1 <?xml version="1.0" encoding="UTF-8"?>
3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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">
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"
235 maxOccurs="unbounded" />
237 <xs:attribute name="start" type="xs:int" />
238 <xs:attribute name="end" type="xs:int" />
239 <xs:attribute name="name" type="xs:string" />
240 <xs:attribute name="colour" type="xs:string" />
241 <xs:attribute name="consThreshold"
243 <xs:attribute name="pidThreshold" type="xs:int" />
244 <xs:attribute name="outlineColour"
246 <xs:attribute name="displayBoxes"
248 <xs:attribute name="displayText"
250 <xs:attribute name="colourText"
252 <xs:attribute name="textCol1" type="xs:int" />
253 <xs:attribute name="textCol2" type="xs:int" />
254 <xs:attribute name="textColThreshold"
256 <xs:attribute name="showUnconserved"
257 type="xs:boolean" use="optional" />
258 <xs:attribute name="ignoreGapsinConsensus"
259 type="xs:boolean" use="optional" default="true" />
260 <xs:attribute name="showConsensusHistogram"
261 type="xs:boolean" use="optional" default="true" />
262 <xs:attribute name="showSequenceLogo"
263 type="xs:boolean" use="optional" default="false" />
264 <xs:attribute name="normaliseSequenceLogo"
265 type="xs:boolean" use="optional" default="false" />
266 <xs:attribute name="id" type="xs:string"
270 Optional sequence group ID (only
271 needs to be unique for this
278 <xs:element name="Viewport" maxOccurs="unbounded">
281 <xs:element name="AnnotationColours"
284 <xs:attribute name="aboveThreshold"
286 <xs:attribute name="annotation"
288 <xs:attribute name="minColour"
290 <xs:attribute name="maxColour"
292 <xs:attribute name="colourScheme"
294 <xs:attribute name="threshold"
296 <xs:attribute name="perSequence"
299 <xs:attribute name="predefinedColours"
304 <xs:element name="hiddenColumns"
305 minOccurs="0" maxOccurs="unbounded">
307 <xs:attribute name="start"
309 <xs:attribute name="end"
313 <xs:element name="calcIdParam"
315 minOccurs="0" maxOccurs="unbounded">
318 <xs:extension base="jvws:WebServiceParameterSet">
319 <xs:attribute name="calcId" type="xs:string" use="required">
321 <xs:documentation>handle for the calculation which uses this parameter set</xs:documentation></xs:annotation>
323 <xs:attribute name="needsUpdate" type="xs:boolean" use="optional" default="false">
324 <xs:annotation><xs:documentation>should the calculation be performed immediately after loading in order to refresh results</xs:documentation></xs:annotation>
326 <xs:attribute name="autoUpdate" type="xs:boolean" use="required">
327 <xs:annotation><xs:documentation>should the calculation be automatically performed on edits</xs:documentation></xs:annotation>
334 <xs:attributeGroup ref="jv:swingwindow" />
335 <xs:attribute name="conservationSelected"
337 <xs:attribute name="pidSelected"
339 <xs:attribute name="bgColour" type="xs:string" />
340 <xs:attribute name="consThreshold"
342 <xs:attribute name="pidThreshold" type="xs:int" />
343 <xs:attribute name="title" type="xs:string" />
344 <xs:attribute name="showFullId"
346 <xs:attribute name="rightAlignIds"
348 <xs:attribute name="showText" type="xs:boolean" />
349 <xs:attribute name="showColourText"
351 <xs:attribute name="showUnconserved"
352 type="xs:boolean" use="optional" default="false" />
353 <xs:attribute name="showBoxes"
355 <xs:attribute name="wrapAlignment"
357 <xs:attribute name="renderGaps"
359 <xs:attribute name="showSequenceFeatures"
361 <xs:attribute name="showNPfeatureTooltip"
362 type="xs:boolean" use="optional" />
363 <xs:attribute name="showDbRefTooltip"
364 type="xs:boolean" use="optional" />
365 <xs:attribute name="followHighlight"
366 type="xs:boolean" use="optional" default="true" />
367 <xs:attribute name="followSelection"
368 type="xs:boolean" use="optional" default="true" />
369 <xs:attribute name="showAnnotation"
371 <xs:attribute name="centreColumnLabels"
372 type="xs:boolean" use="optional" default="false" />
373 <xs:attribute name="showGroupConservation"
374 type="xs:boolean" use="optional" default="false" />
375 <xs:attribute name="showGroupConsensus"
376 type="xs:boolean" use="optional" default="false" />
377 <xs:attribute name="showConsensusHistogram"
378 type="xs:boolean" use="optional" default="true" />
379 <xs:attribute name="showSequenceLogo"
380 type="xs:boolean" use="optional" default="false" />
381 <xs:attribute name="normaliseSequenceLogo"
382 type="xs:boolean" use="optional" default="false" />
383 <xs:attribute name="ignoreGapsinConsensus"
384 type="xs:boolean" use="optional" default="true" />
386 <xs:attribute name="startRes" type="xs:int" />
