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:element name="JalviewModel" type="jv:JalviewModel" />
25 <xs:complexType name="JalviewModel">
27 <xs:element name="creationDate" type="xs:dateTime" />
28 <xs:element name="version" type="xs:string" />
29 <xs:element name="vamsasModel" type="vamsas:VAMSAS" />
31 <xs:element name="JSeq" maxOccurs="unbounded" minOccurs="0">
34 <xs:element name="features" type="jv:feature"
35 minOccurs="0" maxOccurs="unbounded" />
36 <xs:element name="pdbids" minOccurs="0" maxOccurs="unbounded">
39 <xs:extension base="jv:pdbentry">
41 <xs:element name="structureState" minOccurs="0"
42 maxOccurs="unbounded">
45 <xs:extension base="xs:string">
46 <xs:attributeGroup ref="jv:swingwindow" />
47 <xs:attribute name="visible" type="xs:boolean" />
48 <xs:attribute name="viewId" type="xs:string"
108 <xs:attribute name="alignwithAlignPanel"
109 type="xs:boolean" use="optional" default="true">
138 <xs:attribute name="colourwithAlignPanel"
139 type="xs:boolean" use="optional" default="false">
170 <xs:attribute name="colourByJmol" type="xs:boolean"
171 use="optional" default="true">
198 <xs:attribute name="type" type="xs:string"
226 <xs:element name="hiddenSequences" type="xs:int"
227 minOccurs="0" maxOccurs="unbounded" />
228 <xs:element name="rnaViewer" minOccurs="0" maxOccurs="unbounded">
230 <xs:documentation>Reference to a viewer showing RNA structure
231 for this sequence. Schema supports one viewer showing multiple
232 annotations for multiple sequences, though currently only one
233 annotation for one sequence (gapped or trimmed) is used
238 <xs:element name="secondaryStructure" minOccurs="1"
239 maxOccurs="unbounded">
241 <xs:attribute name="title" type="xs:string" />
242 <xs:attribute name="annotationId" type="xs:string"
245 <xs:documentation>id attribute of Annotation in
247 the secondary structure annotation shown
252 <xs:attribute name="gapped" type="xs:boolean">
254 <xs:documentation>if true the RNA structure is shown with gaps, if false without
258 <xs:attribute name="viewerState" type="xs:string">
260 <xs:documentation>name of the project jar entry that holds
261 the VARNA viewer state for the structure
268 <xs:attributeGroup ref="jv:swingwindow" />
269 <xs:attribute name="title" type="xs:string" />
270 <xs:attribute name="viewId" type="xs:string">
272 <xs:documentation>An id unique to the RNA viewer panel
276 <xs:attribute name="dividerLocation" type="xs:int">
278 <xs:documentation>horizontal position of split pane divider
282 <xs:attribute name="selectedRna" type="xs:int">
284 <xs:documentation>Index of the selected structure in the
292 <xs:attribute name="colour" type="xs:int" use="optional" />
293 <xs:attribute name="start" type="xs:int" use="required" />
294 <xs:attribute name="end" type="xs:int" use="required" />
295 <xs:attribute name="id" type="xs:string" use="required" />
296 <xs:attribute name="hidden" type="xs:boolean" />
297 <xs:attribute name="viewreference" type="xs:boolean" use="optional"/>
300 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
303 <xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
304 <xs:element name="annotationColours" type="jv:AnnotationColourScheme"
305 minOccurs="0" maxOccurs="1" />
307 <xs:attribute name="start" type="xs:int" />
308 <xs:attribute name="end" type="xs:int" />
309 <xs:attribute name="name" type="xs:string" />
310 <xs:attribute name="colour" type="xs:string" />
311 <xs:attribute name="consThreshold" type="xs:int" />
312 <xs:attribute name="pidThreshold" type="xs:int" />
313 <xs:attribute name="outlineColour" type="xs:int" />
314 <xs:attribute name="displayBoxes" type="xs:boolean" />
315 <xs:attribute name="displayText" type="xs:boolean" />
316 <xs:attribute name="colourText" type="xs:boolean" />
317 <xs:attribute name="textCol1" type="xs:int" />
318 <xs:attribute name="textCol2" type="xs:int" />
319 <xs:attribute name="textColThreshold" type="xs:int" />
320 <xs:attribute name="showUnconserved" type="xs:boolean"
322 <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
323 use="optional" default="true" />
324 <xs:attribute name="showConsensusHistogram" type="xs:boolean"
325 use="optional" default="true" />
326 <xs:attribute name="showSequenceLogo" type="xs:boolean"
327 use="optional" default="false" />
328 <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
329 use="optional" default="false" />
