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"
297 <xs:element name="hiddenColumns"
298 minOccurs="0" maxOccurs="unbounded">
300 <xs:attribute name="start"
302 <xs:attribute name="end"
306 <xs:element name="calcIdParam"
308 minOccurs="0" maxOccurs="unbounded">
311 <xs:extension base="jvws:WebServiceParameterSet">
312 <xs:attribute name="calcId" type="xs:string" use="required">
314 <xs:documentation>handle for the calculation which uses this parameter set</xs:documentation></xs:annotation>
316 <xs:attribute name="needsUpdate" type="xs:boolean" use="optional" default="false">
317 <xs:annotation><xs:documentation>should the calculation be performed immediately after loading in order to refresh results</xs:documentation></xs:annotation>
319 <xs:attribute name="autoUpdate" type="xs:boolean" use="required">
320 <xs:annotation><xs:documentation>should the calculation be automatically performed on edits</xs:documentation></xs:annotation>
327 <xs:attributeGroup ref="jv:swingwindow" />
328 <xs:attribute name="conservationSelected"
330 <xs:attribute name="pidSelected"
332 <xs:attribute name="bgColour" type="xs:string" />
333 <xs:attribute name="consThreshold"
335 <xs:attribute name="pidThreshold" type="xs:int" />
336 <xs:attribute name="title" type="xs:string" />
337 <xs:attribute name="showFullId"
339 <xs:attribute name="rightAlignIds"
341 <xs:attribute name="showText" type="xs:boolean" />
342 <xs:attribute name="showColourText"
344 <xs:attribute name="showUnconserved"
345 type="xs:boolean" use="optional" default="false" />
346 <xs:attribute name="showBoxes"
348 <xs:attribute name="wrapAlignment"
350 <xs:attribute name="renderGaps"
352 <xs:attribute name="showSequenceFeatures"
354 <xs:attribute name="showNPfeatureTooltip"
355 type="xs:boolean" use="optional" />
356 <xs:attribute name="showDbRefTooltip"
357 type="xs:boolean" use="optional" />
358 <xs:attribute name="followHighlight"
359 type="xs:boolean" use="optional" default="true" />
360 <xs:attribute name="followSelection"
361 type="xs:boolean" use="optional" default="true" />
362 <xs:attribute name="showAnnotation"
364 <xs:attribute name="centreColumnLabels"
365 type="xs:boolean" use="optional" default="false" />
366 <xs:attribute name="showGroupConservation"
367 type="xs:boolean" use="optional" default="false" />
368 <xs:attribute name="showGroupConsensus"
369 type="xs:boolean" use="optional" default="false" />
370 <xs:attribute name="showConsensusHistogram"
371 type="xs:boolean" use="optional" default="true" />
372 <xs:attribute name="showSequenceLogo"
373 type="xs:boolean" use="optional" default="false" />
374 <xs:attribute name="normaliseSequenceLogo"
375 type="xs:boolean" use="optional" default="false" />
376 <xs:attribute name="ignoreGapsinConsensus"
377 type="xs:boolean" use="optional" default="true" />
379 <xs:attribute name="startRes" type="xs:int" />
380 <xs:attribute name="startSeq" type="xs:int" />
381 <xs:attribute name="fontName" type="xs:string" />
382 <xs:attribute name="fontSize" type="xs:int" />
383 <xs:attribute name="fontStyle" type="xs:int" />
384 <xs:attribute name="viewName" type="xs:string" />
385 <xs:attribute name="sequenceSetId"
387 <xs:attribute name="gatheredViews"
389 <xs:attribute name="textCol1" type="xs:int" />
390 <xs:attribute name="textCol2" type="xs:int" />
391 <xs:attribute name="textColThreshold"
393 <xs:attribute name="id" type="xs:ID"
397 unique id used by jalview to
398 synchronize between stored and
405 <xs:element name="UserColours" minOccurs="0"
406 maxOccurs="unbounded">
409 <xs:element name="UserColourScheme"
410 type="jalview:JalviewUserColours" />
412 <xs:attribute name="id" type="xs:string" />
415 <xs:element name="tree" minOccurs="0"
416 maxOccurs="unbounded">
