1 <?xml version="1.0" encoding="UTF-8"?>
3 Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours" xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
20 <xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
21 <xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
22 <xs:import namespace="www.jalview.org/xml/wsparamset" schemaLocation="JalviewWsParamSet.xsd"/>
23 <xs:complexType name="JalviewModel">
25 <xs:element name="creationDate" type="xs:dateTime" />
26 <xs:element name="version" type="xs:string" />
27 <xs:element name="vamsasModel" type="vamsas:VAMSAS" />
29 <xs:element name="JSeq" maxOccurs="unbounded">
32 <xs:element name="features"
33 type="jv:feature" minOccurs="0" maxOccurs="unbounded" />
34 <xs:element name="pdbids" minOccurs="0"
35 maxOccurs="unbounded">
42 name="structureState" minOccurs="0"
43 maxOccurs="unbounded">
49 ref="jv:swingwindow" />
51 name="visible" type="xs:boolean" />
53 name="viewId" type="xs:string" use="optional">
113 name="alignwithAlignPanel" type="xs:boolean"
114 use="optional" default="true">
144 name="colourwithAlignPanel" type="xs:boolean"
145 use="optional" default="false">
177 name="colourByJmol" type="xs:boolean" use="optional"
215 <xs:element name="hiddenSequences"
216 type="xs:int" minOccurs="0" maxOccurs="unbounded" />
218 <xs:attribute name="colour" type="xs:int"
220 <xs:attribute name="start" type="xs:int"
222 <xs:attribute name="end" type="xs:int"
224 <xs:attribute name="id" type="xs:string"
226 <xs:attribute name="hidden" type="xs:boolean" />
229 <xs:element name="JGroup" minOccurs="0"
230 maxOccurs="unbounded">
233 <xs:element name="seq" type="xs:string"
234 maxOccurs="unbounded" />
236 <xs:attribute name="start" type="xs:int" />
237 <xs:attribute name="end" type="xs:int" />
238 <xs:attribute name="name" type="xs:string" />
239 <xs:attribute name="colour" type="xs:string" />
240 <xs:attribute name="consThreshold"
242 <xs:attribute name="pidThreshold" type="xs:int" />
243 <xs:attribute name="outlineColour"
245 <xs:attribute name="displayBoxes"
247 <xs:attribute name="displayText"
249 <xs:attribute name="colourText"
251 <xs:attribute name="textCol1" type="xs:int" />
252 <xs:attribute name="textCol2" type="xs:int" />
253 <xs:attribute name="textColThreshold"
255 <xs:attribute name="showUnconserved"
256 type="xs:boolean" use="optional" />
257 <xs:attribute name="ignoreGapsinConsensus"
258 type="xs:boolean" use="optional" default="true" />
259 <xs:attribute name="showConsensusHistogram"
260 type="xs:boolean" use="optional" default="true" />
261 <xs:attribute name="showSequenceLogo"
262 type="xs:boolean" use="optional" default="false" />
263 <xs:attribute name="normaliseSequenceLogo"
264 type="xs:boolean" use="optional" default="false" />
265 <xs:attribute name="id" type="xs:string"
269 Optional sequence group ID (only
270 needs to be unique for this
277 <xs:element name="Viewport" maxOccurs="unbounded">
280 <xs:element name="AnnotationColours"
283 <xs:attribute name="aboveThreshold"
285 <xs:attribute name="annotation"
287 <xs:attribute name="minColour"
289 <xs:attribute name="maxColour"
291 <xs:attribute name="colourScheme"
293 <xs:attribute name="threshold"
295 <xs:attribute name="perSequence"
298 <xs:attribute name="predefinedColours"
303 <xs:element name="hiddenColumns"
304 minOccurs="0" maxOccurs="unbounded">
306 <xs:attribute name="start"
308 <xs:attribute name="end"
312 <xs:element name="calcIdParam"
314 minOccurs="0" maxOccurs="unbounded">
317 <xs:extension base="jvws:WebServiceParameterSet">
318 <xs:attribute name="calcId" type="xs:string" use="required">
