schemas/vamsas.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!-- edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by MSD (EMBL OUTSTATION THE EBI WELLCOME TRUST GENOME CAMPUS) -->
   3 <!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by lj (jl) -->
   4 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="http://www.vamsas.org" targetNamespace="http://www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
   5         <xs:element name="VAMSAS">
   6                 <xs:complexType>
   7                         <xs:sequence>
   8                                 <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
   9                                 <xs:element ref="vamsas:DataSet" minOccurs="0" maxOccurs="unbounded"/>
  10                         </xs:sequence>
  11                         <xs:attribute name="id" type="xs:ID" use="optional"/>
  12                 </xs:complexType>
  13         </xs:element>
  14         <xs:element name="Tree">
  15                 <xs:complexType>
  16                         <xs:sequence>
  17                                 <xs:element name="title" type="xs:string" minOccurs="0"/>
  18                                 <xs:element name="newick" maxOccurs="unbounded">
  19                                         <xs:complexType>
  20                                                 <xs:simpleContent>
  21                                                         <xs:extension base="xs:string">
  22                                                                 <xs:attribute name="title" type="xs:string" use="optional"/>
  23                                                                 <xs:attribute name="id" type="xs:ID" use="optional"/>
  24                                                         </xs:extension>
  25                                                 </xs:simpleContent>
  26                                         </xs:complexType>
  27                                 </xs:element>
  28                                 <xs:element ref="vamsas:Provenance"/>
  29                         </xs:sequence>
  30                         <xs:attribute name="id" type="xs:ID" use="optional"/>
  31                 </xs:complexType>
  32         </xs:element>
  33         <xs:element name="Provenance">
  34                 <xs:complexType>
  35                         <xs:sequence>
  36                                 <xs:element name="entry" maxOccurs="unbounded">
  37                                         <xs:complexType>
  38                                                 <xs:sequence>
  39                                                         <xs:element name="User" type="xs:string"/>
  40                                                         <xs:element name="Action" type="xs:string"/>
  41                                                         <xs:element name="Date" type="xs:date"/>
  42                                                 </xs:sequence>
  43                                                 <xs:attribute name="id" type="xs:ID" use="optional"/>
  44                                         </xs:complexType>
  45                                 </xs:element>
  46                         </xs:sequence>
  47                 </xs:complexType>
  48         </xs:element>
  49         <xs:element name="DataSet">
  50                 <xs:complexType>
  51                         <xs:sequence>
  52                                 <xs:element name="Sequence" maxOccurs="unbounded">
  53                                         <xs:complexType>
  54                                                 <xs:complexContent>
  55                                                         <xs:extension base="vamsas:SequenceType">
  56                                                                 <xs:sequence>
  57                                                                         <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
  58                                                                                 <xs:complexType>
  59                                                                                         <xs:attribute name="source" type="xs:string"/>
  60                                                                                         <xs:attribute name="version" type="xs:string"/>
  61                                                                                         <xs:attribute name="accessionId" type="xs:string"/>
  62                                                                                         <xs:attribute name="id" type="xs:ID" use="optional"/>
  63                                                                                 </xs:complexType>
  64                                                                         </xs:element>
  65                                                                 </xs:sequence>
  66                                                                 <xs:attribute name="id" type="xs:ID" use="required"/>
  67                                                                 <xs:attribute name="dictionary" type="xs:string"/>
  68                                                         </xs:extension>
  69                                                 </xs:complexContent>
  70                                         </xs:complexType>
  71                                 </xs:element>
  72                                 <xs:element name="DataSetAnnotations" minOccurs="0" maxOccurs="unbounded">
  73                                         <xs:complexType>
  74                                                 <xs:sequence>
  75                                                         <xs:element name="description" type="xs:string" minOccurs="0"/>
  76                                                         <xs:element name="status" type="xs:string" minOccurs="0"/>
  77                                                         <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
  78                                                         <xs:element ref="vamsas:Provenance" maxOccurs="unbounded"/>
  79                                                 </xs:sequence>
  80                                                 <xs:attribute name="type" type="xs:string" use="required"/>
  81                                                 <xs:attribute name="end" type="xs:integer" use="required"/>
  82                                                 <xs:attribute name="begin" type="xs:integer" use="required"/>
  83                                                 <xs:attribute name="seqRef" type="xs:IDREF" use="required"/>
  84                                                 <xs:attribute name="id" type="xs:ID" use="optional"/>
  85                                         </xs:complexType>
  86                                 </xs:element>
  87                                 <xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
  88                                         <xs:complexType>
  89                                                 <xs:sequence>
  90                                                         <xs:element name="AlignmentAnnotations" minOccurs="0" maxOccurs="unbounded">
