schemas/jalview.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <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" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
   3                 <xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
   4         <xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
   5         <xs:complexType name="JalviewModel">
   6                 <xs:sequence>
   7                         <xs:element name="creationDate" type="xs:dateTime"/>
   8                         <xs:element name="version" type="xs:string"/>
   9                         <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>
  10                         <xs:sequence>
  11                                 <xs:element name="JSeq" maxOccurs="unbounded">
  12                                         <xs:complexType>
  13                                                 <xs:sequence>
  14                                                         <xs:element name="features" type="jv:feature" minOccurs="0" maxOccurs="unbounded"/>
  15                                                         <xs:element name="pdbids" minOccurs="0" maxOccurs="unbounded">
  16                                                                 <xs:complexType>
  17                                                                         <xs:complexContent>
  18                                                                                 <xs:extension base="jv:pdbentry">
  19                                                                                         <xs:sequence>
  20                                                                                                 <xs:element name="structureState" minOccurs="0" maxOccurs="unbounded">
  21                                                                                                         <xs:complexType>
  22                                                                                                                 <xs:simpleContent>
  23                                                                                                                         <xs:extension base="xs:string">
  24                                                                                                                                 <xs:attribute name="visible" type="xs:boolean"/>
  25                                                                                                                                 <xs:attribute name="xpos" type="xs:int"/>
  26                                                                                                                                 <xs:attribute name="ypos" type="xs:int"/>
  27                                                                                                                                 <xs:attribute name="width" type="xs:int"/>
  28                                                                                                                                 <xs:attribute name="height" type="xs:int"/>
  29                                                                                                                                 <xs:attribute name="viewId" type="xs:ID" use="optional"/>
  30
  31
  32                                                                                                                         </xs:extension>
  33                                                                                                                 </xs:simpleContent>
  34                                                                                                         </xs:complexType>
  35                                                                                                 </xs:element>
  36                                                                                         </xs:sequence>
  37                                                                                 </xs:extension>
  38                                                                         </xs:complexContent>
  39                                                                 </xs:complexType>
  40                                                         </xs:element>
  41                                                         <xs:element name="hiddenSequences" type="xs:int" minOccurs="0" maxOccurs="unbounded"/>
  42                                                 </xs:sequence>
  43                                                 <xs:attribute name="colour" type="xs:int" use="optional"/>
  44                                                 <xs:attribute name="start" type="xs:int" use="required"/>
  45                                                 <xs:attribute name="end" type="xs:int" use="required"/>
  46                                                 <xs:attribute name="id" type="xs:string" use="required"/>
  47                                                 <xs:attribute name="hidden" type="xs:boolean"/>
  48                                         </xs:complexType>
  49                                 </xs:element>
  50                                 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
  51                                         <xs:complexType>
  52                                                 <xs:sequence>
  53                                                         <xs:element name="seq" type="xs:string" maxOccurs="unbounded"/>
  54                                                 </xs:sequence>
  55                                                 <xs:attribute name="start" type="xs:int"/>
  56                                                 <xs:attribute name="end" type="xs:int"/>
  57                                                 <xs:attribute name="name" type="xs:string"/>
  58                                                 <xs:attribute name="colour" type="xs:string"/>
  59                                                 <xs:attribute name="consThreshold" type="xs:int"/>
  60                                                 <xs:attribute name="pidThreshold" type="xs:int"/>
  61                                                 <xs:attribute name="outlineColour" type="xs:int"/>
  62                                                 <xs:attribute name="displayBoxes" type="xs:boolean"/>
  63                                                 <xs:attribute name="displayText" type="xs:boolean"/>
  64                                                 <xs:attribute name="colourText" type="xs:boolean"/>
