1 <?xml version="1.0" encoding="UTF-8"?>
3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
4 * Copyright (C) 2014 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 <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">
21 <xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
22 <xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
23 <xs:import namespace="www.jalview.org/xml/wsparamset" schemaLocation="JalviewWsParamSet.xsd"/>
24 <xs:complexType name="JalviewModel">
26 <xs:element name="creationDate" type="xs:dateTime" />
27 <xs:element name="version" type="xs:string" />
28 <xs:element name="vamsasModel" type="vamsas:VAMSAS" />
30 <xs:element name="JSeq" maxOccurs="unbounded" minOccurs="0">
33 <xs:element name="features"
34 type="jv:feature" minOccurs="0" maxOccurs="unbounded" />
35 <xs:element name="pdbids" minOccurs="0"
36 maxOccurs="unbounded">
43 name="structureState" minOccurs="0"
44 maxOccurs="unbounded">
50 ref="jv:swingwindow" />
52 name="visible" type="xs:boolean" />
54 name="viewId" type="xs:string" use="optional">
114 name="alignwithAlignPanel" type="xs:boolean"
115 use="optional" default="true">
145 name="colourwithAlignPanel" type="xs:boolean"
146 use="optional" default="false">
178 name="colourByJmol" type="xs:boolean" use="optional"
216 <xs:element name="hiddenSequences"
217 type="xs:int" minOccurs="0" maxOccurs="unbounded" />
219 <xs:attribute name="colour" type="xs:int"
221 <xs:attribute name="start" type="xs:int"
223 <xs:attribute name="end" type="xs:int"
225 <xs:attribute name="id" type="xs:string"
227 <xs:attribute name="hidden" type="xs:boolean" />
230 <xs:element name="JGroup" minOccurs="0"
231 maxOccurs="unbounded">
234 <xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
235 <xs:element name="annotationColours" type="jv:AnnotationColourScheme"
236 minOccurs="0" maxOccurs="1" />
238 <xs:attribute name="start" type="xs:int" />
239 <xs:attribute name="end" type="xs:int" />
240 <xs:attribute name="name" type="xs:string" />
241 <xs:attribute name="colour" type="xs:string" />
242 <xs:attribute name="consThreshold"
244 <xs:attribute name="pidThreshold" type="xs:int" />
245 <xs:attribute name="outlineColour"
247 <xs:attribute name="displayBoxes"
249 <xs:attribute name="displayText"
251 <xs:attribute name="colourText"
253 <xs:attribute name="textCol1" type="xs:int" />
254 <xs:attribute name="textCol2" type="xs:int" />
255 <xs:attribute name="textColThreshold"
257 <xs:attribute name="showUnconserved"
258 type="xs:boolean" use="optional" />
259 <xs:attribute name="ignoreGapsinConsensus"
260 type="xs:boolean" use="optional" default="true" />
261 <xs:attribute name="showConsensusHistogram"
262 type="xs:boolean" use="optional" default="true" />
263 <xs:attribute name="showSequenceLogo"
264 type="xs:boolean" use="optional" default="false" />
265 <xs:attribute name="normaliseSequenceLogo"
266 type="xs:boolean" use="optional" default="false" />
267 <xs:attribute name="id" type="xs:string"
271 Optional sequence group ID (only
272 needs to be unique for this
279 <xs:element name="Viewport" maxOccurs="unbounded" minOccurs="0">
282 <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
283 minOccurs="0" maxOccurs="1">
285 <xs:element name="hiddenColumns"
286 minOccurs="0" maxOccurs="unbounded">
288 <xs:attribute name="start"
290 <xs:attribute name="end"
294 <xs:element name="calcIdParam"
296 minOccurs="0" maxOccurs="unbounded">
299 <xs:extension base="jvws:WebServiceParameterSet">
300 <xs:attribute name="calcId" type="xs:string" use="required">
302 <xs:documentation>handle for the calculation which uses this parameter set</xs:documentation></xs:annotation>
304 <xs:attribute name="needsUpdate" type="xs:boolean" use="optional" default="false">
