+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of
- Jalview. * * Jalview is free software: you can redistribute it and/or * modify
- it under the terms of the GNU General Public License * as published by the
- Free Software Foundation, either version 3 of the License, or (at your option)
- any later version. * * Jalview is distributed in the hope that it will be
- useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General
- Public License for more details. * * You should have received a copy of the
- GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file. -->
-<!--
- Java JAXB binding classes are generated by running command line tool xjc:
- xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
- Note this also generates code for included schemas
--->
-<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">
- <xs:import namespace="www.vamsas.ac.uk/jalview/version2"
- schemaLocation="vamsas.xsd" />
- <xs:import namespace="www.jalview.org/colours"
- schemaLocation="JalviewUserColours.xsd" />
- <xs:import namespace="www.jalview.org/xml/wsparamset"
- schemaLocation="JalviewWsParamSet.xsd" />
- <xs:element name="JalviewModel" type="jv:JalviewModel" />
- <xs:complexType name="JalviewModel">
- <xs:sequence>
- <xs:element name="creationDate" type="xs:dateTime" />
- <xs:element name="version" type="xs:string" />
- <xs:element name="vamsasModel" type="vamsas:VAMSAS" />
- <xs:sequence>
- <xs:element name="JSeq" maxOccurs="unbounded" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="features" type="jv:feature"
- minOccurs="0" maxOccurs="unbounded" />
- <xs:element name="pdbids" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:complexContent>
- <xs:extension base="jv:pdbentry">
- <xs:sequence>
- <xs:element name="structureState" minOccurs="0"
- maxOccurs="unbounded">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:string">
- <xs:attributeGroup ref="jv:swingwindow" />
- <xs:attribute name="visible" type="xs:boolean" />
- <xs:attribute name="viewId" type="xs:string"
- use="optional">
- <xs:annotation>
- <xs:documentation>
- additional
- identifier
- which
- properly
- disambiguates
- the
- structure
- view
- from
- any
- other
- view
- with
- the
- same
- attributes.
- This
- is
- not
- an
- ID,
- because
- it
- is
- possible
- to
- have
- many
- references
- to
- the
- same
- physical
- structure
- view
- from
- different
- sequences
- in
- an
- alignment.
- A
- structureState
- element
- citing
- the
- same
- viewId
- will
- appear
- for
- each
- instance.
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="alignwithAlignPanel"
- type="xs:boolean" use="optional" default="true">
- <xs:annotation>
- <xs:documentation>
- Flag
- set
- if
- the
- alignment
- panel
- containing
- this
- JSeq
- should
- be
- included
- in
- those
- used
- to
- perform
- a
- structure
- superposition
- (since
- Jalview
- 2.7).
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="colourwithAlignPanel"
- type="xs:boolean" use="optional" default="false">
- <xs:annotation>
- <xs:documentation>
- Flag
- set
- if
- the
- alignment
- panel
- containing
- this
- JSeq
- should
- be
- included
- in
- those
- used
- to
- colour
- its
- associated
- sequences
- in
- this
- structureState(since
- Jalview
- 2.7).
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="colourByJmol" type="xs:boolean"
- use="optional" default="true">
- <xs:annotation>
- <xs:documentation>
- Flag
- set
- if
- the
- structure
- display
- is
- coloured
- by
- the
- Jmol
- state,
- rather
- than
- by
- one
- or
- more
- linked
- alignment
- views.
