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. -->
14 Java JAXB binding classes are generated by running command line tool xjc:
15 xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
16 Note this also generates code for included schemas
18 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
19 xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours"
20 xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset"
21 targetNamespace="www.jalview.org" elementFormDefault="qualified"
22 attributeFormDefault="unqualified">
23 <xs:import namespace="www.vamsas.ac.uk/jalview/version2"
24 schemaLocation="vamsas.xsd" />
25 <xs:import namespace="www.jalview.org/colours"
26 schemaLocation="JalviewUserColours.xsd" />
27 <xs:import namespace="www.jalview.org/xml/wsparamset"
28 schemaLocation="JalviewWsParamSet.xsd" />
29 <xs:element name="JalviewModel" type="jv:JalviewModel" />
30 <xs:complexType name="JalviewModel">
32 <xs:element name="creationDate" type="xs:dateTime" />
33 <xs:element name="version" type="xs:string" />
34 <xs:element name="vamsasModel" type="vamsas:VAMSAS" />
36 <xs:element name="JSeq" maxOccurs="unbounded" minOccurs="0">
39 <xs:element name="features"
40 type="jv:feature" minOccurs="0" maxOccurs="unbounded" />
41 <xs:element name="pdbids" minOccurs="0"
42 maxOccurs="unbounded">
49 name="structureState" minOccurs="0"
50 maxOccurs="unbounded">
56 ref="jv:swingwindow" />
58 name="visible" type="xs:boolean" />
60 name="viewId" type="xs:string" use="optional">
120 name="alignwithAlignPanel" type="xs:boolean"
121 use="optional" default="true">
151 name="colourwithAlignPanel" type="xs:boolean"
152 use="optional" default="false">
184 name="colourByJmol" type="xs:boolean" use="optional"
213 name="type" type="xs:string" use="optional">
240 <xs:element name="hiddenSequences"
241 type="xs:int" minOccurs="0" maxOccurs="unbounded" />
242 <xs:element name="rnaViewer" minOccurs="0"
243 maxOccurs="unbounded">
246 Reference to a viewer showing
247 RNA structure for this sequence.
248 Schema supports one viewer
249 showing multiple annotations for
250 multiple sequences, though
251 currently only one annotation
252 for one sequence (gapped or
259 name="secondaryStructure" minOccurs="1"
260 maxOccurs="unbounded">
263 name="title" type="xs:string" />
265 name="annotationId" type="xs:string" use="required">
283 name="gapped" type="xs:boolean">
297 name="viewerState" type="xs:string">
315 ref="jv:swingwindow" />
316 <xs:attribute name="title"
318 <xs:attribute name="viewId"
322 An id unique to the RNA
327 <xs:attribute name="dividerLocation"
331 horizontal position of
336 <xs:attribute name="selectedRna"
340 Index of the selected
341 structure in the viewer
349 <xs:attribute name="colour" type="xs:int" use="optional" />
350 <xs:attribute name="start" type="xs:int" use="required" />
351 <xs:attribute name="end" type="xs:int" use="required" />
352 <xs:attribute name="id" type="xs:string" use="required" />
353 <xs:attribute name="hidden" type="xs:boolean" />
354 <xs:attribute name="viewreference" type="xs:boolean" use="optional"/>
357 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
360 <xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
361 <xs:element name="annotationColours" type="jv:AnnotationColourScheme"
362 minOccurs="0" maxOccurs="1" />
364 <xs:attribute name="start" type="xs:int" />
365 <xs:attribute name="end" type="xs:int" />
366 <xs:attribute name="name" type="xs:string" />
367 <xs:attribute name="colour" type="xs:string" />
368 <xs:attribute name="consThreshold" type="xs:int" />
369 <xs:attribute name="pidThreshold" type="xs:int" />
370 <xs:attribute name="outlineColour" type="xs:int" />
371 <xs:attribute name="displayBoxes" type="xs:boolean" />
372 <xs:attribute name="displayText" type="xs:boolean" />
373 <xs:attribute name="colourText" type="xs:boolean" />
374 <xs:attribute name="textCol1" type="xs:int" />
375 <xs:attribute name="textCol2" type="xs:int" />
376 <xs:attribute name="textColThreshold" type="xs:int" />
377 <xs:attribute name="showUnconserved" type="xs:boolean"
379 <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
