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