  65                                                 <xs:attribute name="textCol1" type="xs:int"/>
  66                                                 <xs:attribute name="textCol2" type="xs:int"/>
  67                                                 <xs:attribute name="textColThreshold" type="xs:int"/>
  68                                         </xs:complexType>
  69                                 </xs:element>
  70                                 <xs:element name="Viewport" maxOccurs="unbounded">
  71                                         <xs:complexType>
  72                                                 <xs:sequence>
  73                                                         <xs:element name="AnnotationColours" minOccurs="0">
  74                                                                 <xs:complexType>
  75                                                                         <xs:attribute name="aboveThreshold" type="xs:int"/>
  76                                                                         <xs:attribute name="annotation" type="xs:string"/>
  77                                                                         <xs:attribute name="minColour" type="xs:int"/>
  78                                                                         <xs:attribute name="maxColour" type="xs:int"/>
  79                                                                         <xs:attribute name="colourScheme" type="xs:string"/>
  80                                                                         <xs:attribute name="threshold" type="xs:float"/>
  81                                                                 </xs:complexType>
  82                                                         </xs:element>
  83                                                         <xs:element name="hiddenColumns" minOccurs="0" maxOccurs="unbounded">
  84                                                                 <xs:complexType>
  85                                                                         <xs:attribute name="start" type="xs:int"/>
  86                                                                         <xs:attribute name="end" type="xs:int"/>
  87                                                                 </xs:complexType>
  88                                                         </xs:element>
  89                                                 </xs:sequence>
  90                                                 <xs:attribute name="conservationSelected" type="xs:boolean"/>
  91                                                 <xs:attribute name="pidSelected" type="xs:boolean"/>
  92                                                 <xs:attribute name="bgColour" type="xs:string"/>
  93                                                 <xs:attribute name="consThreshold" type="xs:int"/>
  94                                                 <xs:attribute name="pidThreshold" type="xs:int"/>
  95                                                 <xs:attribute name="title" type="xs:string"/>
  96                                                 <xs:attribute name="showFullId" type="xs:boolean"/>
  97                                                 <xs:attribute name="rightAlignIds" type="xs:boolean"/>
  98                                                 <xs:attribute name="showText" type="xs:boolean"/>
  99                                                 <xs:attribute name="showColourText" type="xs:boolean"/>
 100                                                 <xs:attribute name="showBoxes" type="xs:boolean"/>
 101                                                 <xs:attribute name="wrapAlignment" type="xs:boolean"/>
 102                                                 <xs:attribute name="renderGaps" type="xs:boolean"/>
 103                                                 <xs:attribute name="showSequenceFeatures" type="xs:boolean"/>
 104                                                 <xs:attribute name="showAnnotation" type="xs:boolean"/>
 105                                                 <xs:attribute name="xpos" type="xs:int"/>
 106                                                 <xs:attribute name="ypos" type="xs:int"/>
 107                                                 <xs:attribute name="width" type="xs:int"/>
 108                                                 <xs:attribute name="height" type="xs:int"/>
 109                                                 <xs:attribute name="startRes" type="xs:int"/>
 110                                                 <xs:attribute name="startSeq" type="xs:int"/>
 111                                                 <xs:attribute name="fontName" type="xs:string"/>
 112                                                 <xs:attribute name="fontSize" type="xs:int"/>
 113                                                 <xs:attribute name="fontStyle" type="xs:int"/>
 114                                                 <xs:attribute name="viewName" type="xs:string"/>
 115                                                 <xs:attribute name="sequenceSetId" type="xs:string"/>
 116                                                 <xs:attribute name="gatheredViews" type="xs:boolean"/>
 117                                                 <xs:attribute name="textCol1" type="xs:int"/>
 118                                                 <xs:attribute name="textCol2" type="xs:int"/>
 119                                                 <xs:attribute name="textColThreshold" type="xs:int"/>
 120                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 121                                                         <xs:annotation>
 122                                                                 <xs:documentation>
 123                                                                         unique id used by jalview to synchronize between stored and instantiated views
 124                                                                 </xs:documentation>
 125                                                         </xs:annotation>
 126                                                 </xs:attribute>
 127                                         </xs:complexType>
 128                                 </xs:element>
 129                                 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
 130                                         <xs:complexType>
 131                                                 <xs:sequence>
 132                                                         <xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
