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="fontName" type="xs:string" />
500 <xs:attribute name="fontSize" type="xs:int" />
501 <xs:attribute name="fontStyle" type="xs:int" />
502 <xs:attribute name="scaleProteinAsCdna" type="xs:boolean" use="optional" default="true" />
503 <xs:attribute name="viewName" type="xs:string" />
504 <xs:attribute name="sequenceSetId" type="xs:string" />
505 <xs:attribute name="gatheredViews" type="xs:boolean" />
506 <xs:attribute name="textCol1" type="xs:int" />
507 <xs:attribute name="textCol2" type="xs:int" />
508 <xs:attribute name="textColThreshold" type="xs:int" />
509 <xs:attribute name="id" type="xs:ID" use="optional">
512 unique id used by jalview to
519 <xs:attribute name="complementId" type="xs:string"
523 The viewport id of this viewport's
524 (cdna/protein) coding complement, if any
528 <xs:attribute name="showComplementFeatures" type="xs:boolean" use="optional" default="false" />
529 <xs:attribute name="showComplementFeaturesOnTop" type="xs:boolean" use="optional" default="false" />
532 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
535 <xs:element name="UserColourScheme" type="jalview:JalviewUserColours" />
537 <xs:attribute name="id" type="xs:string" />
540 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
542 <xs:sequence minOccurs="0">
543 <xs:element name="title" type="xs:string" />
544 <xs:element name="newick" type="xs:string" />
546 <xs:attribute name="fontName" type="xs:string" />
547 <xs:attribute name="fontSize" type="xs:int" />
548 <xs:attribute name="fontStyle" type="xs:int" />
549 <xs:attribute name="threshold" type="xs:float" />
550 <xs:attribute name="showBootstrap" type="xs:boolean" />
551 <xs:attribute name="showDistances" type="xs:boolean" />
552 <xs:attribute name="markUnlinked" type="xs:boolean" />
553 <xs:attribute name="fitToWindow" type="xs:boolean" />
554 <xs:attribute name="currentTree" type="xs:boolean" />
555 <xs:attribute name="id" type="xs:ID" use="optional">
558 Tree ID added for binding tree
561 document trees in jalview 2.4.1
565 <xs:attributeGroup ref="jv:swingwindow" />
566 <xs:attribute name="linkToAllViews" use="optional" default="false" type="xs:boolean" />
569 <xs:element name="PcaViewer" minOccurs="0" maxOccurs="unbounded">
572 <xs:element name="sequencePoint" minOccurs="1" maxOccurs="unbounded">
574 <xs:attribute name="sequenceRef" type="xs:string" />
575 <xs:attributeGroup ref="jv:position" />
578 <xs:element name="axis" minOccurs="3" maxOccurs="3">
581 endpoints of X, Y and Z axes in that order
585 <xs:attributeGroup ref="jv:position" />
588 <xs:element name="seqPointMin">
590 <xs:attributeGroup ref="jv:position" />
593 <xs:element name="seqPointMax">
595 <xs:attributeGroup ref="jv:position" />
598 <xs:element name="pcaData" type="jv:PcaDataType" />
600 <xs:attribute name="title" type="xs:string" />
601 <xs:attribute name="scoreModelName" type="xs:string" />
602 <xs:attribute name="xDim" type="xs:int" />
603 <xs:attribute name="yDim" type="xs:int" />
604 <xs:attribute name="zDim" type="xs:int" />
605 <xs:attribute name="bgColour" type="xs:int" />
606 <xs:attribute name="scaleFactor" type="xs:float" />
607 <xs:attribute name="showLabels" type="xs:boolean" />
608 <xs:attribute name="linkToAllViews" type="xs:boolean" />
609 <xs:attributeGroup ref="jv:SimilarityParams" />
610 <xs:attributeGroup ref="jv:swingwindow" />
613 <xs:element name="FeatureSettings" minOccurs="0">
616 <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
619 <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
621 <xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
624 <xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
626 <xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
630 <xs:attribute name="type" type="xs:string" use="required" />
631 <xs:attribute name="colour" type="xs:int" use="required" />
632 <xs:attribute name="display" type="xs:boolean"
634 <xs:attribute name="order" type="xs:float" use="optional" />
635 <xs:attribute name="mincolour" type="xs:int" use="optional">
638 Optional minimum colour
645 <xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
646 <xs:attribute name="threshold" type="xs:float"
651 graduated feature colour
655 <xs:attribute name="threshstate" type="xs:int"