305 <xs:annotation><xs:documentation>should the calculation be performed immediately after loading in order to refresh results</xs:documentation></xs:annotation>
307 <xs:attribute name="autoUpdate" type="xs:boolean" use="required">
308 <xs:annotation><xs:documentation>should the calculation be automatically performed on edits</xs:documentation></xs:annotation>
315 <xs:attributeGroup ref="jv:swingwindow" />
316 <xs:attribute name="conservationSelected"
318 <xs:attribute name="pidSelected"
320 <xs:attribute name="bgColour" type="xs:string" />
321 <xs:attribute name="consThreshold"
323 <xs:attribute name="pidThreshold" type="xs:int" />
324 <xs:attribute name="title" type="xs:string" />
325 <xs:attribute name="showFullId"
327 <xs:attribute name="rightAlignIds"
329 <xs:attribute name="showText" type="xs:boolean" />
330 <xs:attribute name="showColourText"
332 <xs:attribute name="showUnconserved"
333 type="xs:boolean" use="optional" default="false" />
334 <xs:attribute name="showBoxes"
336 <xs:attribute name="wrapAlignment"
338 <xs:attribute name="renderGaps"
340 <xs:attribute name="showSequenceFeatures"
342 <xs:attribute name="showNPfeatureTooltip"
343 type="xs:boolean" use="optional" />
344 <xs:attribute name="showDbRefTooltip"
345 type="xs:boolean" use="optional" />
346 <xs:attribute name="followHighlight"
347 type="xs:boolean" use="optional" default="true" />
348 <xs:attribute name="followSelection"
349 type="xs:boolean" use="optional" default="true" />
350 <xs:attribute name="showAnnotation"
352 <xs:attribute name="centreColumnLabels"
353 type="xs:boolean" use="optional" default="false" />
354 <xs:attribute name="showGroupConservation"
355 type="xs:boolean" use="optional" default="false" />
356 <xs:attribute name="showGroupConsensus"
357 type="xs:boolean" use="optional" default="false" />
358 <xs:attribute name="showConsensusHistogram"
359 type="xs:boolean" use="optional" default="true" />
360 <xs:attribute name="showSequenceLogo"
361 type="xs:boolean" use="optional" default="false" />
362 <xs:attribute name="normaliseSequenceLogo"
363 type="xs:boolean" use="optional" default="false" />
364 <xs:attribute name="ignoreGapsinConsensus"
365 type="xs:boolean" use="optional" default="true" />
367 <xs:attribute name="startRes" type="xs:int" />
368 <xs:attribute name="startSeq" type="xs:int" />
369 <xs:attribute name="fontName" type="xs:string" />
370 <xs:attribute name="fontSize" type="xs:int" />
371 <xs:attribute name="fontStyle" type="xs:int" />
372 <xs:attribute name="viewName" type="xs:string" />
373 <xs:attribute name="sequenceSetId"
375 <xs:attribute name="gatheredViews"
377 <xs:attribute name="textCol1" type="xs:int" />
378 <xs:attribute name="textCol2" type="xs:int" />
379 <xs:attribute name="textColThreshold"
381 <xs:attribute name="id" type="xs:ID"
385 unique id used by jalview to
386 synchronize between stored and
393 <xs:element name="UserColours" minOccurs="0"
394 maxOccurs="unbounded">
397 <xs:element name="UserColourScheme"
398 type="jalview:JalviewUserColours" />
400 <xs:attribute name="id" type="xs:string" />
403 <xs:element name="tree" minOccurs="0"
404 maxOccurs="unbounded">
406 <xs:sequence minOccurs="0">
407 <xs:element name="title" type="xs:string" />
408 <xs:element name="newick" type="xs:string" />
410 <xs:attribute name="fontName" type="xs:string" />
411 <xs:attribute name="fontSize" type="xs:int" />
412 <xs:attribute name="fontStyle" type="xs:int" />
413 <xs:attribute name="threshold" type="xs:float" />
414 <xs:attribute name="showBootstrap"
416 <xs:attribute name="showDistances"
418 <xs:attribute name="markUnlinked"
420 <xs:attribute name="fitToWindow"
422 <xs:attribute name="currentTree"