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="type" type="xs:string"
- use="optional">
- <xs:annotation>
- <xs:documentation>
- An
- identifier
- for
- the
- viewer
- type,
- currently
- either
- JMOL
- or
- CHIMERA
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:extension>
- </xs:complexContent>
- </xs:complexType>
- </xs:element>
- <xs:element name="hiddenSequences" type="xs:int"
- minOccurs="0" maxOccurs="unbounded" />
- <xs:element name="rnaViewer" minOccurs="0" maxOccurs="unbounded">
- <xs:annotation>
- <xs:documentation>Reference to a viewer showing RNA structure
- for this sequence. Schema supports one viewer showing multiple
- annotations for multiple sequences, though currently only one
- annotation for one sequence (gapped or trimmed) is used
- </xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="secondaryStructure" minOccurs="1"
- maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="title" type="xs:string" />
- <xs:attribute name="annotationId" type="xs:string"
- use="required">
- <xs:annotation>
- <xs:documentation>id attribute of Annotation in
- vamsasModel for
- the secondary structure annotation shown
- in the viewer
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="gapped" type="xs:boolean">
- <xs:annotation>
- <xs:documentation>if true the RNA structure is shown with gaps, if false without
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="viewerState" type="xs:string">
- <xs:annotation>
- <xs:documentation>name of the project jar entry that holds
- the VARNA viewer state for the structure
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attributeGroup ref="jv:swingwindow" />
- <xs:attribute name="title" type="xs:string" />
- <xs:attribute name="viewId" type="xs:string">
- <xs:annotation>
- <xs:documentation>An id unique to the RNA viewer panel
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="dividerLocation" type="xs:int">
- <xs:annotation>
- <xs:documentation>horizontal position of split pane divider
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="selectedRna" type="xs:int">
- <xs:annotation>
- <xs:documentation>Index of the selected structure in the
- viewer panel
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="colour" type="xs:int" use="optional" />
- <xs:attribute name="start" type="xs:int" use="required" />
- <xs:attribute name="end" type="xs:int" use="required" />
- <xs:attribute name="id" type="xs:string" use="required" />
- <xs:attribute name="hidden" type="xs:boolean" />
- <xs:attribute name="viewreference" type="xs:boolean" use="optional"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
- <xs:element name="annotationColours" type="jv:AnnotationColourScheme"
- minOccurs="0" maxOccurs="1" />
- </xs:sequence>
- <xs:attribute name="start" type="xs:int" />
- <xs:attribute name="end" type="xs:int" />
- <xs:attribute name="name" type="xs:string" />
- <xs:attribute name="colour" type="xs:string" />
- <xs:attribute name="consThreshold" type="xs:int" />
- <xs:attribute name="pidThreshold" type="xs:int" />
- <xs:attribute name="outlineColour" type="xs:int" />
- <xs:attribute name="displayBoxes" type="xs:boolean" />
- <xs:attribute name="displayText" type="xs:boolean" />
- <xs:attribute name="colourText" type="xs:boolean" />
- <xs:attribute name="textCol1" type="xs:int" />
- <xs:attribute name="textCol2" type="xs:int" />
- <xs:attribute name="textColThreshold" type="xs:int" />
- <xs:attribute name="showUnconserved" type="xs:boolean"
- use="optional" />
- <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
- use="optional" default="true" />
- <xs:attribute name="showConsensusHistogram" type="xs:boolean"
- use="optional" default="true" />
- <xs:attribute name="showSequenceLogo" type="xs:boolean"
- use="optional" default="false" />
- <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
- use="optional" default="false" />
- <xs:attribute name="id" type="xs:string" use="optional">
- <xs:annotation>
- <xs:documentation>
- Optional sequence group ID (only
- needs to be
- unique for this
- alignment)
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="Viewport" maxOccurs="unbounded"
- minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
- minOccurs="0" maxOccurs="1">
- </xs:element>
- <xs:element name="hiddenColumns" minOccurs="0"
- maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="start" type="xs:int" />
