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:extension>
  30                                                                                                                 </xs:simpleContent>
  31                                                                                                         </xs:complexType>
  32                                                                                                 </xs:element>
  33                                                                                         </xs:sequence>
  34                                                                                 </xs:extension>
  35                                                                         </xs:complexContent>
  36                                                                 </xs:complexType>
  37                                                         </xs:element>
  38                                                         <xs:element name="hiddenSequences" type="xs:int" minOccurs="0" maxOccurs="unbounded"/>
  39                                                 </xs:sequence>
  40                                                 <xs:attribute name="colour" type="xs:int" use="optional"/>
  41                                                 <xs:attribute name="start" type="xs:int" use="required"/>
  42                                                 <xs:attribute name="end" type="xs:int" use="required"/>
  43                                                 <xs:attribute name="id" type="xs:int" use="required"/>
  44                                                 <xs:attribute name="hidden" type="xs:boolean"/>
  45                                         </xs:complexType>
  46                                 </xs:element>
  47                                 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
  48                                         <xs:complexType>
  49                                                 <xs:sequence>
  50                                                         <xs:element name="seq" type="xs:int" maxOccurs="unbounded"/>
  51                                                 </xs:sequence>
  52                                                 <xs:attribute name="start" type="xs:int"/>
  53                                                 <xs:attribute name="end" type="xs:int"/>
  54                                                 <xs:attribute name="name" type="xs:string"/>
  55                                                 <xs:attribute name="colour" type="xs:string"/>
  56                                                 <xs:attribute name="consThreshold" type="xs:int"/>
  57                                                 <xs:attribute name="pidThreshold" type="xs:int"/>
  58                                                 <xs:attribute name="outlineColour" type="xs:int"/>
  59                                                 <xs:attribute name="displayBoxes" type="xs:boolean"/>
  60                                                 <xs:attribute name="displayText" type="xs:boolean"/>
  61                                                 <xs:attribute name="colourText" type="xs:boolean"/>
  62                                                 <xs:attribute name="textCol1" type="xs:int"/>
  63                                                 <xs:attribute name="textCol2" type="xs:int"/>
  64                                                 <xs:attribute name="textColThreshold" type="xs:int"/>
  65                                         </xs:complexType>
  66                                 </xs:element>
  67                                 <xs:element name="Viewport" maxOccurs="unbounded">
  68                                         <xs:complexType>
  69                                                 <xs:sequence>
  70                                                         <xs:element name="AnnotationColours" minOccurs="0">
  71                                                                 <xs:complexType>
  72                                                                         <xs:attribute name="aboveThreshold" type="xs:int"/>
  73                                                                         <xs:attribute name="annotation" type="xs:string"/>
  74                                                                         <xs:attribute name="minColour" type="xs:int"/>
  75                                                                         <xs:attribute name="maxColour" type="xs:int"/>
  76                                                                         <xs:attribute name="colourScheme" type="xs:string"/>
  77                                                                         <xs:attribute name="threshold" type="xs:float"/>
  78                                                                 </xs:complexType>
  79                                                         </xs:element>
  80                                                         <xs:element name="hiddenColumns" minOccurs="0" maxOccurs="unbounded">
  81                                                                 <xs:complexType>
  82                                                                         <xs:attribute name="start" type="xs:int"/>
  83                                                                         <xs:attribute name="end" type="xs:int"/>
  84                                                                 </xs:complexType>
  85                                                         </xs:element>
  86                                                 </xs:sequence>
  87                                                 <xs:attribute name="conservationSelected" type="xs:boolean"/>
  88                                                 <xs:attribute name="pidSelected" type="xs:boolean"/>
  89                                                 <xs:attribute name="bgColour" type="xs:string"/>
  90                                                 <xs:attribute name="consThreshold" type="xs:int"/>
  91                                                 <xs:attribute name="pidThreshold" type="xs:int"/>
  92                                                 <xs:attribute name="title" type="xs:string"/>
  93                                                 <xs:attribute name="showFullId" type="xs:boolean"/>
  94                                                 <xs:attribute name="rightAlignIds" type="xs:boolean"/>
  95                                                 <xs:attribute name="showText" type="xs:boolean"/>
  96                                                 <xs:attribute name="showColourText" type="xs:boolean"/>
  97                                                 <xs:attribute name="showBoxes" type="xs:boolean"/>
  98                                                 <xs:attribute name="wrapAlignment" type="xs:boolean"/>
  99                                                 <xs:attribute name="renderGaps" type="xs:boolean"/>
 100                                                 <xs:attribute name="showSequenceFeatures" type="xs:boolean"/>
 101                                                 <xs:attribute name="showAnnotation" type="xs:boolean"/>
 102                                                 <xs:attribute name="xpos" type="xs:int"/>
 103                                                 <xs:attribute name="ypos" type="xs:int"/>
 104                                                 <xs:attribute name="width" type="xs:int"/>
 105                                                 <xs:attribute name="height" type="xs:int"/>
 106                                                 <xs:attribute name="startRes" type="xs:int"/>