380 use="optional" default="true" />
381 <xs:attribute name="showConsensusHistogram" type="xs:boolean"
382 use="optional" default="true" />
383 <xs:attribute name="showSequenceLogo" type="xs:boolean"
384 use="optional" default="false" />
385 <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
386 use="optional" default="false" />
387 <xs:attribute name="id" type="xs:string" use="optional">
390 Optional sequence group ID (only
399 <xs:element name="Viewport" maxOccurs="unbounded"
403 <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
404 minOccurs="0" maxOccurs="1">
406 <xs:element name="hiddenColumns" minOccurs="0"
407 maxOccurs="unbounded">
409 <xs:attribute name="start" type="xs:int" />
410 <xs:attribute name="end" type="xs:int" />
413 <xs:element name="calcIdParam" minOccurs="0"
414 maxOccurs="unbounded">
417 <xs:extension base="jvws:WebServiceParameterSet">
418 <xs:attribute name="calcId" type="xs:string"
421 <xs:documentation>handle for the calculation which uses
426 <xs:attribute name="needsUpdate" type="xs:boolean"
427 use="optional" default="false">
429 <xs:documentation>should the calculation be performed
430 immediately after loading in order to refresh results
434 <xs:attribute name="autoUpdate" type="xs:boolean"
437 <xs:documentation>should the calculation be automatically
446 <xs:element name="overview" minOccurs="0">
448 <xs:attributeGroup ref="jv:swingwindow" />
449 <xs:attribute name="showHidden" type="xs:boolean" />
450 <xs:attribute name="residueColour" type="xs:int" />
451 <xs:attribute name="gapColour" type="xs:int" />
452 <xs:attribute name="hiddenColour" type="xs:int" />
453 <xs:attribute name="title" type="xs:string" />
457 <xs:attributeGroup ref="jv:swingwindow" />
458 <xs:attribute name="conservationSelected" type="xs:boolean" />
459 <xs:attribute name="pidSelected" type="xs:boolean" />
460 <xs:attribute name="bgColour" type="xs:string" />
461 <xs:attribute name="consThreshold" type="xs:int" />
462 <xs:attribute name="pidThreshold" type="xs:int" />
463 <xs:attribute name="title" type="xs:string" />
464 <xs:attribute name="showFullId" type="xs:boolean" />
465 <xs:attribute name="rightAlignIds" type="xs:boolean" />
466 <xs:attribute name="showText" type="xs:boolean" />
467 <xs:attribute name="showColourText" type="xs:boolean" />
468 <xs:attribute name="showUnconserved" type="xs:boolean"
469 use="optional" default="false" />
470 <xs:attribute name="showBoxes" type="xs:boolean" />
471 <xs:attribute name="wrapAlignment" type="xs:boolean" />
472 <xs:attribute name="renderGaps" type="xs:boolean" />
473 <xs:attribute name="showSequenceFeatures" type="xs:boolean" />
474 <xs:attribute name="showNPfeatureTooltip" type="xs:boolean"
476 <xs:attribute name="showDbRefTooltip" type="xs:boolean"
478 <xs:attribute name="followHighlight" type="xs:boolean"
479 use="optional" default="true" />
480 <xs:attribute name="followSelection" type="xs:boolean"
481 use="optional" default="true" />
482 <xs:attribute name="showAnnotation" type="xs:boolean" />
483 <xs:attribute name="centreColumnLabels" type="xs:boolean"
484 use="optional" default="false" />
485 <xs:attribute name="showGroupConservation" type="xs:boolean"
486 use="optional" default="false" />
487 <xs:attribute name="showGroupConsensus" type="xs:boolean"
488 use="optional" default="false" />
489 <xs:attribute name="showConsensusHistogram" type="xs:boolean"
490 use="optional" default="true" />
491 <xs:attribute name="showSequenceLogo" type="xs:boolean"
492 use="optional" default="false" />
493 <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
494 use="optional" default="false" />
495 <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
496 use="optional" default="true" />
497 <xs:attribute name="startRes" type="xs:int" />
498 <xs:attribute name="startSeq" type="xs:int" />
499 <xs:attribute name="charWidth" type="xs:int" />
500 <xs:attribute name="charHeight" type="xs:int" />
501 <xs:attribute name="fontName" type="xs:string" />
502 <xs:attribute name="fontSize" type="xs:int" />
503 <xs:attribute name="fontStyle" type="xs:int" />
504 <xs:attribute name="scaleProteinAsCdna" type="xs:boolean" use="optional" default="true" />