424 <xs:attribute name="id" type="xs:ID"
428 Tree ID added for binding tree
429 visualization settings to vamsas
430 document trees in jalview 2.4.1
434 <xs:attributeGroup ref="jv:swingwindow" />
437 <xs:element name="FeatureSettings" minOccurs="0">
440 <xs:element name="setting" minOccurs="0"
441 maxOccurs="unbounded">
443 <xs:attribute name="type"
444 type="xs:string" use="required" />
445 <xs:attribute name="colour"
446 type="xs:int" use="required" />
447 <xs:attribute name="display"
448 type="xs:boolean" use="required" />
449 <xs:attribute name="order"
450 type="xs:float" use="optional" />
451 <xs:attribute name="mincolour"
452 type="xs:int" use="optional">
455 Optional minimum colour
456 for graduated feature
461 <xs:attribute name="threshold"
462 type="xs:float" use="optional">
466 graduated feature colour
470 <xs:attribute name="threshstate"
471 type="xs:int" use="optional">
475 graduated feature colour
479 <xs:attribute name="max"
480 type="xs:float" use="optional" />
481 <xs:attribute name="min"
482 type="xs:float" use="optional" />
483 <xs:attribute name="colourByLabel"
484 type="xs:boolean" use="optional" />
485 <xs:attribute name="autoScale"
486 type="xs:boolean" use="optional" />
489 <xs:element name="group" minOccurs="0"
490 maxOccurs="unbounded">
492 <xs:attribute name="name"
493 type="xs:string" use="required" />
494 <xs:attribute name="display"
495 type="xs:boolean" use="required" />
504 <xs:complexType name="feature">
506 <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
508 <xs:attribute name="key" type="xs:string" use="required"/>
509 <xs:attribute name="value" type="xs:string" use="required"/>
513 <xs:attribute name="begin" type="xs:int" use="required"/>
514 <xs:attribute name="end" type="xs:int" use="required"/>
515 <xs:attribute name="type" type="xs:string" use="required"/>
516 <xs:attribute name="description" type="xs:string" use="optional"/>
517 <xs:attribute name="status" type="xs:string" use="optional"/>
518 <xs:attribute name="featureGroup" type="xs:string" use="optional"/>
519 <xs:attribute name="score" type="xs:float" use="optional"/>
521 <xs:complexType name="pdbentry">
522 <xs:sequence minOccurs="0" maxOccurs="unbounded">
523 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
525 <xs:attribute name="name" type="xs:string" use="required"/>
526 <xs:attribute name="value" type="xs:string" use="required"/>
530 <xs:attribute name="id" type="xs:string" use="required"/>
531 <xs:attribute name="type" type="xs:string" use="optional"/>
532 <xs:attribute name="file" type="xs:string"/>
535 <xs:complexType name="reportWindow">
537 <xs:documentation>Generic type for windows containing mime-typed data associated with other jalview windows</xs:documentation>
541 <xs:attribute name="id" type="xs:string" use="required"/>
542 <xs:attribute name="type" type="xs:string" use="optional"/>
543 <xs:attribute name="file" type="xs:string" use="optional"/>
546 <xs:attributeGroup name="swingwindow">
549 base attributes for windows displayed in Jalview desktop.
552 <xs:attribute name="width" type="xs:int"/>
553 <xs:attribute name="height" type="xs:int"/>
554 <xs:attribute name="xpos" type="xs:int"/>
555 <xs:attribute name="ypos" type="xs:int"/>
557 <xs:complexType name="AnnotationColourScheme">
558 <xs:attribute name="aboveThreshold" type="xs:int" />
559 <xs:attribute name="annotation" type="xs:string" />
560 <xs:attribute name="minColour" type="xs:int" />
561 <xs:attribute name="maxColour" type="xs:int" />
562 <xs:attribute name="colourScheme" type="xs:string" />
563 <xs:attribute name="threshold" type="xs:float" />
564 <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
565 <xs:attribute name="predefinedColours" type="xs:boolean"