1 <?xml version="1.0" encoding="UTF-8"?>
3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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"
207 name="chimeraSession" type="xs:string" use="optional">
210 Full path name to a saved Chimera session file (usually a .py file).
223 <xs:element name="hiddenSequences"
224 type="xs:int" minOccurs="0" maxOccurs="unbounded" />
226 <xs:attribute name="colour" type="xs:int"
228 <xs:attribute name="start" type="xs:int"
230 <xs:attribute name="end" type="xs:int"
232 <xs:attribute name="id" type="xs:string"
234 <xs:attribute name="hidden" type="xs:boolean" />
237 <xs:element name="JGroup" minOccurs="0"
238 maxOccurs="unbounded">
241 <xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
242 <xs:element name="annotationColours" type="jv:AnnotationColourScheme"
243 minOccurs="0" maxOccurs="1" />
245 <xs:attribute name="start" type="xs:int" />
246 <xs:attribute name="end" type="xs:int" />
247 <xs:attribute name="name" type="xs:string" />
248 <xs:attribute name="colour" type="xs:string" />
249 <xs:attribute name="consThreshold"
251 <xs:attribute name="pidThreshold" type="xs:int" />
252 <xs:attribute name="outlineColour"
254 <xs:attribute name="displayBoxes"
256 <xs:attribute name="displayText"
258 <xs:attribute name="colourText"
260 <xs:attribute name="textCol1" type="xs:int" />
261 <xs:attribute name="textCol2" type="xs:int" />
262 <xs:attribute name="textColThreshold"
264 <xs:attribute name="showUnconserved"
265 type="xs:boolean" use="optional" />
266 <xs:attribute name="ignoreGapsinConsensus"
267 type="xs:boolean" use="optional" default="true" />
268 <xs:attribute name="showConsensusHistogram"
269 type="xs:boolean" use="optional" default="true" />
270 <xs:attribute name="showSequenceLogo"
271 type="xs:boolean" use="optional" default="false" />
272 <xs:attribute name="normaliseSequenceLogo"
273 type="xs:boolean" use="optional" default="false" />
274 <xs:attribute name="id" type="xs:string"
278 Optional sequence group ID (only
279 needs to be unique for this
286 <xs:element name="Viewport" maxOccurs="unbounded" minOccurs="0">
289 <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
290 minOccurs="0" maxOccurs="1">
292 <xs:element name="hiddenColumns"
293 minOccurs="0" maxOccurs="unbounded">
295 <xs:attribute name="start"
297 <xs:attribute name="end"
301 <xs:element name="calcIdParam"
303 minOccurs="0" maxOccurs="unbounded">
306 <xs:extension base="jvws:WebServiceParameterSet">
307 <xs:attribute name="calcId" type="xs:string" use="required">
309 <xs:documentation>handle for the calculation which uses this parameter set</xs:documentation></xs:annotation>
311 <xs:attribute name="needsUpdate" type="xs:boolean" use="optional" default="false">
312 <xs:annotation><xs:documentation>should the calculation be performed immediately after loading in order to refresh results</xs:documentation></xs:annotation>
314 <xs:attribute name="autoUpdate" type="xs:boolean" use="required">
315 <xs:annotation><xs:documentation>should the calculation be automatically performed on edits</xs:documentation></xs:annotation>
322 <xs:attributeGroup ref="jv:swingwindow" />
323 <xs:attribute name="conservationSelected"
325 <xs:attribute name="pidSelected"
327 <xs:attribute name="bgColour" type="xs:string" />
328 <xs:attribute name="consThreshold"
330 <xs:attribute name="pidThreshold" type="xs:int" />
331 <xs:attribute name="title" type="xs:string" />
332 <xs:attribute name="showFullId"
334 <xs:attribute name="rightAlignIds"
336 <xs:attribute name="showText" type="xs:boolean" />
337 <xs:attribute name="showColourText"
339 <xs:attribute name="showUnconserved"
340 type="xs:boolean" use="optional" default="false" />
341 <xs:attribute name="showBoxes"
343 <xs:attribute name="wrapAlignment"
345 <xs:attribute name="renderGaps"
347 <xs:attribute name="showSequenceFeatures"
349 <xs:attribute name="showNPfeatureTooltip"
350 type="xs:boolean" use="optional" />
351 <xs:attribute name="showDbRefTooltip"
352 type="xs:boolean" use="optional" />
353 <xs:attribute name="followHighlight"
354 type="xs:boolean" use="optional" default="true" />
355 <xs:attribute name="followSelection"
356 type="xs:boolean" use="optional" default="true" />
357 <xs:attribute name="showAnnotation"
359 <xs:attribute name="centreColumnLabels"
360 type="xs:boolean" use="optional" default="false" />
361 <xs:attribute name="showGroupConservation"
362 type="xs:boolean" use="optional" default="false" />
363 <xs:attribute name="showGroupConsensus"
364 type="xs:boolean" use="optional" default="false" />
365 <xs:attribute name="showConsensusHistogram"
366 type="xs:boolean" use="optional" default="true" />
367 <xs:attribute name="showSequenceLogo"
368 type="xs:boolean" use="optional" default="false" />
369 <xs:attribute name="normaliseSequenceLogo"
370 type="xs:boolean" use="optional" default="false" />
371 <xs:attribute name="ignoreGapsinConsensus"
372 type="xs:boolean" use="optional" default="true" />
374 <xs:attribute name="startRes" type="xs:int" />
