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="Version" type="xs:string"/>
   6                 <xs:annotation>
   7                         <xs:documentation>DESCRIPTION</xs:documentation>
   8         </xs:annotation>
   9
  10         <xs:complexType name="LockFile">
  11                 <xs:simpleContent>
  12                         <xs:extension base="xs:string"/>
  13                 </xs:simpleContent>
  14         </xs:complexType>
  15         <xs:element name="VAMSAS">
  16         <xs:complexType>
  17
  18                 <xs:sequence>
  19                         <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
  20                         <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
  21                 </xs:sequence>
  22                 <xs:attribute name="id" type="xs:ID"  use="optional"/>
  23                 </xs:complexType>
  24     </xs:element>
  25     <xs:element name="Tree">
  26                 <xs:complexType>
  27                 <xs:sequence>
  28                         <xs:element name="title" type="xs:string" minOccurs="0" maxOccurs="1"/>
  29                         <xs:element name="newick" minOccurs="1" maxOccurs="unbounded">
  30                           <xs:complexType>
  31                           <xs:simpleContent>
  32                           <xs:extension base="xs:string">
  33                           <xs:attribute name="title" type="xs:string"  use="optional"/>
  34                           <xs:attribute name="id" type="xs:ID"  use="optional"/>
  35                           </xs:extension>
  36                           </xs:simpleContent>
  37                           </xs:complexType>
  38                         </xs:element>
  39                         <xs:element ref="vamsas:Provenance" minOccurs="1" maxOccurs="1"/>
  40                     </xs:sequence>
  41                 <xs:attribute name="id" type="xs:ID"  use="optional"/>
  42         </xs:complexType>
  43         </xs:element>
  44         <xs:element name="Provenance">
  45                 <xs:complexType>
  46                         <xs:sequence>
  47                                 <xs:element name="entry" minOccurs="0" maxOccurs="unbounded">
  48                                         <xs:complexType>
  49                                                 <xs:sequence>
  50                                                         <xs:element name="User" type="xs:string"/>
  51                                                         <xs:element name="Action" type="xs:string"/>
  52                                                         <xs:element name="Date" type="xs:date"/>
  53                                                 </xs:sequence>
  54                                                 <xs:attribute name="id" type="xs:ID"  use="optional"/>
  55                                         </xs:complexType>
  56                                 </xs:element>
  57                         </xs:sequence>
  58                 </xs:complexType>
  59         </xs:element>
  60
  61         <xs:element name="SequenceSet">
  62                 <xs:complexType>
  63                         <xs:sequence>
  64                                 <xs:element name="Sequence" maxOccurs="unbounded">
  65                                         <xs:complexType>
  66                                                 <xs:complexContent>
  67                                                         <xs:extension base="vamsas:SequenceType">
  68                                                                 <xs:sequence>
  69                                                                     <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
  70                                                                         <xs:complexType>
  71                                                                                 <xs:attribute name="source"/>
  72                                                                                 <xs:attribute name="version"/>
  73                                                                                 <xs:attribute name="accessionId"/>
  74                                                                                 <xs:attribute name="id" type="xs:ID"  use="optional"/>
  75                                                                         </xs:complexType>
  76                                                                         </xs:element>
  77                                                                 </xs:sequence>
  78                                                                 <xs:attribute name="id" type="xs:ID"  use="required"/>
  79                                                                 <xs:attribute name="dictionary" type="xs:string"/>
  80                                                         </xs:extension>
  81                                                 </xs:complexContent>
  82                                         </xs:complexType>
  83                                 </xs:element>
  84                                 <xs:element name="SequenceSetAnnotations" minOccurs="0" maxOccurs="unbounded">
  85                                         <xs:complexType>
  86                                                 <xs:sequence>
  87                                                         <xs:element name="description" type="xs:string" minOccurs="0"/>
  88                                                         <xs:element name="status" type="xs:string" minOccurs="0"/>
  89                                                         <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
  90                                                         <xs:element ref="vamsas:Provenance" minOccurs="0" maxOccurs="unbounded"/>
  91                                                 </xs:sequence>
  92                                                 <xs:attribute name="type" type="xs:string" use="required"/>
  93                                                 <xs:attribute name="end" type="xs:string" use="required"/>
  94                                                 <xs:attribute name="begin" type="xs:string" use="required"/>
  95                                                 <xs:attribute name="seqRef" type="xs:IDREF" use="required"/>
  96                                                 <xs:attribute name="id" type="xs:ID"  use="optional"/>
  97                                         </xs:complexType>
  98                                 </xs:element>
  99                                 <xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