- <xs:attribute name="end" type="xs:int" />
- </xs:complexType>
- </xs:element>
- <xs:element name="calcIdParam" minOccurs="0"
- maxOccurs="unbounded">
- <xs:complexType>
- <xs:complexContent>
- <xs:extension base="jvws:WebServiceParameterSet">
- <xs:attribute name="calcId" type="xs:string"
- use="required">
- <xs:annotation>
- <xs:documentation>handle for the calculation which uses
- this parameter set
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="needsUpdate" type="xs:boolean"
- use="optional" default="false">
- <xs:annotation>
- <xs:documentation>should the calculation be performed
- immediately after loading in order to refresh results
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="autoUpdate" type="xs:boolean"
- use="required">
- <xs:annotation>
- <xs:documentation>should the calculation be automatically
- performed on edits
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:extension>
- </xs:complexContent>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attributeGroup ref="jv:swingwindow" />
- <xs:attribute name="conservationSelected" type="xs:boolean" />
- <xs:attribute name="pidSelected" type="xs:boolean" />
- <xs:attribute name="bgColour" type="xs:string" />
- <xs:attribute name="consThreshold" type="xs:int" />
- <xs:attribute name="pidThreshold" type="xs:int" />
- <xs:attribute name="title" type="xs:string" />
- <xs:attribute name="showFullId" type="xs:boolean" />
- <xs:attribute name="rightAlignIds" type="xs:boolean" />
- <xs:attribute name="showText" type="xs:boolean" />
- <xs:attribute name="showColourText" type="xs:boolean" />
- <xs:attribute name="showUnconserved" type="xs:boolean"
- use="optional" default="false" />
- <xs:attribute name="showBoxes" type="xs:boolean" />
- <xs:attribute name="wrapAlignment" type="xs:boolean" />
- <xs:attribute name="renderGaps" type="xs:boolean" />
- <xs:attribute name="showSequenceFeatures" type="xs:boolean" />
- <xs:attribute name="showNPfeatureTooltip" type="xs:boolean"
- use="optional" />
- <xs:attribute name="showDbRefTooltip" type="xs:boolean"
- use="optional" />
- <xs:attribute name="followHighlight" type="xs:boolean"
- use="optional" default="true" />
- <xs:attribute name="followSelection" type="xs:boolean"
- use="optional" default="true" />
- <xs:attribute name="showAnnotation" type="xs:boolean" />
- <xs:attribute name="centreColumnLabels" type="xs:boolean"
- use="optional" default="false" />
- <xs:attribute name="showGroupConservation" type="xs:boolean"
- use="optional" default="false" />
- <xs:attribute name="showGroupConsensus" type="xs:boolean"
- use="optional" default="false" />
- <xs:attribute name="showConsensusHistogram" type="xs:boolean"
- use="optional" default="true" />
- <xs:attribute name="showSequenceLogo" type="xs:boolean"
- use="optional" default="false" />
- <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
- use="optional" default="false" />
- <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
- use="optional" default="true" />
- <xs:attribute name="startRes" type="xs:int" />
- <xs:attribute name="startSeq" type="xs:int" />
- <xs:attribute name="fontName" type="xs:string" />
- <xs:attribute name="fontSize" type="xs:int" />
- <xs:attribute name="fontStyle" type="xs:int" />
- <xs:attribute name="scaleProteinAsCdna" type="xs:boolean" use="optional" default="true" />
- <xs:attribute name="viewName" type="xs:string" />
- <xs:attribute name="sequenceSetId" type="xs:string" />
- <xs:attribute name="gatheredViews" type="xs:boolean" />
- <xs:attribute name="textCol1" type="xs:int" />
- <xs:attribute name="textCol2" type="xs:int" />
- <xs:attribute name="textColThreshold" type="xs:int" />
- <xs:attribute name="id" type="xs:ID" use="optional">
- <xs:annotation>
- <xs:documentation>
- unique id used by jalview to
- synchronize
- between stored and
- instantiated views
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="complementId" type="xs:string"
- use="optional">
- <xs:annotation>
- <xs:documentation>
- The viewport id of this viewport's
- (cdna/protein) coding complement, if any
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="UserColourScheme" type="jalview:JalviewUserColours" />
- </xs:sequence>
- <xs:attribute name="id" type="xs:string" />
- </xs:complexType>
- </xs:element>