 107                                                 <xs:attribute name="startSeq" type="xs:int"/>
 108                                                 <xs:attribute name="fontName" type="xs:string"/>
 109                                                 <xs:attribute name="fontSize" type="xs:int"/>
 110                                                 <xs:attribute name="fontStyle" type="xs:int"/>
 111                                                 <xs:attribute name="viewName" type="xs:string"/>
 112                                                 <xs:attribute name="sequenceSetId" type="xs:string"/>
 113                                                 <xs:attribute name="gatheredViews" type="xs:boolean"/>
 114                                                 <xs:attribute name="textCol1" type="xs:int"/>
 115                                                 <xs:attribute name="textCol2" type="xs:int"/>
 116                                                 <xs:attribute name="textColThreshold" type="xs:int"/>
 117                                         </xs:complexType>
 118                                 </xs:element>
 119                                 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
 120                                         <xs:complexType>
 121                                                 <xs:sequence>
 122                                                         <xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
 123                                                 </xs:sequence>
 124                                                 <xs:attribute name="id" type="xs:string"/>
 125                                         </xs:complexType>
 126                                 </xs:element>
 127                                 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
 128                                         <xs:complexType>
 129                                                 <xs:sequence minOccurs="0">
 130                                                         <xs:element name="title" type="xs:string"/>
 131                                                         <xs:element name="newick" type="xs:string"/>
 132                                                 </xs:sequence>
 133                                                 <xs:attribute name="width" type="xs:int"/>
 134                                                 <xs:attribute name="height" type="xs:int"/>
 135                                                 <xs:attribute name="xpos" type="xs:int"/>
 136                                                 <xs:attribute name="ypos" type="xs:int"/>
 137                                                 <xs:attribute name="fontName" type="xs:string"/>
 138                                                 <xs:attribute name="fontSize" type="xs:int"/>
 139                                                 <xs:attribute name="fontStyle" type="xs:int"/>
 140                                                 <xs:attribute name="threshold" type="xs:float"/>
 141                                                 <xs:attribute name="showBootstrap" type="xs:boolean"/>
 142                                                 <xs:attribute name="showDistances" type="xs:boolean"/>
 143                                                 <xs:attribute name="markUnlinked" type="xs:boolean"/>
 144                                                 <xs:attribute name="fitToWindow" type="xs:boolean"/>
 145                                                 <xs:attribute name="currentTree" type="xs:boolean"/>
 146                                         </xs:complexType>
 147                                 </xs:element>
 148                                 <xs:element name="FeatureSettings" minOccurs="0">
 149                                         <xs:complexType>
 150                                                 <xs:sequence>
 151                                                         <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
 152                                                                 <xs:complexType>
 153                                                                         <xs:attribute name="type" type="xs:string" use="required"/>
 154                                                                         <xs:attribute name="colour" type="xs:int" use="required"/>
 155                                                                         <xs:attribute name="display" type="xs:boolean" use="required"/>
 156                                                                         <xs:attribute name="order" type="xs:float" use="optional"/>
 157                                                                 </xs:complexType>
 158                                                         </xs:element>
 159                                                         <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
 160                                                                 <xs:complexType>
 161                                                                         <xs:attribute name="name" type="xs:string" use="required"/>
 162                                                                         <xs:attribute name="display" type="xs:boolean" use="required"/>
 163                                                                 </xs:complexType>
 164                                                         </xs:element>
 165                                                 </xs:sequence>
 166                                         </xs:complexType>
 167                                 </xs:element>
 168                         </xs:sequence>
 169                 </xs:sequence>
 170         </xs:complexType>
 171         <xs:complexType name="feature">
 172                 <xs:sequence>
 173                         <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 174                                 <xs:complexType>
 175                                         <xs:attribute name="key" type="xs:string" use="required"/>
 176                                         <xs:attribute name="value" type="xs:string" use="required"/>
 177                                 </xs:complexType>
 178                         </xs:element>
 179                 </xs:sequence>
 180                 <xs:attribute name="begin" type="xs:int" use="required"/>
 181                 <xs:attribute name="end" type="xs:int" use="required"/>
 182                 <xs:attribute name="type" type="xs:string" use="required"/>
 183                 <xs:attribute name="description" type="xs:string" use="optional"/>
 184                 <xs:attribute name="status" type="xs:string" use="optional"/>
 185                 <xs:attribute name="featureGroup" type="xs:string" use="optional"/>
 186                 <xs:attribute name="score" type="xs:float" use="optional"/>
 187         </xs:complexType>
 188         <xs:complexType name="pdbentry">
 189                 <xs:sequence minOccurs="0" maxOccurs="unbounded">
 190                         <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
 191                                 <xs:complexType>
 192                                         <xs:attribute name="name" type="xs:string" use="required"/>
 193                                         <xs:attribute name="value" type="xs:string" use="required"/>
 194                                 </xs:complexType>
 195                         </xs:element>
 196                 </xs:sequence>
 197                 <xs:attribute name="id" type="xs:string" use="required"/>
 198                 <xs:attribute name="type" type="xs:string" use="optional"/>
 199                 <xs:attribute name="file" type="xs:string"/>
 200         </xs:complexType>
 201 </xs:schema>