660 graduated feature colour
664 <xs:attribute name="max" type="xs:float" use="optional" />
665 <xs:attribute name="min" type="xs:float" use="optional" />
666 <xs:attribute name="colourByLabel" type="xs:boolean"
668 <xs:attribute name="autoScale" type="xs:boolean"
672 <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
674 <xs:attribute name="name" type="xs:string" use="required" />
675 <xs:attribute name="display" type="xs:boolean"
685 <xs:complexType name="feature">
687 <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
689 <xs:attribute name="key" type="xs:string" use="required" />
690 <xs:attribute name="key2" type="xs:string" use="optional">
692 <xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
695 <xs:attribute name="value" type="xs:string" use="required" />
699 <xs:attribute name="begin" type="xs:int" use="required" />
700 <xs:attribute name="end" type="xs:int" use="required" />
701 <xs:attribute name="type" type="xs:string" use="required" />
702 <xs:attribute name="description" type="xs:string" use="optional" />
703 <xs:attribute name="status" type="xs:string" use="optional" />
704 <xs:attribute name="featureGroup" type="xs:string" use="optional" />
705 <xs:attribute name="score" type="xs:float" use="optional" />
707 <xs:complexType name="pdbentry">
708 <xs:sequence minOccurs="0" maxOccurs="unbounded">
709 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
711 <xs:attribute name="name" type="xs:string" use="required" />
712 <xs:attribute name="value" type="xs:string" use="required" />
716 <xs:attribute name="id" type="xs:string" use="required" />
717 <xs:attribute name="type" type="xs:string" use="optional" />
718 <xs:attribute name="file" type="xs:string" />
720 <!-- <xs:complexType name="reportWindow"> <xs:annotation> <xs:documentation>Generic
721 type for windows containing mime-typed data associated with other jalview
722 windows</xs:documentation> </xs:annotation> <xs:sequence> </xs:sequence>
723 <xs:attribute name="id" type="xs:string" use="required"/> <xs:attribute name="type"
724 type="xs:string" use="optional"/> <xs:attribute name="file" type="xs:string"
725 use="optional"/> </xs:complexType> -->
726 <xs:attributeGroup name="swingwindow">
729 base attributes for windows displayed in Jalview
733 <xs:attribute name="width" type="xs:int" />
734 <xs:attribute name="height" type="xs:int" />
735 <xs:attribute name="xpos" type="xs:int" />
736 <xs:attribute name="ypos" type="xs:int" />
738 <xs:complexType name="AnnotationColourScheme">
739 <xs:attribute name="aboveThreshold" type="xs:int" />
740 <xs:attribute name="annotation" type="xs:string" />
741 <xs:attribute name="minColour" type="xs:int" />
742 <xs:attribute name="maxColour" type="xs:int" />
743 <xs:attribute name="colourScheme" type="xs:string" />
744 <xs:attribute name="threshold" type="xs:float" />
745 <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
746 <xs:attribute name="predefinedColours" type="xs:boolean"
749 <xs:attributeGroup name="SimilarityParams">
752 parameters that condition a similarity score calculation
755 <xs:attribute name="includeGaps" type="xs:boolean" />
756 <xs:attribute name="matchGaps" type="xs:boolean" />
757 <xs:attribute name="includeGappedColumns" type="xs:boolean" />
758 <xs:attribute name="denominateByShortestLength" type="xs:boolean" />
760 <xs:attributeGroup name="position">
761 <xs:attribute name="xPos" type="xs:float" />
762 <xs:attribute name="yPos" type="xs:float" />
763 <xs:attribute name="zPos" type="xs:float" />
765 <xs:complexType name="PcaDataType">
768 The results of a PCA calculation
772 <xs:element name="pairwiseMatrix" type="jv:DoubleMatrix" />
773 <xs:element name="tridiagonalMatrix" type="jv:DoubleMatrix" />
774 <xs:element name="eigenMatrix" type="jv:DoubleMatrix" />
777 <xs:complexType name="DoubleVector">
779 <xs:element name="v" type="xs:double" minOccurs="0" maxOccurs="unbounded" />
782 <xs:complexType name="DoubleMatrix">
784 <xs:element name="row" type="jv:DoubleVector" minOccurs="0" maxOccurs="unbounded" />
785 <xs:element name="D" minOccurs="0" type="jv:DoubleVector" />
786 <xs:element name="E" minOccurs="0" type="jv:DoubleVector" />
788 <xs:attribute name="rows" type="xs:int" />
789 <xs:attribute name="columns" type="xs:int" />