- <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence minOccurs="0">
- <xs:element name="title" type="xs:string" />
- <xs:element name="newick" type="xs:string" />
- </xs:sequence>
- <xs:attribute name="fontName" type="xs:string" />
- <xs:attribute name="fontSize" type="xs:int" />
- <xs:attribute name="fontStyle" type="xs:int" />
- <xs:attribute name="threshold" type="xs:float" />
- <xs:attribute name="showBootstrap" type="xs:boolean" />
- <xs:attribute name="showDistances" type="xs:boolean" />
- <xs:attribute name="markUnlinked" type="xs:boolean" />
- <xs:attribute name="fitToWindow" type="xs:boolean" />
- <xs:attribute name="currentTree" type="xs:boolean" />
- <xs:attribute name="id" type="xs:ID" use="optional">
- <xs:annotation>
- <xs:documentation>
- Tree ID added for binding tree
- visualization
- settings to vamsas
- document trees in jalview 2.4.1
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attributeGroup ref="jv:swingwindow" />
- <xs:attribute name="linkToAllViews" use="optional" default="false" type="xs:boolean" />
- </xs:complexType>
- </xs:element>
- <xs:element name="PcaViewer" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="sequencePoint" minOccurs="1" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="sequenceRef" type="xs:string" />
- <xs:attributeGroup ref="jv:position" />
- </xs:complexType>
- </xs:element>
- <xs:element name="axis" minOccurs="3" maxOccurs="3">
- <xs:annotation>
- <xs:documentation>
- endpoints of X, Y and Z axes in that order
- </xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:attributeGroup ref="jv:position" />
- </xs:complexType>
- </xs:element>
- <xs:element name="seqPointMin">
- <xs:complexType>
- <xs:attributeGroup ref="jv:position" />
- </xs:complexType>
- </xs:element>
- <xs:element name="seqPointMax">
- <xs:complexType>
- <xs:attributeGroup ref="jv:position" />
- </xs:complexType>
- </xs:element>
- <xs:element name="pcaData" type="jv:PcaDataType" />
- </xs:sequence>
- <xs:attribute name="title" type="xs:string" />
- <xs:attribute name="scoreModelName" type="xs:string" />
- <xs:attribute name="xDim" type="xs:int" />
- <xs:attribute name="yDim" type="xs:int" />
- <xs:attribute name="zDim" type="xs:int" />
- <xs:attribute name="bgColour" type="xs:int" />
- <xs:attribute name="scaleFactor" type="xs:float" />
- <xs:attribute name="showLabels" type="xs:boolean" />
- <xs:attribute name="linkToAllViews" type="xs:boolean" />
- <xs:attributeGroup ref="jv:SimilarityParams" />
- <xs:attributeGroup ref="jv:swingwindow" />
- </xs:complexType>
- </xs:element>
- <xs:element name="FeatureSettings" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
- <xs:annotation>
- <xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
- </xs:annotation>
- </xs:element>
- <xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
- <xs:annotation>
- <xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
- </xs:annotation>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="type" type="xs:string" use="required" />
- <xs:attribute name="colour" type="xs:int" use="required" />
- <xs:attribute name="display" type="xs:boolean"
- use="required" />
- <xs:attribute name="order" type="xs:float" use="optional" />
- <xs:attribute name="mincolour" type="xs:int" use="optional">
- <xs:annotation>
- <xs:documentation>
- Optional minimum colour
- for graduated
- feature
- colour
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
- <xs:attribute name="threshold" type="xs:float"
- use="optional">
- <xs:annotation>
- <xs:documentation>
- threshold value for
- graduated feature colour
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="threshstate" type="xs:int"
- use="optional">
- <xs:annotation>
- <xs:documentation>
- threshold type for
- graduated feature colour
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="max" type="xs:float" use="optional" />
- <xs:attribute name="min" type="xs:float" use="optional" />
- <xs:attribute name="colourByLabel" type="xs:boolean"
- use="optional" />
- <xs:attribute name="autoScale" type="xs:boolean"
- use="optional" />
- </xs:complexType>
- </xs:element>
- <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="name" type="xs:string" use="required" />
- <xs:attribute name="display" type="xs:boolean"
- use="required" />
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:sequence>
- </xs:complexType>