 133                                                 </xs:sequence>
 134                                                 <xs:attribute name="id" type="xs:string"/>
 135                                         </xs:complexType>
 136                                 </xs:element>
 137                                 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
 138                                         <xs:complexType>
 139                                                 <xs:sequence minOccurs="0">
 140                                                         <xs:element name="title" type="xs:string"/>
 141                                                         <xs:element name="newick" type="xs:string"/>
 142                                                 </xs:sequence>
 143                                                 <xs:attribute name="width" type="xs:int"/>
 144                                                 <xs:attribute name="height" type="xs:int"/>
 145                                                 <xs:attribute name="xpos" type="xs:int"/>
 146                                                 <xs:attribute name="ypos" type="xs:int"/>
 147                                                 <xs:attribute name="fontName" type="xs:string"/>
 148                                                 <xs:attribute name="fontSize" type="xs:int"/>
 149                                                 <xs:attribute name="fontStyle" type="xs:int"/>
 150                                                 <xs:attribute name="threshold" type="xs:float"/>
 151                                                 <xs:attribute name="showBootstrap" type="xs:boolean"/>
 152                                                 <xs:attribute name="showDistances" type="xs:boolean"/>
 153                                                 <xs:attribute name="markUnlinked" type="xs:boolean"/>
 154                                                 <xs:attribute name="fitToWindow" type="xs:boolean"/>
 155                                                 <xs:attribute name="currentTree" type="xs:boolean"/>
 156                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 157                                                         <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>
 158                                                 </xs:attribute>
 159                                         </xs:complexType>
 160                                 </xs:element>
 161                                 <xs:element name="FeatureSettings" minOccurs="0">
 162                                         <xs:complexType>
 163                                                 <xs:sequence>
 164                                                         <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
 165                                                                 <xs:complexType>
 166                                                                         <xs:attribute name="type" type="xs:string" use="required"/>
 167                                                                         <xs:attribute name="colour" type="xs:int" use="required"/>
 168                                                                         <xs:attribute name="display" type="xs:boolean" use="required"/>
 169                                                                         <xs:attribute name="order" type="xs:float" use="optional"/>
 170                                                                 </xs:complexType>
 171                                                         </xs:element>
 172                                                         <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
 173                                                                 <xs:complexType>
 174                                                                         <xs:attribute name="name" type="xs:string" use="required"/>
 175                                                                         <xs:attribute name="display" type="xs:boolean" use="required"/>
 176                                                                 </xs:complexType>
 177                                                         </xs:element>
 178                                                 </xs:sequence>
 179                                         </xs:complexType>
 180                                 </xs:element>
 181                         </xs:sequence>
 182                 </xs:sequence>
 183         </xs:complexType>
 184         <xs:complexType name="feature">
 185                 <xs:sequence>
 186                         <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 187                                 <xs:complexType>
 188                                         <xs:attribute name="key" type="xs:string" use="required"/>
 189                                         <xs:attribute name="value" type="xs:string" use="required"/>
 190                                 </xs:complexType>
 191                         </xs:element>
 192                 </xs:sequence>
 193                 <xs:attribute name="begin" type="xs:int" use="required"/>
 194                 <xs:attribute name="end" type="xs:int" use="required"/>
 195                 <xs:attribute name="type" type="xs:string" use="required"/>
 196                 <xs:attribute name="description" type="xs:string" use="optional"/>
 197                 <xs:attribute name="status" type="xs:string" use="optional"/>
 198                 <xs:attribute name="featureGroup" type="xs:string" use="optional"/>
 199                 <xs:attribute name="score" type="xs:float" use="optional"/>
 200         </xs:complexType>
 201         <xs:complexType name="pdbentry">
 202                 <xs:sequence minOccurs="0" maxOccurs="unbounded">
 203                         <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
 204                                 <xs:complexType>
 205                                         <xs:attribute name="name" type="xs:string" use="required"/>
 206                                         <xs:attribute name="value" type="xs:string" use="required"/>
 207                                 </xs:complexType>
 208                         </xs:element>
 209                 </xs:sequence>
 210                 <xs:attribute name="id" type="xs:string" use="required"/>
 211                 <xs:attribute name="type" type="xs:string" use="optional"/>
 212                 <xs:attribute name="file" type="xs:string"/>
 213         </xs:complexType>
 214 </xs:schema>