schemas/jalview.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>\r
   2 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"\r
   3                                  xmlns:vamsas="www.vamsas.org"\r
   4                                  xmlns:jalview="www.jalview.org/colours"\r
   5                                  xmlns:jv="www.jalview.org" \r
   6                                  targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">\r
   7                                  \r
   8         <xs:import schemaLocation="vamsas.xsd" namespace="www.vamsas.org"/>\r
   9         <xs:import schemaLocation="jalviewUserColours.xsd" namespace="www.jalview.org/colours"/>\r
  10         <xs:complexType name="JalviewModel">\r
  11                 <xs:sequence>\r
  12                         <xs:element name="creationDate" type="xs:dateTime"/>\r
  13                         <xs:element name="version" type="xs:string"/>\r
  14                         <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>\r
  15                         <xs:sequence>\r
  16                                 <xs:element name="JSeq" maxOccurs="unbounded">\r
  17                                         <xs:complexType>\r
  18                                                 <xs:sequence>\r
  19                                                          <xs:element name="features" type="jv:feature" minOccurs="0" maxOccurs="unbounded"/>\r
  20                                                          <xs:element name="pdbids" type="jv:pdbentry" minOccurs="0" maxOccurs="unbounded"/>\r
  21                                               </xs:sequence>\r
  22                                               \r
  23                                                     <xs:attribute name="colour" type="xs:int" use="optional"/>\r
  24                                                         <xs:attribute name="start" type="xs:int" use="required"/>\r
  25                                                         <xs:attribute name="end" type="xs:int" use="required"/>\r
  26                                                         <xs:attribute name="id" type="xs:int" use="required"/>\r
  27                                                 </xs:complexType>\r
  28                                 </xs:element>\r
  29                                 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">\r
  30                                         <xs:complexType>\r
  31                                                 <xs:sequence minOccurs="1">\r
  32                                                         <xs:element name="seq" maxOccurs="unbounded" type="xs:int"/>\r
  33                                                 </xs:sequence>\r
  34                                                 <xs:attribute name="start" type="xs:int"/>\r
  35                                                 <xs:attribute name="end" type="xs:int"/>\r
  36                                                 <xs:attribute name="name" type="xs:string"/>\r
  37                                                 <xs:attribute name="colour" type="xs:string"/>\r
  38                                                 <xs:attribute name="consThreshold" type="xs:int"/>\r
  39                                                 <xs:attribute name="pidThreshold" type="xs:int"/>\r
  40                                                 <xs:attribute name="outlineColour" type="xs:int"/>\r
  41                                                 <xs:attribute name="displayBoxes" type="xs:boolean"/>\r
  42                                                 <xs:attribute name="displayText" type="xs:boolean"/>\r
  43                                                 <xs:attribute name="colourText" type="xs:boolean"/>\r
  44                                         </xs:complexType>\r
  45                                 </xs:element>\r
  46                                 <xs:element name="Viewport" maxOccurs="unbounded">\r
  47                                         <xs:complexType>\r
  48                                                 <xs:attribute name="conservationSelected" type="xs:boolean"/>\r
  49                                                 <xs:attribute name="pidSelected" type="xs:boolean"/>\r
  50                                                 <xs:attribute name="bgColour" type="xs:string"/>\r
  51                                                 <xs:attribute name="consThreshold" type="xs:int"/>\r
  52                                                 <xs:attribute name="pidThreshold" type="xs:int"/>\r
  53                                                 <xs:attribute name="title" type="xs:string"/>\r
  54                                                 <xs:attribute name="showFullId" type="xs:boolean"/>\r
  55                                                 <xs:attribute name="showText" type="xs:boolean"/>\r
  56                                                 <xs:attribute name="showColourText" type="xs:boolean"/>\r
  57                                                 <xs:attribute name="showBoxes" type="xs:boolean"/>\r
  58                                                 <xs:attribute name="wrapAlignment" type="xs:boolean"/>\r
  59                                                 <xs:attribute name="renderGaps" type="xs:boolean"/>\r
  60                                                 <xs:attribute name="showSequenceFeatures" type="xs:boolean"/>\r
  61                                                 <xs:attribute name="showAnnotation" type="xs:boolean"/>\r
  62                                                 <xs:attribute name="showConservation" type="xs:boolean"/>\r
  63                                                 <xs:attribute name="showQuality" type="xs:boolean"/>\r
  64                                                 <xs:attribute name="showIdentity" type="xs:boolean"/>\r
  65                                                 <xs:attribute name="xpos" type="xs:int"/>\r
  66                                                 <xs:attribute name="ypos" type="xs:int"/>\r