330 <xs:attribute name="id" type="xs:string" use="optional">
333 Optional sequence group ID (only
342 <xs:element name="Viewport" maxOccurs="unbounded"
346 <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
347 minOccurs="0" maxOccurs="1">
349 <xs:element name="hiddenColumns" minOccurs="0"
350 maxOccurs="unbounded">
352 <xs:attribute name="start" type="xs:int" />
353 <xs:attribute name="end" type="xs:int" />
356 <xs:element name="calcIdParam" minOccurs="0"
357 maxOccurs="unbounded">
360 <xs:extension base="jvws:WebServiceParameterSet">
361 <xs:attribute name="calcId" type="xs:string"
364 <xs:documentation>handle for the calculation which uses
369 <xs:attribute name="needsUpdate" type="xs:boolean"
370 use="optional" default="false">
372 <xs:documentation>should the calculation be performed
373 immediately after loading in order to refresh results
377 <xs:attribute name="autoUpdate" type="xs:boolean"
380 <xs:documentation>should the calculation be automatically
390 <xs:attributeGroup ref="jv:swingwindow" />
391 <xs:attribute name="conservationSelected" type="xs:boolean" />
392 <xs:attribute name="pidSelected" type="xs:boolean" />
393 <xs:attribute name="bgColour" type="xs:string" />
394 <xs:attribute name="consThreshold" type="xs:int" />
395 <xs:attribute name="pidThreshold" type="xs:int" />
396 <xs:attribute name="title" type="xs:string" />
397 <xs:attribute name="showFullId" type="xs:boolean" />
398 <xs:attribute name="rightAlignIds" type="xs:boolean" />
399 <xs:attribute name="showText" type="xs:boolean" />
400 <xs:attribute name="showColourText" type="xs:boolean" />
401 <xs:attribute name="showUnconserved" type="xs:boolean"
402 use="optional" default="false" />
403 <xs:attribute name="showBoxes" type="xs:boolean" />
404 <xs:attribute name="wrapAlignment" type="xs:boolean" />
405 <xs:attribute name="renderGaps" type="xs:boolean" />
406 <xs:attribute name="showSequenceFeatures" type="xs:boolean" />
407 <xs:attribute name="showNPfeatureTooltip" type="xs:boolean"
409 <xs:attribute name="showDbRefTooltip" type="xs:boolean"
411 <xs:attribute name="followHighlight" type="xs:boolean"
412 use="optional" default="true" />
413 <xs:attribute name="followSelection" type="xs:boolean"
414 use="optional" default="true" />
415 <xs:attribute name="showAnnotation" type="xs:boolean" />
416 <xs:attribute name="centreColumnLabels" type="xs:boolean"
417 use="optional" default="false" />
418 <xs:attribute name="showGroupConservation" type="xs:boolean"
419 use="optional" default="false" />
420 <xs:attribute name="showGroupConsensus" type="xs:boolean"
421 use="optional" default="false" />
422 <xs:attribute name="showConsensusHistogram" type="xs:boolean"
423 use="optional" default="true" />
424 <xs:attribute name="showSequenceLogo" type="xs:boolean"
425 use="optional" default="false" />
426 <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
427 use="optional" default="false" />
428 <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
429 use="optional" default="true" />
430 <xs:attribute name="startRes" type="xs:int" />
431 <xs:attribute name="startSeq" type="xs:int" />
432 <xs:attribute name="fontName" type="xs:string" />
433 <xs:attribute name="fontSize" type="xs:int" />
434 <xs:attribute name="fontStyle" type="xs:int" />
435 <xs:attribute name="scaleProteinAsCdna" type="xs:boolean" use="optional" default="true" />
436 <xs:attribute name="viewName" type="xs:string" />
437 <xs:attribute name="sequenceSetId" type="xs:string" />
438 <xs:attribute name="gatheredViews" type="xs:boolean" />
439 <xs:attribute name="textCol1" type="xs:int" />
440 <xs:attribute name="textCol2" type="xs:int" />
441 <xs:attribute name="textColThreshold" type="xs:int" />
442 <xs:attribute name="id" type="xs:ID" use="optional">
445 unique id used by jalview to
452 <xs:attribute name="complementId" type="xs:string"
456 The viewport id of this viewport's
457 (cdna/protein) coding complement, if any
463 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
466 <xs:element name="UserColourScheme" type="jalview:JalviewUserColours" />
468 <xs:attribute name="id" type="xs:string" />
471 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
473 <xs:sequence minOccurs="0">
474 <xs:element name="title" type="xs:string" />
475 <xs:element name="newick" type="xs:string" />
477 <xs:attribute name="fontName" type="xs:string" />
478 <xs:attribute name="fontSize" type="xs:int" />