505 <xs:attribute name="viewName" type="xs:string" />
506 <xs:attribute name="sequenceSetId" type="xs:string" />
507 <xs:attribute name="gatheredViews" type="xs:boolean" />
508 <xs:attribute name="textCol1" type="xs:int" />
509 <xs:attribute name="textCol2" type="xs:int" />
510 <xs:attribute name="textColThreshold" type="xs:int" />
511 <xs:attribute name="id" type="xs:ID" use="optional">
514 unique id used by jalview to
521 <xs:attribute name="complementId" type="xs:string"
525 The viewport id of this viewport's
526 (cdna/protein) coding complement, if any
530 <xs:attribute name="showComplementFeatures" type="xs:boolean" use="optional" default="false" />
531 <xs:attribute name="showComplementFeaturesOnTop" type="xs:boolean" use="optional" default="false" />
534 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
537 <xs:element name="UserColourScheme" type="jalview:JalviewUserColours" />
539 <xs:attribute name="id" type="xs:string" />
542 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
544 <xs:sequence minOccurs="0">
545 <xs:element name="title" type="xs:string" />
546 <xs:element name="newick" type="xs:string" />
548 <xs:attribute name="fontName" type="xs:string" />
549 <xs:attribute name="fontSize" type="xs:int" />
550 <xs:attribute name="fontStyle" type="xs:int" />
551 <xs:attribute name="threshold" type="xs:float" />
552 <xs:attribute name="showBootstrap" type="xs:boolean" />
553 <xs:attribute name="showDistances" type="xs:boolean" />
554 <xs:attribute name="markUnlinked" type="xs:boolean" />
555 <xs:attribute name="fitToWindow" type="xs:boolean" />
556 <xs:attribute name="currentTree" type="xs:boolean" />
557 <xs:attribute name="id" type="xs:ID" use="optional">
560 Tree ID added for binding tree
563 document trees in jalview 2.4.1
567 <xs:attributeGroup ref="jv:swingwindow" />
568 <xs:attribute name="linkToAllViews" use="optional" default="false" type="xs:boolean" />
571 <xs:element name="PcaViewer" minOccurs="0" maxOccurs="unbounded">
574 <xs:element name="sequencePoint" minOccurs="1" maxOccurs="unbounded">
576 <xs:attribute name="sequenceRef" type="xs:string" />
577 <xs:attributeGroup ref="jv:position" />
580 <xs:element name="axis" minOccurs="3" maxOccurs="3">
583 endpoints of X, Y and Z axes in that order
587 <xs:attributeGroup ref="jv:position" />
590 <xs:element name="seqPointMin">
592 <xs:attributeGroup ref="jv:position" />
595 <xs:element name="seqPointMax">
597 <xs:attributeGroup ref="jv:position" />
600 <xs:element name="pcaData" type="jv:PcaDataType" />
602 <xs:attribute name="title" type="xs:string" />
603 <xs:attribute name="scoreModelName" type="xs:string" />
604 <xs:attribute name="xDim" type="xs:int" />
605 <xs:attribute name="yDim" type="xs:int" />
606 <xs:attribute name="zDim" type="xs:int" />
607 <xs:attribute name="bgColour" type="xs:int" />
608 <xs:attribute name="scaleFactor" type="xs:float" />
609 <xs:attribute name="showLabels" type="xs:boolean" />
610 <xs:attribute name="linkToAllViews" type="xs:boolean" />
611 <xs:attributeGroup ref="jv:SimilarityParams" />
612 <xs:attributeGroup ref="jv:swingwindow" />
615 <xs:element name="FeatureSettings" minOccurs="0">
618 <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
621 <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
623 <xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
626 <xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
628 <xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
632 <xs:attribute name="type" type="xs:string" use="required" />
633 <xs:attribute name="colour" type="xs:int" use="required" />
634 <xs:attribute name="display" type="xs:boolean"
636 <xs:attribute name="order" type="xs:float" use="optional" />
637 <xs:attribute name="mincolour" type="xs:int" use="optional">
640 Optional minimum colour
647 <xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
648 <xs:attribute name="threshold" type="xs:float"
653 graduated feature colour
657 <xs:attribute name="threshstate" type="xs:int"
662 graduated feature colour
666 <xs:attribute name="max" type="xs:float" use="optional" />