- <xs:complexType name="feature">
- <xs:sequence>
- <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="key" type="xs:string" use="required" />
- <xs:attribute name="key2" type="xs:string" use="optional">
- <xs:annotation>
- <xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="value" type="xs:string" use="required" />
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="begin" type="xs:int" use="required" />
- <xs:attribute name="end" type="xs:int" use="required" />
- <xs:attribute name="type" type="xs:string" use="required" />
- <xs:attribute name="description" type="xs:string" use="optional" />
- <xs:attribute name="status" type="xs:string" use="optional" />
- <xs:attribute name="featureGroup" type="xs:string" use="optional" />
- <xs:attribute name="score" type="xs:float" use="optional" />
- </xs:complexType>
- <xs:complexType name="pdbentry">
- <xs:sequence minOccurs="0" maxOccurs="unbounded">
- <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="name" type="xs:string" use="required" />
- <xs:attribute name="value" type="xs:string" use="required" />
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="id" type="xs:string" use="required" />
- <xs:attribute name="type" type="xs:string" use="optional" />
- <xs:attribute name="file" type="xs:string" />
- </xs:complexType>
- <!-- <xs:complexType name="reportWindow"> <xs:annotation> <xs:documentation>Generic
- type for windows containing mime-typed data associated with other jalview
- windows</xs:documentation> </xs:annotation> <xs:sequence> </xs:sequence>
- <xs:attribute name="id" type="xs:string" use="required"/> <xs:attribute name="type"
- type="xs:string" use="optional"/> <xs:attribute name="file" type="xs:string"
- use="optional"/> </xs:complexType> -->
- <xs:attributeGroup name="swingwindow">
- <xs:annotation>
- <xs:documentation>
- base attributes for windows displayed in Jalview
- desktop.
- </xs:documentation>
- </xs:annotation>
- <xs:attribute name="width" type="xs:int" />
- <xs:attribute name="height" type="xs:int" />
- <xs:attribute name="xpos" type="xs:int" />
- <xs:attribute name="ypos" type="xs:int" />
- </xs:attributeGroup>
- <xs:complexType name="AnnotationColourScheme">
- <xs:attribute name="aboveThreshold" type="xs:int" />
- <xs:attribute name="annotation" type="xs:string" />
- <xs:attribute name="minColour" type="xs:int" />
- <xs:attribute name="maxColour" type="xs:int" />
- <xs:attribute name="colourScheme" type="xs:string" />
- <xs:attribute name="threshold" type="xs:float" />
- <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
- <xs:attribute name="predefinedColours" type="xs:boolean"
- use="optional" />
- </xs:complexType>
- <xs:attributeGroup name="SimilarityParams">
- <xs:annotation>
- <xs:documentation>
- parameters that condition a similarity score calculation
- </xs:documentation>
- </xs:annotation>
- <xs:attribute name="includeGaps" type="xs:boolean" />
- <xs:attribute name="matchGaps" type="xs:boolean" />
- <xs:attribute name="includeGappedColumns" type="xs:boolean" />
- <xs:attribute name="denominateByShortestLength" type="xs:boolean" />
- </xs:attributeGroup>
- <xs:attributeGroup name="position">
- <xs:attribute name="xPos" type="xs:float" />
- <xs:attribute name="yPos" type="xs:float" />
- <xs:attribute name="zPos" type="xs:float" />
- </xs:attributeGroup>
- <xs:complexType name="PcaDataType">
- <xs:annotation>
- <xs:documentation>
- The results of a PCA calculation
- </xs:documentation>
- </xs:annotation>
- <xs:sequence>
- <xs:element name="pairwiseMatrix" type="jv:DoubleMatrix" />
- <xs:element name="tridiagonalMatrix" type="jv:DoubleMatrix" />
- <xs:element name="eigenMatrix" type="jv:DoubleMatrix" />
- </xs:sequence>
- </xs:complexType>
- <xs:complexType name="DoubleVector">
- <xs:sequence>
- <xs:element name="v" type="xs:double" minOccurs="0" maxOccurs="unbounded" />
- </xs:sequence>
- </xs:complexType>
- <xs:complexType name="DoubleMatrix">
- <xs:sequence>
- <xs:element name="row" type="jv:DoubleVector" minOccurs="0" maxOccurs="unbounded" />
- <xs:element name="D" minOccurs="0" type="jv:DoubleVector" />
- <xs:element name="E" minOccurs="0" type="jv:DoubleVector" />
- </xs:sequence>
- <xs:attribute name="rows" type="xs:int" />
- <xs:attribute name="columns" type="xs:int" />
- </xs:complexType>
-</xs:schema>
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