479 <xs:attribute name="fontStyle" type="xs:int" />
480 <xs:attribute name="threshold" type="xs:float" />
481 <xs:attribute name="showBootstrap" type="xs:boolean" />
482 <xs:attribute name="showDistances" type="xs:boolean" />
483 <xs:attribute name="markUnlinked" type="xs:boolean" />
484 <xs:attribute name="fitToWindow" type="xs:boolean" />
485 <xs:attribute name="currentTree" type="xs:boolean" />
486 <xs:attribute name="id" type="xs:ID" use="optional">
489 Tree ID added for binding tree
492 document trees in jalview 2.4.1
496 <xs:attributeGroup ref="jv:swingwindow" />
499 <xs:element name="FeatureSettings" minOccurs="0">
502 <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
505 <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
507 <xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
510 <xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
512 <xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
516 <xs:attribute name="type" type="xs:string" use="required" />
517 <xs:attribute name="colour" type="xs:int" use="required" />
518 <xs:attribute name="display" type="xs:boolean"
520 <xs:attribute name="order" type="xs:float" use="optional" />
521 <xs:attribute name="mincolour" type="xs:int" use="optional">
524 Optional minimum colour
531 <xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
532 <xs:attribute name="threshold" type="xs:float"
537 graduated feature colour
541 <xs:attribute name="threshstate" type="xs:int"
546 graduated feature colour
550 <xs:attribute name="max" type="xs:float" use="optional" />
551 <xs:attribute name="min" type="xs:float" use="optional" />
552 <xs:attribute name="colourByLabel" type="xs:boolean"
554 <xs:attribute name="autoScale" type="xs:boolean"
558 <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
560 <xs:attribute name="name" type="xs:string" use="required" />
561 <xs:attribute name="display" type="xs:boolean"
571 <xs:complexType name="feature">
573 <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
575 <xs:attribute name="key" type="xs:string" use="required" />
576 <xs:attribute name="key2" type="xs:string" use="optional">
578 <xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
581 <xs:attribute name="value" type="xs:string" use="required" />
585 <xs:attribute name="begin" type="xs:int" use="required" />
586 <xs:attribute name="end" type="xs:int" use="required" />
587 <xs:attribute name="type" type="xs:string" use="required" />
588 <xs:attribute name="description" type="xs:string" use="optional" />
589 <xs:attribute name="status" type="xs:string" use="optional" />
590 <xs:attribute name="featureGroup" type="xs:string" use="optional" />
591 <xs:attribute name="score" type="xs:float" use="optional" />
593 <xs:complexType name="pdbentry">
594 <xs:sequence minOccurs="0" maxOccurs="unbounded">
595 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
597 <xs:attribute name="name" type="xs:string" use="required" />
598 <xs:attribute name="value" type="xs:string" use="required" />
602 <xs:attribute name="id" type="xs:string" use="required" />
603 <xs:attribute name="type" type="xs:string" use="optional" />
604 <xs:attribute name="file" type="xs:string" />
606 <!-- <xs:complexType name="reportWindow"> <xs:annotation> <xs:documentation>Generic
607 type for windows containing mime-typed data associated with other jalview
608 windows</xs:documentation> </xs:annotation> <xs:sequence> </xs:sequence>
609 <xs:attribute name="id" type="xs:string" use="required"/> <xs:attribute name="type"
610 type="xs:string" use="optional"/> <xs:attribute name="file" type="xs:string"
611 use="optional"/> </xs:complexType> -->
612 <xs:attributeGroup name="swingwindow">
615 base attributes for windows displayed in Jalview
619 <xs:attribute name="width" type="xs:int" />
620 <xs:attribute name="height" type="xs:int" />
621 <xs:attribute name="xpos" type="xs:int" />
622 <xs:attribute name="ypos" type="xs:int" />
624 <xs:complexType name="AnnotationColourScheme">
625 <xs:attribute name="aboveThreshold" type="xs:int" />
626 <xs:attribute name="annotation" type="xs:string" />
627 <xs:attribute name="minColour" type="xs:int" />
628 <xs:attribute name="maxColour" type="xs:int" />
629 <xs:attribute name="colourScheme" type="xs:string" />
630 <xs:attribute name="threshold" type="xs:float" />
631 <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
632 <xs:attribute name="predefinedColours" type="xs:boolean"