 100                                         <xs:complexType>
 101                                                 <xs:sequence>
 102                                                         <xs:element name="AlignmentAnnotations" minOccurs="0">
 103                                                                 <xs:complexType>
 104                                                                         <xs:sequence>
 105                                                                                 <xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/>
 106                                                                                 <xs:element name="label" type="xs:string"/>
 107                                                                                 <xs:element name="description" type="xs:string"/>
 108                                                                                 <xs:element ref="vamsas:Provenance"/>
 109                                                                         </xs:sequence>
 110                                                                         <xs:attribute name="graph" type="xs:boolean" use="required"/>
 111                                                                         <xs:attribute name="id" type="xs:ID"  use="optional"/>
 112                                                                 </xs:complexType>
 113                                                         </xs:element>
 114                                                         <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
 115                                                         <xs:element name="alignmentSequence" minOccurs="2" maxOccurs="unbounded">
 116                                                                 <xs:complexType>
 117                                                                         <xs:complexContent>
 118                                                                                 <xs:extension base="vamsas:SequenceType">
 119                                                                                         <xs:attribute name="id" type="xs:ID"  use="optional"/>
 120                                                                                         <xs:attribute name="refid" type="xs:IDREF" use="required"/>
 121                                                                                 </xs:extension>
 122                                                                         </xs:complexContent>
 123                                                                 </xs:complexType>
 124                                                         </xs:element>
 125                                                         <xs:element ref="vamsas:Provenance"/>
 126                                                 </xs:sequence>
 127                                                 <xs:attribute name="id" type="xs:ID"  use="optional"/>
 128                                         </xs:complexType>
 129                                 </xs:element>
 130                                 <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
 131                                 <xs:element ref="vamsas:Provenance"/>
 132                         </xs:sequence>
 133                         <xs:attribute name="gapChar" type="xs:string" use="required"/>
 134                         <xs:attribute name="aligned" type="xs:boolean" use="optional"/>
 135                         <xs:attribute name="id" type="xs:ID"   use="optional"/>
 136                 </xs:complexType>
 137         </xs:element>
 138         <xs:element name="annotationElement">
 139                 <xs:complexType>
 140                         <xs:sequence>
 141                                 <xs:element name="displayCharacter" type="xs:string"/>
 142                                 <xs:element name="description" type="xs:string"/>
 143                                 <xs:element name="secondaryStructure">
 144                                         <xs:simpleType>
 145                                                 <xs:restriction base="xs:string">
 146                                                         <xs:length value="1"/>
 147                                                 </xs:restriction>
 148                                         </xs:simpleType>
 149                                 </xs:element>
 150                                 <xs:element name="value" type="xs:float"/>
 151                         </xs:sequence>
 152                         <xs:attribute name="position" type="xs:int" use="required"/>
 153                         <xs:attribute name="id" type="xs:ID"   use="optional"/>
 154                 </xs:complexType>
 155         </xs:element>
 156     <xs:complexType name="SequenceType">
 157                 <xs:sequence>
 158                         <xs:element name="sequence" type="xs:string"/>
 159                         <xs:element name="name" type="xs:string"/>
 160                 </xs:sequence>
 161                 <xs:attribute name="start" type="xs:int" use="required"/>
 162                 <xs:attribute name="end" type="xs:int" use="required"/>
 163         </xs:complexType>
 164
 165     <xs:complexType name="ApplicationData">
 166                 <xs:sequence>
 167                         <xs:element name="Application">
 168                                 <xs:complexType>
 169                                         <xs:sequence>
 170                                           <xs:element name="User">
 171                                           <xs:complexType>
 172                                                 <xs:attribute name="fullname" type="xs:string"/>
 173                                                 <xs:attribute name="organization" type="xs:string"/>
 174                                                 <xs:attribute name="data" type="xs:string"/>
 175                                           </xs:complexType>
 176                                           </xs:element>
 177                                         </xs:sequence>
 178                                         <xs:attribute name="version" type="xs:string"/>
 179                                         <xs:attribute name="name" type="xs:string"/>
 180                                         <xs:attribute name="urn" type="xs:string"/>
 181                                         <xs:attribute name="data" type="xs:string"/>
 182                                 </xs:complexType>
 183                         </xs:element>
 184                 </xs:sequence>
 185         </xs:complexType>
 186 </xs:schema>