320 <xs:documentation>handle for the calculation which uses this parameter set</xs:documentation></xs:annotation>
322 <xs:attribute name="needsUpdate" type="xs:boolean" use="optional" default="false">
323 <xs:annotation><xs:documentation>should the calculation be performed immediately after loading in order to refresh results</xs:documentation></xs:annotation>
325 <xs:attribute name="autoUpdate" type="xs:boolean" use="required">
326 <xs:annotation><xs:documentation>should the calculation be automatically performed on edits</xs:documentation></xs:annotation>
333 <xs:attributeGroup ref="jv:swingwindow" />
334 <xs:attribute name="conservationSelected"
336 <xs:attribute name="pidSelected"
338 <xs:attribute name="bgColour" type="xs:string" />
339 <xs:attribute name="consThreshold"
341 <xs:attribute name="pidThreshold" type="xs:int" />
342 <xs:attribute name="title" type="xs:string" />
343 <xs:attribute name="showFullId"
345 <xs:attribute name="rightAlignIds"
347 <xs:attribute name="showText" type="xs:boolean" />
348 <xs:attribute name="showColourText"
350 <xs:attribute name="showUnconserved"
351 type="xs:boolean" use="optional" default="false" />
352 <xs:attribute name="showBoxes"
354 <xs:attribute name="wrapAlignment"
356 <xs:attribute name="renderGaps"
358 <xs:attribute name="showSequenceFeatures"
360 <xs:attribute name="showNPfeatureTooltip"
361 type="xs:boolean" use="optional" />
362 <xs:attribute name="showDbRefTooltip"
363 type="xs:boolean" use="optional" />
364 <xs:attribute name="followHighlight"
365 type="xs:boolean" use="optional" default="true" />
366 <xs:attribute name="followSelection"
367 type="xs:boolean" use="optional" default="true" />
368 <xs:attribute name="showAnnotation"
370 <xs:attribute name="centreColumnLabels"
371 type="xs:boolean" use="optional" default="false" />
372 <xs:attribute name="showGroupConservation"
373 type="xs:boolean" use="optional" default="false" />
374 <xs:attribute name="showGroupConsensus"
375 type="xs:boolean" use="optional" default="false" />
376 <xs:attribute name="showConsensusHistogram"
377 type="xs:boolean" use="optional" default="true" />
378 <xs:attribute name="showSequenceLogo"
379 type="xs:boolean" use="optional" default="false" />
380 <xs:attribute name="normaliseSequenceLogo"
381 type="xs:boolean" use="optional" default="false" />
382 <xs:attribute name="ignoreGapsinConsensus"
383 type="xs:boolean" use="optional" default="true" />
385 <xs:attribute name="startRes" type="xs:int" />
386 <xs:attribute name="startSeq" type="xs:int" />
387 <xs:attribute name="fontName" type="xs:string" />
388 <xs:attribute name="fontSize" type="xs:int" />
389 <xs:attribute name="fontStyle" type="xs:int" />
390 <xs:attribute name="viewName" type="xs:string" />
391 <xs:attribute name="sequenceSetId"
393 <xs:attribute name="gatheredViews"
395 <xs:attribute name="textCol1" type="xs:int" />
396 <xs:attribute name="textCol2" type="xs:int" />
397 <xs:attribute name="textColThreshold"
399 <xs:attribute name="id" type="xs:ID"
403 unique id used by jalview to
404 synchronize between stored and
411 <xs:element name="UserColours" minOccurs="0"
412 maxOccurs="unbounded">
415 <xs:element name="UserColourScheme"
416 type="jalview:JalviewUserColours" />
418 <xs:attribute name="id" type="xs:string" />
421 <xs:element name="tree" minOccurs="0"
422 maxOccurs="unbounded">
424 <xs:sequence minOccurs="0">
425 <xs:element name="title" type="xs:string" />
426 <xs:element name="newick" type="xs:string" />
428 <xs:attribute name="fontName" type="xs:string" />
