1 <?xml version="1.0" encoding="UTF-8"?>
2 <!-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of
4 Jalview. * * Jalview is free software: you can redistribute it and/or * modify
5 it under the terms of the GNU General Public License * as published by the
6 Free Software Foundation, either version 3 of the License, or (at your option)
7 any later version. * * Jalview is distributed in the hope that it will be
8 useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of
9 MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General
10 Public License for more details. * * You should have received a copy of the
11 GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
12 * The Jalview Authors are detailed in the 'AUTHORS' file. -->
13 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
14 xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours"
15 xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset"
16 targetNamespace="www.jalview.org" elementFormDefault="qualified"
17 attributeFormDefault="unqualified">
18 <xs:import namespace="www.vamsas.ac.uk/jalview/version2"
19 schemaLocation="vamsas.xsd" />
20 <xs:import namespace="www.jalview.org/colours"
21 schemaLocation="JalviewUserColours.xsd" />
22 <xs:import namespace="www.jalview.org/xml/wsparamset"
23 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" type="jv:feature"
34 minOccurs="0" maxOccurs="unbounded" />
35 <xs:element name="pdbids" minOccurs="0" maxOccurs="unbounded">
38 <xs:extension base="jv:pdbentry">
40 <xs:element name="structureState" minOccurs="0"
41 maxOccurs="unbounded">
44 <xs:extension base="xs:string">
45 <xs:attributeGroup ref="jv:swingwindow" />
46 <xs:attribute name="visible" type="xs:boolean" />
47 <xs:attribute name="viewId" type="xs:string"
107 <xs:attribute name="alignwithAlignPanel"
108 type="xs:boolean" use="optional" default="true">
137 <xs:attribute name="colourwithAlignPanel"
138 type="xs:boolean" use="optional" default="false">
169 <xs:attribute name="colourByJmol" type="xs:boolean"
170 use="optional" default="true">
197 <xs:attribute name="type" type="xs:string"
225 <xs:element name="hiddenSequences" type="xs:int"
226 minOccurs="0" maxOccurs="unbounded" />
227 <xs:element name="rnaViewer" minOccurs="0" maxOccurs="unbounded">
229 <xs:documentation>Reference to a viewer showing RNA structure
230 for this sequence. Schema supports one viewer showing multiple
231 annotations for multiple sequences, though currently only one
232 annotation for one sequence (gapped or trimmed) is used
237 <xs:element name="secondaryStructure" minOccurs="1"
238 maxOccurs="unbounded">
240 <xs:attribute name="title" type="xs:string" />
241 <xs:attribute name="annotationId" type="xs:string"
244 <xs:documentation>id attribute of Annotation in
246 the secondary structure annotation shown
251 <xs:attribute name="gapped" type="xs:boolean">
253 <xs:documentation>if true the RNA structure is shown with gaps, if false without
257 <xs:attribute name="viewerState" type="xs:string">
259 <xs:documentation>name of the project jar entry that holds
260 the VARNA viewer state for the structure
267 <xs:attributeGroup ref="jv:swingwindow" />
268 <xs:attribute name="title" type="xs:string" />
269 <xs:attribute name="viewId" type="xs:string">
271 <xs:documentation>An id unique to the RNA viewer panel
275 <xs:attribute name="dividerLocation" type="xs:int">
277 <xs:documentation>horizontal position of split pane divider
281 <xs:attribute name="selectedRna" type="xs:int">
283 <xs:documentation>Index of the selected structure in the
291 <xs:attribute name="colour" type="xs:int" use="optional" />
292 <xs:attribute name="start" type="xs:int" use="required" />
293 <xs:attribute name="end" type="xs:int" use="required" />
294 <xs:attribute name="id" type="xs:string" use="required" />
295 <xs:attribute name="hidden" type="xs:boolean" />
298 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
301 <xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
302 <xs:element name="annotationColours" type="jv:AnnotationColourScheme"
303 minOccurs="0" maxOccurs="1" />
305 <xs:attribute name="start" type="xs:int" />
306 <xs:attribute name="end" type="xs:int" />
307 <xs:attribute name="name" type="xs:string" />
308 <xs:attribute name="colour" type="xs:string" />
309 <xs:attribute name="consThreshold" type="xs:int" />
310 <xs:attribute name="pidThreshold" type="xs:int" />
311 <xs:attribute name="outlineColour" type="xs:int" />
312 <xs:attribute name="displayBoxes" type="xs:boolean" />