375 <xs:attribute name="startSeq" type="xs:int" />
376 <xs:attribute name="fontName" type="xs:string" />
377 <xs:attribute name="fontSize" type="xs:int" />
378 <xs:attribute name="fontStyle" type="xs:int" />
379 <xs:attribute name="viewName" type="xs:string" />
380 <xs:attribute name="sequenceSetId"
382 <xs:attribute name="gatheredViews"
384 <xs:attribute name="textCol1" type="xs:int" />
385 <xs:attribute name="textCol2" type="xs:int" />
386 <xs:attribute name="textColThreshold"
388 <xs:attribute name="id" type="xs:ID"
392 unique id used by jalview to
393 synchronize between stored and
400 <xs:element name="UserColours" minOccurs="0"
401 maxOccurs="unbounded">
404 <xs:element name="UserColourScheme"
405 type="jalview:JalviewUserColours" />
407 <xs:attribute name="id" type="xs:string" />
410 <xs:element name="tree" minOccurs="0"
411 maxOccurs="unbounded">
413 <xs:sequence minOccurs="0">
414 <xs:element name="title" type="xs:string" />
415 <xs:element name="newick" type="xs:string" />
417 <xs:attribute name="fontName" type="xs:string" />
418 <xs:attribute name="fontSize" type="xs:int" />
419 <xs:attribute name="fontStyle" type="xs:int" />
420 <xs:attribute name="threshold" type="xs:float" />
421 <xs:attribute name="showBootstrap"
423 <xs:attribute name="showDistances"
425 <xs:attribute name="markUnlinked"
427 <xs:attribute name="fitToWindow"
429 <xs:attribute name="currentTree"
431 <xs:attribute name="id" type="xs:ID"
435 Tree ID added for binding tree
436 visualization settings to vamsas
437 document trees in jalview 2.4.1
441 <xs:attributeGroup ref="jv:swingwindow" />
444 <xs:element name="FeatureSettings" minOccurs="0">
447 <xs:element name="setting" minOccurs="0"
448 maxOccurs="unbounded">
450 <xs:attribute name="type"
451 type="xs:string" use="required" />
452 <xs:attribute name="colour"
453 type="xs:int" use="required" />
454 <xs:attribute name="display"
455 type="xs:boolean" use="required" />
456 <xs:attribute name="order"
457 type="xs:float" use="optional" />
458 <xs:attribute name="mincolour"
459 type="xs:int" use="optional">
462 Optional minimum colour
463 for graduated feature
468 <xs:attribute name="threshold"
469 type="xs:float" use="optional">
473 graduated feature colour
477 <xs:attribute name="threshstate"
478 type="xs:int" use="optional">
482 graduated feature colour
486 <xs:attribute name="max"
487 type="xs:float" use="optional" />
488 <xs:attribute name="min"
489 type="xs:float" use="optional" />
490 <xs:attribute name="colourByLabel"
491 type="xs:boolean" use="optional" />
492 <xs:attribute name="autoScale"
493 type="xs:boolean" use="optional" />
496 <xs:element name="group" minOccurs="0"
497 maxOccurs="unbounded">
499 <xs:attribute name="name"
500 type="xs:string" use="required" />
501 <xs:attribute name="display"
502 type="xs:boolean" use="required" />
511 <xs:complexType name="feature">
513 <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
515 <xs:attribute name="key" type="xs:string" use="required"/>
516 <xs:attribute name="value" type="xs:string" use="required"/>
520 <xs:attribute name="begin" type="xs:int" use="required"/>
521 <xs:attribute name="end" type="xs:int" use="required"/>
522 <xs:attribute name="type" type="xs:string" use="required"/>
523 <xs:attribute name="description" type="xs:string" use="optional"/>
524 <xs:attribute name="status" type="xs:string" use="optional"/>
525 <xs:attribute name="featureGroup" type="xs:string" use="optional"/>
526 <xs:attribute name="score" type="xs:float" use="optional"/>
528 <xs:complexType name="pdbentry">
529 <xs:sequence minOccurs="0" maxOccurs="unbounded">
530 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
532 <xs:attribute name="name" type="xs:string" use="required"/>
533 <xs:attribute name="value" type="xs:string" use="required"/>
537 <xs:attribute name="id" type="xs:string" use="required"/>
538 <xs:attribute name="type" type="xs:string" use="optional"/>
539 <xs:attribute name="file" type="xs:string"/>
542 <xs:complexType name="reportWindow">
544 <xs:documentation>Generic type for windows containing mime-typed data associated with other jalview windows</xs:documentation>
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" use="optional"/>
553 <xs:attributeGroup name="swingwindow">
556 base attributes for windows displayed in Jalview desktop.
559 <xs:attribute name="width" type="xs:int"/>
560 <xs:attribute name="height" type="xs:int"/>
561 <xs:attribute name="xpos" type="xs:int"/>
562 <xs:attribute name="ypos" type="xs:int"/>
564 <xs:complexType name="AnnotationColourScheme">
565 <xs:attribute name="aboveThreshold" type="xs:int" />
566 <xs:attribute name="annotation" type="xs:string" />
567 <xs:attribute name="minColour" type="xs:int" />
568 <xs:attribute name="maxColour" type="xs:int" />
569 <xs:attribute name="colourScheme" type="xs:string" />
570 <xs:attribute name="threshold" type="xs:float" />
571 <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
572 <xs:attribute name="predefinedColours" type="xs:boolean"