schemas/jalview.xsd

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