313 <xs:attribute name="displayText" type="xs:boolean" />
314 <xs:attribute name="colourText" type="xs:boolean" />
315 <xs:attribute name="textCol1" type="xs:int" />
316 <xs:attribute name="textCol2" type="xs:int" />
317 <xs:attribute name="textColThreshold" type="xs:int" />
318 <xs:attribute name="showUnconserved" type="xs:boolean"
320 <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
321 use="optional" default="true" />
322 <xs:attribute name="showConsensusHistogram" type="xs:boolean"
323 use="optional" default="true" />
324 <xs:attribute name="showSequenceLogo" type="xs:boolean"
325 use="optional" default="false" />
326 <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
327 use="optional" default="false" />
328 <xs:attribute name="id" type="xs:string" use="optional">
331 Optional sequence group ID (only
340 <xs:element name="Viewport" maxOccurs="unbounded"
344 <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
345 minOccurs="0" maxOccurs="1">
347 <xs:element name="hiddenColumns" minOccurs="0"
348 maxOccurs="unbounded">
350 <xs:attribute name="start" type="xs:int" />
351 <xs:attribute name="end" type="xs:int" />
354 <xs:element name="calcIdParam" minOccurs="0"
355 maxOccurs="unbounded">
358 <xs:extension base="jvws:WebServiceParameterSet">
359 <xs:attribute name="calcId" type="xs:string"
362 <xs:documentation>handle for the calculation which uses
367 <xs:attribute name="needsUpdate" type="xs:boolean"
368 use="optional" default="false">
370 <xs:documentation>should the calculation be performed
371 immediately after loading in order to refresh results
375 <xs:attribute name="autoUpdate" type="xs:boolean"
378 <xs:documentation>should the calculation be automatically
388 <xs:attributeGroup ref="jv:swingwindow" />
389 <xs:attribute name="conservationSelected" type="xs:boolean" />
390 <xs:attribute name="pidSelected" type="xs:boolean" />
391 <xs:attribute name="bgColour" type="xs:string" />
392 <xs:attribute name="consThreshold" type="xs:int" />
393 <xs:attribute name="pidThreshold" type="xs:int" />
394 <xs:attribute name="title" type="xs:string" />
395 <xs:attribute name="showFullId" type="xs:boolean" />
396 <xs:attribute name="rightAlignIds" type="xs:boolean" />
397 <xs:attribute name="showText" type="xs:boolean" />
398 <xs:attribute name="showColourText" type="xs:boolean" />
399 <xs:attribute name="showUnconserved" type="xs:boolean"
400 use="optional" default="false" />
401 <xs:attribute name="showBoxes" type="xs:boolean" />
402 <xs:attribute name="wrapAlignment" type="xs:boolean" />
403 <xs:attribute name="renderGaps" type="xs:boolean" />
404 <xs:attribute name="showSequenceFeatures" type="xs:boolean" />
405 <xs:attribute name="showNPfeatureTooltip" type="xs:boolean"
407 <xs:attribute name="showDbRefTooltip" type="xs:boolean"
409 <xs:attribute name="followHighlight" type="xs:boolean"
410 use="optional" default="true" />
411 <xs:attribute name="followSelection" type="xs:boolean"
412 use="optional" default="true" />
413 <xs:attribute name="showAnnotation" type="xs:boolean" />
414 <xs:attribute name="centreColumnLabels" type="xs:boolean"
415 use="optional" default="false" />
416 <xs:attribute name="showGroupConservation" type="xs:boolean"
417 use="optional" default="false" />
418 <xs:attribute name="showGroupConsensus" type="xs:boolean"
419 use="optional" default="false" />
420 <xs:attribute name="showConsensusHistogram" type="xs:boolean"
421 use="optional" default="true" />
422 <xs:attribute name="showSequenceLogo" type="xs:boolean"
423 use="optional" default="false" />
424 <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
425 use="optional" default="false" />
426 <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
427 use="optional" default="true" />
428 <xs:attribute name="startRes" type="xs:int" />
429 <xs:attribute name="startSeq" type="xs:int" />
430 <xs:attribute name="fontName" type="xs:string" />
431 <xs:attribute name="fontSize" type="xs:int" />
432 <xs:attribute name="fontStyle" type="xs:int" />
433 <xs:attribute name="viewName" type="xs:string" />
434 <xs:attribute name="sequenceSetId" type="xs:string" />
435 <xs:attribute name="gatheredViews" type="xs:boolean" />
436 <xs:attribute name="textCol1" type="xs:int" />
437 <xs:attribute name="textCol2" type="xs:int" />
438 <xs:attribute name="textColThreshold" type="xs:int" />
439 <xs:attribute name="id" type="xs:ID" use="optional">
442 unique id used by jalview to
449 <xs:attribute name="complementId" type="xs:string"
453 The viewport id of this viewport's