  91                                                                 <xs:complexType>
  92                                                                         <xs:sequence>
  93                                                                                 <xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/>
  94                                                                                 <xs:element name="label" type="xs:string"/>
  95                                                                                 <xs:element name="description" type="xs:string"/>
  96                                                                                 <xs:element ref="vamsas:Provenance"/>
  97                                                                         </xs:sequence>
  98                                                                         <xs:attribute name="graph" type="xs:boolean" use="required"/>
  99                                                                         <xs:attribute name="id" type="xs:ID" use="optional"/>
 100                                                                 </xs:complexType>
 101                                                         </xs:element>
 102                                                         <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
 103                                                         <xs:element name="alignmentSequence" maxOccurs="unbounded">
 104                                                                 <xs:complexType>
 105                                                                         <xs:complexContent>
 106                                                                                 <xs:extension base="vamsas:SequenceType">
 107                                                                                         <xs:attribute name="id" type="xs:ID" use="optional"/>
 108                                                                                         <xs:attribute name="refid" type="xs:IDREF" use="required"/>
 109                                                                                 </xs:extension>
 110                                                                         </xs:complexContent>
 111                                                                 </xs:complexType>
 112                                                         </xs:element>
 113                                                         <xs:element ref="vamsas:Provenance"/>
 114                                                 </xs:sequence>
 115                                                 <xs:attribute name="gapChar" type="xs:string" use="required"/>
 116                                                 <xs:attribute name="aligned" type="xs:boolean" use="optional"/>
 117                                                 <xs:attribute name="id" type="xs:ID" use="optional"/>
 118                                         </xs:complexType>
 119                                 </xs:element>
 120                                 <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
 121                                 <xs:element ref="vamsas:Provenance"/>
 122                         </xs:sequence>
 123                         <xs:attribute name="id" type="xs:ID" use="optional"/>
 124                 </xs:complexType>
 125         </xs:element>
 126         <xs:element name="annotationElement">
 127                 <xs:complexType>
 128                         <xs:sequence>
 129                                 <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
 130                                 <xs:element name="description" type="xs:string" minOccurs="0"/>
 131                                 <xs:element name="secondaryStructure" minOccurs="0">
 132                                         <xs:simpleType>
 133                                                 <xs:restriction base="xs:string">
 134                                                         <xs:length value="1"/>
 135                                                 </xs:restriction>
 136                                         </xs:simpleType>
 137                                 </xs:element>
 138                                 <xs:element name="value" type="xs:float" minOccurs="0"/>
 139                         </xs:sequence>
 140                         <xs:attribute name="position" type="xs:integer" use="required"/>
 141                         <xs:attribute name="id" type="xs:ID" use="optional"/>
 142                 </xs:complexType>
 143         </xs:element>
 144         <xs:complexType name="SequenceType">
 145                 <xs:sequence>
 146                         <xs:element name="sequence" type="xs:string"/>
 147                         <xs:element name="name" type="xs:string"/>
 148                 </xs:sequence>
 149                 <xs:attribute name="start" type="xs:integer" use="required"/>
 150                 <xs:attribute name="end" type="xs:integer" use="required"/>
 151         </xs:complexType>
 152         <xs:element name="ApplicationData">
 153                 <xs:complexType>
 154                         <xs:complexContent>
 155                                 <xs:extension base="vamsas:appData">
 156                                         <xs:sequence>
 157                                                 <xs:element name="User" maxOccurs="unbounded" minOccurs="0">
 158                                                         <xs:complexType>
 159                                                                 <xs:complexContent>
 160                                                                         <xs:extension base="vamsas:appData">
 161                                                                                 <xs:attribute name="fullname" type="xs:string" use="required"/>
 162                                                                                 <xs:attribute name="organization" type="xs:string" use="required"/>
 163                                                                         </xs:extension>
 164                                                                 </xs:complexContent>
 165                                                         </xs:complexType>
 166                                                 </xs:element>
 167                                         </xs:sequence>
 168                                         <xs:attribute name="version" type="xs:string" use="required"/>
 169                                         <xs:attribute name="name" type="xs:string" use="required"/>
 170                                         <xs:attribute name="urn" type="xs:string" use="required"/>
 171                                 </xs:extension>
 172                         </xs:complexContent>
 173                 </xs:complexType>
 174         </xs:element>
 175         <xs:complexType name="appData">
 176                 <xs:choice>
 177                         <xs:element name="data" type="xs:base64Binary"/>
 178                         <xs:element name="dataReference" type="xs:string"/>
 179                 </xs:choice>
 180         </xs:complexType>
 181 </xs:schema>