping e.g. CdsToPeptide
147 <xs:element name="AlcodonFrame">
150 <xs:element name="alcodon" minOccurs="0"
151 maxOccurs="unbounded">
155 specifies a series of aligned codons from an
156 associated DNA sequence alignment that when translated
157 correspond to columns of a peptide alignment.
159 either all pos1,2,3 attributes specified, or none at all
160 (indicating a gapped column with no translated peptide).
163 <xs:attribute name="pos1" type="xs:integer"
165 <xs:attribute name="pos2" type="xs:integer"
167 <xs:attribute name="pos3" type="xs:integer"
171 <xs:element name="alcodMap" minOccurs="0"
172 maxOccurs="unbounded">
175 <xs:element ref="vamsas:Mapping" maxOccurs="1"
179 a Mapping entry and an associated protein
185 <xs:attribute name="dnasq" type="xs:string"
189 internal jalview id for the dnasq for this
201 <xs:element name="Sequence">
204 <xs:extension base="vamsas:SequenceType">
206 <xs:element name="DBRef" minOccurs="0"
207 maxOccurs="unbounded">
210 <xs:element ref="vamsas:Mapping" minOccurs="0"
213 <xs:attribute name="source" type="xs:string" />
214 <xs:attribute name="version" type="xs:string" />
215 <xs:attribute name="accessionId" type="xs:string" />
216 <xs:attribute name="locus" type="xs:boolean"
220 true for gene locus mapping, source=species,
221 version=assembly, accession=chromosome
225 <xs:attribute name="canonical" type="xs:boolean"
229 true for the representative accession for
230 databases where multiple accessions map to the same entry
238 <xs:attribute name="dsseqid" type="xs:string"
242 dataset sequence id for this sequence. Will be
243 created as union of sequences.
247 <xs:attribute name="biotype" type="xs:string"
251 Biotype of the sequence (if known)
259 <xs:element name="Annotation">
262 <xs:element ref="vamsas:annotationElement" minOccurs="0"
263 maxOccurs="unbounded" />
264 <xs:element name="label" type="xs:string" />
265 <xs:element name="description" type="xs:string"
267 <xs:element name="thresholdLine" minOccurs="0">
269 <xs:attribute name="label" type="xs:string" />
270 <xs:attribute name="value" type="xs:float" />
271 <xs:attribute name="colour" type="xs:int" />
274 <xs:element name="contactmatrix"
275 type="vamsas:MapOnAMatrixType" maxOccurs="unbounded" minOccurs="0">
277 <xs:element name="property" type="vamsas:property"
278 minOccurs="0" maxOccurs="unbounded" />
280 <xs:attribute name="graph" type="xs:boolean"
282 <xs:attribute name="graphType" type="xs:int"
284 <xs:attribute name="sequenceRef" type="xs:string"
286 <xs:attribute name="groupRef" type="xs:string"
288 <xs:attribute name="graphColour" type="xs:int"
290 <xs:attribute name="graphGroup" type="xs:int"
292 <xs:attribute name="graphHeight" type="xs:int"
295 <xs:documentation>height in pixels for the graph if this is a
296 graph-type annotation.
300 <xs:attribute name="id" type="xs:string" use="optional" />
301 <xs:attribute name="scoreOnly" type="xs:boolean"
302 use="optional" default="false" />
303 <xs:attribute name="score" type="xs:double"
305 <xs:attribute name="visible" type="xs:boolean"
307 <xs:attribute name="centreColLabels" type="xs:boolean"
309 <xs:attribute name="scaleColLabels" type="xs:boolean"
311 <xs:attribute name="showAllColLabels" type="xs:boolean"
315 <xs:attribute name="autoCalculated" type="xs:boolean"
316 use="optional" default="false">
318 <xs:documentation>is an autocalculated annotation row
322 <xs:attribute name="belowAlignment" type="xs:boolean"
323 use="optional" default="true">
325 <xs:documentation>is to be shown below the alignment - introduced
326 in Jalview 2.8 for visualizing T-COFFEE alignment scores
330 <xs:attribute name="calcId" type="xs:string"
333 <xs:documentation>Optional string identifier used to group sets of
334 annotation produced by a particular calculation. Values are opaque
335 strings but have semantic meaning to Jalview's renderer, data
336 importer and calculation system.