454 (cdna/protein) coding complement, if any
460 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
463 <xs:element name="UserColourScheme" type="jalview:JalviewUserColours" />
465 <xs:attribute name="id" type="xs:string" />
468 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
470 <xs:sequence minOccurs="0">
471 <xs:element name="title" type="xs:string" />
472 <xs:element name="newick" type="xs:string" />
474 <xs:attribute name="fontName" type="xs:string" />
475 <xs:attribute name="fontSize" type="xs:int" />
476 <xs:attribute name="fontStyle" type="xs:int" />
477 <xs:attribute name="threshold" type="xs:float" />
478 <xs:attribute name="showBootstrap" type="xs:boolean" />
479 <xs:attribute name="showDistances" type="xs:boolean" />
480 <xs:attribute name="markUnlinked" type="xs:boolean" />
481 <xs:attribute name="fitToWindow" type="xs:boolean" />
482 <xs:attribute name="currentTree" type="xs:boolean" />
483 <xs:attribute name="id" type="xs:ID" use="optional">
486 Tree ID added for binding tree
489 document trees in jalview 2.4.1
493 <xs:attributeGroup ref="jv:swingwindow" />
496 <xs:element name="FeatureSettings" minOccurs="0">
499 <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
501 <xs:attribute name="type" type="xs:string" use="required" />
502 <xs:attribute name="colour" type="xs:int" use="required" />
503 <xs:attribute name="display" type="xs:boolean"
505 <xs:attribute name="order" type="xs:float" use="optional" />
506 <xs:attribute name="mincolour" type="xs:int" use="optional">
509 Optional minimum colour
516 <xs:attribute name="threshold" type="xs:float"
521 graduated feature colour
525 <xs:attribute name="threshstate" type="xs:int"
530 graduated feature colour
534 <xs:attribute name="max" type="xs:float" use="optional" />
535 <xs:attribute name="min" type="xs:float" use="optional" />
536 <xs:attribute name="colourByLabel" type="xs:boolean"
538 <xs:attribute name="autoScale" type="xs:boolean"
542 <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
544 <xs:attribute name="name" type="xs:string" use="required" />
545 <xs:attribute name="display" type="xs:boolean"
555 <xs:complexType name="feature">
557 <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
559 <xs:attribute name="key" type="xs:string" use="required" />
560 <xs:attribute name="value" type="xs:string" use="required" />
564 <xs:attribute name="begin" type="xs:int" use="required" />
565 <xs:attribute name="end" type="xs:int" use="required" />
566 <xs:attribute name="type" type="xs:string" use="required" />
567 <xs:attribute name="description" type="xs:string" use="optional" />
568 <xs:attribute name="status" type="xs:string" use="optional" />
569 <xs:attribute name="featureGroup" type="xs:string" use="optional" />
570 <xs:attribute name="score" type="xs:float" use="optional" />
572 <xs:complexType name="pdbentry">
573 <xs:sequence minOccurs="0" maxOccurs="unbounded">
574 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
576 <xs:attribute name="name" type="xs:string" use="required" />
577 <xs:attribute name="value" type="xs:string" use="required" />
581 <xs:attribute name="id" type="xs:string" use="required" />
582 <xs:attribute name="type" type="xs:string" use="optional" />
583 <xs:attribute name="file" type="xs:string" />
585 <!-- <xs:complexType name="reportWindow"> <xs:annotation> <xs:documentation>Generic
586 type for windows containing mime-typed data associated with other jalview
587 windows</xs:documentation> </xs:annotation> <xs:sequence> </xs:sequence>
588 <xs:attribute name="id" type="xs:string" use="required"/> <xs:attribute name="type"
589 type="xs:string" use="optional"/> <xs:attribute name="file" type="xs:string"
590 use="optional"/> </xs:complexType> -->
591 <xs:attributeGroup name="swingwindow">
594 base attributes for windows displayed in Jalview
598 <xs:attribute name="width" type="xs:int" />
599 <xs:attribute name="height" type="xs:int" />
600 <xs:attribute name="xpos" type="xs:int" />
601 <xs:attribute name="ypos" type="xs:int" />
603 <xs:complexType name="AnnotationColourScheme">
604 <xs:attribute name="aboveThreshold" type="xs:int" />
605 <xs:attribute name="annotation" type="xs:string" />
606 <xs:attribute name="minColour" type="xs:int" />
607 <xs:attribute name="maxColour" type="xs:int" />
608 <xs:attribute name="colourScheme" type="xs:string" />
609 <xs:attribute name="threshold" type="xs:float" />
610 <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
611 <xs:attribute name="predefinedColours" type="xs:boolean"