  67                                                 <xs:attribute name="width" type="xs:int"/>\r
  68                                                 <xs:attribute name="height" type="xs:int"/>\r
  69                                                 <xs:attribute name="startRes" type="xs:int"/>\r
  70                                                 <xs:attribute name="startSeq" type="xs:int"/>\r
  71                                                 <xs:attribute name="fontName" type="xs:string"/>\r
  72                                                 <xs:attribute name="fontSize" type="xs:int"/>\r
  73                                                 <xs:attribute name="fontStyle" type="xs:int"/>\r
  74                                         </xs:complexType>\r
  75                                 </xs:element>\r
  76                                 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">\r
  77                                         <xs:complexType>\r
  78                                                 <xs:sequence minOccurs="1">\r
  79                                                         <xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>\r
  80                                                 </xs:sequence>\r
  81                                                 <xs:attribute name="id" type="xs:string"/>\r
  82                                         </xs:complexType>\r
  83                                 </xs:element>\r
  84                                 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">\r
  85                                         <xs:complexType>\r
  86                                                 <xs:sequence minOccurs="0" maxOccurs="1">\r
  87                                                         <xs:element name="title" type="xs:string"/>\r
  88                                                         <xs:element name="newick" type="xs:string"/>\r
  89                                                 </xs:sequence>\r
  90                                                 <xs:attribute name="width" type="xs:int"/>\r
  91                                                 <xs:attribute name="height" type="xs:int"/>\r
  92                                                 <xs:attribute name="xpos" type="xs:int"/>\r
  93                                                 <xs:attribute name="ypos" type="xs:int"/>\r
  94                                                 <xs:attribute name="fontName" type="xs:string"/>\r
  95                                                 <xs:attribute name="fontSize" type="xs:int"/>\r
  96                                                 <xs:attribute name="fontStyle" type="xs:int"/>\r
  97                                                 <xs:attribute name="threshold" type="xs:float"/>\r
  98                                                 <xs:attribute name="showBootstrap" type="xs:boolean"/>\r
  99                                                 <xs:attribute name="showDistances" type="xs:boolean"/>\r
 100                                                 <xs:attribute name="markUnlinked" type="xs:boolean"/>\r
 101                                                 <xs:attribute name="fitToWindow" type="xs:boolean"/>\r
 102                                                 <xs:attribute name="currentTree" type="xs:boolean"/>\r
 103                                         </xs:complexType>\r
 104                                 </xs:element>\r
 105                                 \r
 106                                 <xs:element name="FeatureSettings" minOccurs="0" maxOccurs="1">\r
 107                                                 <xs:complexType>\r
 108                                 <xs:sequence>\r
 109                                         <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">\r
 110                                                 <xs:complexType>\r
 111                                                         <xs:attribute name="type" type="xs:string" use="required"/>\r
 112                                                         <xs:attribute name="colour" type="xs:int" use="required"/>\r
 113                                                         <xs:attribute name="display" type="xs:boolean" use="required"/>\r
 114                                                 </xs:complexType>\r
 115                                         </xs:element>\r
 116                                 </xs:sequence>\r
 117                                 </xs:complexType>\r
 118                                 </xs:element>\r
 119                                 \r
 120                         </xs:sequence>\r
 121                 </xs:sequence>\r
 122         </xs:complexType>\r
 123         \r
 124         <xs:complexType name="feature">\r
 125                 <xs:attribute name="begin" type="xs:int" use="required"/>\r
 126                 <xs:attribute name="end" type="xs:int" use="required"/>\r
 127                 <xs:attribute name="type" type="xs:string" use="required"/>\r
 128                 <xs:attribute name="description" type="xs:string" use="optional"/>\r
 129                 <xs:attribute name="status" type="xs:string" use="optional"/>\r
 130         </xs:complexType>\r
 131                 \r
 132         <xs:complexType name="pdbentry">\r
 133                 <xs:sequence minOccurs="0" maxOccurs="unbounded">\r
 134                         <xs:element name="property" minOccurs="0" maxOccurs="unbounded">\r
 135                                 <xs:complexType>\r
 136                                         <xs:attribute name="name" type="xs:string" use="required"/>\r
 137                                         <xs:attribute name="value" type="xs:string" use="required"/>\r
 138                                 </xs:complexType>\r
 139                         </xs:element>\r
 140                 </xs:sequence>\r
 141                 <xs:attribute name="id" type="xs:string" use="required"/>\r
 142                 <xs:attribute name="type" type="xs:string" use="optional"/>\r
 143         </xs:complexType>\r
 144         \r
 145 </xs:schema>\r