429 <xs:attribute name="fontSize" type="xs:int" />
430 <xs:attribute name="fontStyle" type="xs:int" />
431 <xs:attribute name="threshold" type="xs:float" />
432 <xs:attribute name="showBootstrap"
434 <xs:attribute name="showDistances"
436 <xs:attribute name="markUnlinked"
438 <xs:attribute name="fitToWindow"
440 <xs:attribute name="currentTree"
442 <xs:attribute name="id" type="xs:ID"
446 Tree ID added for binding tree
447 visualization settings to vamsas
448 document trees in jalview 2.4.1
452 <xs:attributeGroup ref="jv:swingwindow" />
455 <xs:element name="FeatureSettings" minOccurs="0">
458 <xs:element name="setting" minOccurs="0"
459 maxOccurs="unbounded">
461 <xs:attribute name="type"
462 type="xs:string" use="required" />
463 <xs:attribute name="colour"
464 type="xs:int" use="required" />
465 <xs:attribute name="display"
466 type="xs:boolean" use="required" />
467 <xs:attribute name="order"
468 type="xs:float" use="optional" />
469 <xs:attribute name="mincolour"
470 type="xs:int" use="optional">
473 Optional minimum colour
474 for graduated feature
479 <xs:attribute name="threshold"
480 type="xs:float" use="optional">
484 graduated feature colour
488 <xs:attribute name="threshstate"
489 type="xs:int" use="optional">
493 graduated feature colour
497 <xs:attribute name="max"
498 type="xs:float" use="optional" />
499 <xs:attribute name="min"
500 type="xs:float" use="optional" />
501 <xs:attribute name="colourByLabel"
502 type="xs:boolean" use="optional" />
503 <xs:attribute name="autoScale"
504 type="xs:boolean" use="optional" />
507 <xs:element name="group" minOccurs="0"
508 maxOccurs="unbounded">
510 <xs:attribute name="name"
511 type="xs:string" use="required" />
512 <xs:attribute name="display"
513 type="xs:boolean" use="required" />
522 <xs:complexType name="feature">
524 <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
526 <xs:attribute name="key" type="xs:string" use="required"/>
527 <xs:attribute name="value" type="xs:string" use="required"/>
531 <xs:attribute name="begin" type="xs:int" use="required"/>
532 <xs:attribute name="end" type="xs:int" use="required"/>
533 <xs:attribute name="type" type="xs:string" use="required"/>
534 <xs:attribute name="description" type="xs:string" use="optional"/>
535 <xs:attribute name="status" type="xs:string" use="optional"/>
536 <xs:attribute name="featureGroup" type="xs:string" use="optional"/>
537 <xs:attribute name="score" type="xs:float" use="optional"/>
539 <xs:complexType name="pdbentry">
540 <xs:sequence minOccurs="0" maxOccurs="unbounded">
541 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
543 <xs:attribute name="name" type="xs:string" use="required"/>
544 <xs:attribute name="value" type="xs:string" use="required"/>
548 <xs:attribute name="id" type="xs:string" use="required"/>
549 <xs:attribute name="type" type="xs:string" use="optional"/>
550 <xs:attribute name="file" type="xs:string"/>
553 <xs:complexType name="reportWindow">
555 <xs:documentation>Generic type for windows containing mime-typed data associated with other jalview windows</xs:documentation>
559 <xs:attribute name="id" type="xs:string" use="required"/>
560 <xs:attribute name="type" type="xs:string" use="optional"/>
561 <xs:attribute name="file" type="xs:string" use="optional"/>
564 <xs:attributeGroup name="swingwindow">
567 base attributes for windows displayed in Jalview desktop.
570 <xs:attribute name="width" type="xs:int"/>
571 <xs:attribute name="height" type="xs:int"/>
572 <xs:attribute name="xpos" type="xs:int"/>
573 <xs:attribute name="ypos" type="xs:int"/>