667 <xs:attribute name="min" type="xs:float" use="optional" />
668 <xs:attribute name="colourByLabel" type="xs:boolean"
670 <xs:attribute name="autoScale" type="xs:boolean"
674 <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
676 <xs:attribute name="name" type="xs:string" use="required" />
677 <xs:attribute name="display" type="xs:boolean"
687 <xs:complexType name="feature">
689 <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
691 <xs:attribute name="key" type="xs:string" use="required" />
692 <xs:attribute name="key2" type="xs:string" use="optional">
694 <xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
697 <xs:attribute name="value" type="xs:string" use="required" />
701 <xs:attribute name="begin" type="xs:int" use="required" />
702 <xs:attribute name="end" type="xs:int" use="required" />
703 <xs:attribute name="type" type="xs:string" use="required" />
704 <xs:attribute name="description" type="xs:string" use="optional" />
705 <xs:attribute name="status" type="xs:string" use="optional" />
706 <xs:attribute name="featureGroup" type="xs:string" use="optional" />
707 <xs:attribute name="score" type="xs:float" use="optional" />
709 <xs:complexType name="pdbentry">
710 <xs:sequence minOccurs="0" maxOccurs="unbounded">
711 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
713 <xs:attribute name="name" type="xs:string" use="required" />
714 <xs:attribute name="value" type="xs:string" use="required" />
718 <xs:attribute name="id" type="xs:string" use="required" />
719 <xs:attribute name="type" type="xs:string" use="optional" />
720 <xs:attribute name="file" type="xs:string" />
722 <!-- <xs:complexType name="reportWindow"> <xs:annotation> <xs:documentation>Generic
723 type for windows containing mime-typed data associated with other jalview
724 windows</xs:documentation> </xs:annotation> <xs:sequence> </xs:sequence>
725 <xs:attribute name="id" type="xs:string" use="required"/> <xs:attribute name="type"
726 type="xs:string" use="optional"/> <xs:attribute name="file" type="xs:string"
727 use="optional"/> </xs:complexType> -->
728 <xs:attributeGroup name="swingwindow">
731 base attributes for windows displayed in Jalview
735 <xs:attribute name="width" type="xs:int" />
736 <xs:attribute name="height" type="xs:int" />
737 <xs:attribute name="xpos" type="xs:int" />
738 <xs:attribute name="ypos" type="xs:int" />
740 <xs:complexType name="AnnotationColourScheme">
741 <xs:attribute name="aboveThreshold" type="xs:int" />
742 <xs:attribute name="annotation" type="xs:string" />
743 <xs:attribute name="minColour" type="xs:int" />
744 <xs:attribute name="maxColour" type="xs:int" />
745 <xs:attribute name="colourScheme" type="xs:string" />
746 <xs:attribute name="threshold" type="xs:float" />
747 <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
748 <xs:attribute name="predefinedColours" type="xs:boolean"
751 <xs:attributeGroup name="SimilarityParams">
754 parameters that condition a similarity score calculation
757 <xs:attribute name="includeGaps" type="xs:boolean" />
758 <xs:attribute name="matchGaps" type="xs:boolean" />
759 <xs:attribute name="includeGappedColumns" type="xs:boolean" />
760 <xs:attribute name="denominateByShortestLength" type="xs:boolean" />
762 <xs:attributeGroup name="position">
763 <xs:attribute name="xPos" type="xs:float" />
764 <xs:attribute name="yPos" type="xs:float" />
765 <xs:attribute name="zPos" type="xs:float" />
767 <xs:complexType name="PcaDataType">
770 The results of a PCA calculation
774 <xs:element name="pairwiseMatrix" type="jv:DoubleMatrix" />
775 <xs:element name="tridiagonalMatrix" type="jv:DoubleMatrix" />
776 <xs:element name="eigenMatrix" type="jv:DoubleMatrix" />
779 <xs:complexType name="DoubleVector">
781 <xs:element name="v" type="xs:double" minOccurs="0" maxOccurs="unbounded" />
784 <xs:complexType name="DoubleMatrix">
786 <xs:element name="row" type="jv:DoubleVector" minOccurs="0" maxOccurs="unbounded" />
787 <xs:element name="D" minOccurs="0" type="jv:DoubleVector" />
788 <xs:element name="E" minOccurs="0" type="jv:DoubleVector" />
790 <xs:attribute name="rows" type="xs:int" />
791 <xs:attribute name="columns" type="xs:int" />