387 <xs:attribute name="startSeq" type="xs:int" />
388 <xs:attribute name="fontName" type="xs:string" />
389 <xs:attribute name="fontSize" type="xs:int" />
390 <xs:attribute name="fontStyle" type="xs:int" />
391 <xs:attribute name="viewName" type="xs:string" />
392 <xs:attribute name="sequenceSetId"
394 <xs:attribute name="gatheredViews"
396 <xs:attribute name="textCol1" type="xs:int" />
397 <xs:attribute name="textCol2" type="xs:int" />
398 <xs:attribute name="textColThreshold"
400 <xs:attribute name="id" type="xs:ID"
404 unique id used by jalview to
405 synchronize between stored and
412 <xs:element name="UserColours" minOccurs="0"
413 maxOccurs="unbounded">
416 <xs:element name="UserColourScheme"
417 type="jalview:JalviewUserColours" />
419 <xs:attribute name="id" type="xs:string" />
422 <xs:element name="tree" minOccurs="0"
423 maxOccurs="unbounded">
425 <xs:sequence minOccurs="0">
426 <xs:element name="title" type="xs:string" />
427 <xs:element name="newick" type="xs:string" />
429 <xs:attribute name="fontName" type="xs:string" />
430 <xs:attribute name="fontSize" type="xs:int" />
431 <xs:attribute name="fontStyle" type="xs:int" />
432 <xs:attribute name="threshold" type="xs:float" />
433 <xs:attribute name="showBootstrap"
435 <xs:attribute name="showDistances"
437 <xs:attribute name="markUnlinked"
439 <xs:attribute name="fitToWindow"
441 <xs:attribute name="currentTree"
443 <xs:attribute name="id" type="xs:ID"
447 Tree ID added for binding tree
448 visualization settings to vamsas
449 document trees in jalview 2.4.1
453 <xs:attributeGroup ref="jv:swingwindow" />
456 <xs:element name="FeatureSettings" minOccurs="0">
459 <xs:element name="setting" minOccurs="0"
460 maxOccurs="unbounded">
462 <xs:attribute name="type"
463 type="xs:string" use="required" />
464 <xs:attribute name="colour"
465 type="xs:int" use="required" />
466 <xs:attribute name="display"
467 type="xs:boolean" use="required" />
468 <xs:attribute name="order"
469 type="xs:float" use="optional" />
470 <xs:attribute name="mincolour"
471 type="xs:int" use="optional">
474 Optional minimum colour
475 for graduated feature
480 <xs:attribute name="threshold"
481 type="xs:float" use="optional">
485 graduated feature colour
489 <xs:attribute name="threshstate"
490 type="xs:int" use="optional">
494 graduated feature colour
498 <xs:attribute name="max"
499 type="xs:float" use="optional" />
500 <xs:attribute name="min"
501 type="xs:float" use="optional" />
502 <xs:attribute name="colourByLabel"
503 type="xs:boolean" use="optional" />
504 <xs:attribute name="autoScale"
505 type="xs:boolean" use="optional" />
508 <xs:element name="group" minOccurs="0"
509 maxOccurs="unbounded">
511 <xs:attribute name="name"
512 type="xs:string" use="required" />
513 <xs:attribute name="display"
514 type="xs:boolean" use="required" />
523 <xs:complexType name="feature">
525 <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
527 <xs:attribute name="key" type="xs:string" use="required"/>
528 <xs:attribute name="value" type="xs:string" use="required"/>
532 <xs:attribute name="begin" type="xs:int" use="required"/>
533 <xs:attribute name="end" type="xs:int" use="required"/>
534 <xs:attribute name="type" type="xs:string" use="required"/>
535 <xs:attribute name="description" type="xs:string" use="optional"/>
536 <xs:attribute name="status" type="xs:string" use="optional"/>
537 <xs:attribute name="featureGroup" type="xs:string" use="optional"/>
538 <xs:attribute name="score" type="xs:float" use="optional"/>
540 <xs:complexType name="pdbentry">
541 <xs:sequence minOccurs="0" maxOccurs="unbounded">
542 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
544 <xs:attribute name="name" type="xs:string" use="required"/>
545 <xs:attribute name="value" type="xs:string" use="required"/>
549 <xs:attribute name="id" type="xs:string" use="required"/>
550 <xs:attribute name="type" type="xs:string" use="optional"/>
551 <xs:attribute name="file" type="xs:string"/>
554 <xs:complexType name="reportWindow">
556 <xs:documentation>Generic type for windows containing mime-typed data associated with other jalview windows</xs:documentation>
560 <xs:attribute name="id" type="xs:string" use="required"/>
561 <xs:attribute name="type" type="xs:string" use="optional"/>
562 <xs:attribute name="file" type="xs:string" use="optional"/>
565 <xs:attributeGroup name="swingwindow">
568 base attributes for windows displayed in Jalview desktop.
571 <xs:attribute name="width" type="xs:int"/>
572 <xs:attribute name="height" type="xs:int"/>
573 <xs:attribute name="xpos" type="xs:int"/>
574 <xs:attribute name="ypos" type="xs:int"/>