342 <xs:element name="SequenceSet">
345 <xs:element ref="vamsas:Sequence" minOccurs="0"
346 maxOccurs="unbounded" />
347 <xs:element ref="vamsas:Annotation" minOccurs="0"
348 maxOccurs="unbounded" />
349 <xs:element name="sequenceSetProperties" minOccurs="0"
350 maxOccurs="unbounded">
352 <xs:attribute name="key" type="xs:string" />
353 <xs:attribute name="value" type="xs:string" />
356 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0"
357 maxOccurs="unbounded" />
358 <xs:element name="Matrix" type="vamsas:MatrixType"
359 minOccurs="0" maxOccurs="unbounded">
361 <xs:documentation>Matrices referred to by this set of sequences.
366 <xs:attribute name="gapChar" type="xs:string"
368 <xs:attribute name="datasetId" type="xs:string"
372 reference to set where jalview will gather the
373 dataset sequences for all sequences in the set.
379 <xs:element name="annotationElement">
382 <xs:element name="displayCharacter" type="xs:string"
384 <xs:element name="description" type="xs:string"
386 <xs:element name="secondaryStructure" minOccurs="0">
388 <xs:restriction base="xs:string">
389 <xs:length value="1" />
393 <xs:element name="value" type="xs:float" minOccurs="0" />
395 <xs:attribute name="position" type="xs:int"
397 <xs:attribute name="colour" type="xs:int" use="optional" />
400 <xs:complexType name="SequenceType">
402 <xs:element name="sequence" type="xs:string" minOccurs="0" />
403 <xs:element name="name" type="xs:string" minOccurs="0" />
405 <xs:attribute name="id" type="xs:string" />
406 <xs:attribute name="description" type="xs:string" />
408 <xs:complexType name="MatrixType">
410 <xs:documentation>Represents matrix data imported to Jalview, and the
411 results of any derived calculations (independent of a particular
417 <xs:element name="elements" type="xs:string" minOccurs="1"
420 <xs:documentation>serialised representation of matrix as one or
421 more sets of comma separated values
425 <xs:element name="groups" type="xs:string" minOccurs="0"
426 maxOccurs="unbounded">
428 <xs:documentation>Comma separated series of longs formed from
429 bitsets defining partitions on the rows/columns of the matrix
433 <xs:element name="newick" type="xs:string" minOccurs="0"
434 maxOccurs="unbounded">
436 <xs:documentation>tree computed for this</xs:documentation>
439 <xs:element name="property" type="vamsas:property"
440 minOccurs="0" maxOccurs="unbounded" />
443 <xs:attribute name="type" type="xs:string" use="required" />
444 <xs:attribute name="rows" type="xs:integer"
446 <xs:attribute name="cols" type="xs:integer"
448 <xs:attribute name="treeMethod" type="xs:string"
450 <xs:attribute name="cutHeight" type="xs:double"
452 <xs:attribute name="id" type="xs:string" use="required" />
455 <xs:complexType name="MapOnAMatrixType">
457 <xs:documentation>Defines a mapping from the local frame to a matrix
458 and its associated data specified by MatrixType
462 <xs:element name="property" type="vamsas:property"
463 minOccurs="0" maxOccurs="unbounded" />
464 <xs:element name="mapping" type="vamsas:mapListType"
465 minOccurs="0" maxOccurs="1">
467 <xs:documentation>mapping from the matrix row and column positions
469 associated reference frame
475 <xs:attribute name="matrix" type="xs:string"
479 <xs:documentation>reference to the matrix type this Map refers to
483 <xs:attribute name="id" type="xs:string" use="optional" />
485 <xs:complexType name="property">
486 <xs:attribute name="name" type="xs:string" />
487 <xs:attribute name="value" type="xs:string" />