418 <xs:sequence minOccurs="0">
419 <xs:element name="title" type="xs:string" />
420 <xs:element name="newick" type="xs:string" />
422 <xs:attribute name="fontName" type="xs:string" />
423 <xs:attribute name="fontSize" type="xs:int" />
424 <xs:attribute name="fontStyle" type="xs:int" />
425 <xs:attribute name="threshold" type="xs:float" />
426 <xs:attribute name="showBootstrap"
428 <xs:attribute name="showDistances"
430 <xs:attribute name="markUnlinked"
432 <xs:attribute name="fitToWindow"
434 <xs:attribute name="currentTree"
436 <xs:attribute name="id" type="xs:ID"
440 Tree ID added for binding tree
441 visualization settings to vamsas
442 document trees in jalview 2.4.1
446 <xs:attributeGroup ref="jv:swingwindow" />
449 <xs:element name="FeatureSettings" minOccurs="0">
452 <xs:element name="setting" minOccurs="0"
453 maxOccurs="unbounded">
455 <xs:attribute name="type"
456 type="xs:string" use="required" />
457 <xs:attribute name="colour"
458 type="xs:int" use="required" />
459 <xs:attribute name="display"
460 type="xs:boolean" use="required" />
461 <xs:attribute name="order"
462 type="xs:float" use="optional" />
463 <xs:attribute name="mincolour"
464 type="xs:int" use="optional">
467 Optional minimum colour
468 for graduated feature
473 <xs:attribute name="threshold"
474 type="xs:float" use="optional">
478 graduated feature colour
482 <xs:attribute name="threshstate"
483 type="xs:int" use="optional">
487 graduated feature colour
491 <xs:attribute name="max"
492 type="xs:float" use="optional" />
493 <xs:attribute name="min"
494 type="xs:float" use="optional" />
495 <xs:attribute name="colourByLabel"
496 type="xs:boolean" use="optional" />
497 <xs:attribute name="autoScale"
498 type="xs:boolean" use="optional" />
501 <xs:element name="group" minOccurs="0"
502 maxOccurs="unbounded">
504 <xs:attribute name="name"
505 type="xs:string" use="required" />
506 <xs:attribute name="display"
507 type="xs:boolean" use="required" />
516 <xs:complexType name="feature">
518 <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
520 <xs:attribute name="key" type="xs:string" use="required"/>
521 <xs:attribute name="value" type="xs:string" use="required"/>
525 <xs:attribute name="begin" type="xs:int" use="required"/>
526 <xs:attribute name="end" type="xs:int" use="required"/>
527 <xs:attribute name="type" type="xs:string" use="required"/>
528 <xs:attribute name="description" type="xs:string" use="optional"/>
529 <xs:attribute name="status" type="xs:string" use="optional"/>
530 <xs:attribute name="featureGroup" type="xs:string" use="optional"/>
531 <xs:attribute name="score" type="xs:float" use="optional"/>
533 <xs:complexType name="pdbentry">
534 <xs:sequence minOccurs="0" maxOccurs="unbounded">
535 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
537 <xs:attribute name="name" type="xs:string" use="required"/>
538 <xs:attribute name="value" type="xs:string" use="required"/>
542 <xs:attribute name="id" type="xs:string" use="required"/>
543 <xs:attribute name="type" type="xs:string" use="optional"/>
544 <xs:attribute name="file" type="xs:string"/>
547 <xs:complexType name="reportWindow">
549 <xs:documentation>Generic type for windows containing mime-typed data associated with other jalview windows</xs:documentation>
553 <xs:attribute name="id" type="xs:string" use="required"/>
554 <xs:attribute name="type" type="xs:string" use="optional"/>
555 <xs:attribute name="file" type="xs:string" use="optional"/>
558 <xs:attributeGroup name="swingwindow">
561 base attributes for windows displayed in Jalview desktop.
564 <xs:attribute name="width" type="xs:int"/>
565 <xs:attribute name="height" type="xs:int"/>
566 <xs:attribute name="xpos" type="xs:int"/>
567 <xs:attribute name="ypos" type="xs:int"/>