schemas/vamsas15_9.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 name="Dendro" type="vamsas:TreeType" minOccurs="0" maxOccurs="unbounded"/>
  14                         <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
  15                 </xs:sequence>
  16
  17         <xs:attribute name="id" type="xs:ID"/>
  18     </xs:complexType>
  19         <xs:element name="Provenance">
  20                 <xs:complexType>
  21                         <xs:sequence maxOccurs="unbounded">
  22                                 <xs:element name="entry">
  23                                         <xs:complexType>
  24                                                 <xs:sequence>
  25                                                         <xs:element name="User" type="xs:string"/>
  26                                                         <xs:element name="Action" type="xs:string"/>
  27                                                         <xs:element name="Date" type="xs:date"/>
  28                                                 </xs:sequence>
  29                                         <xs:attribute name="id" type="xs:ID"/>
  30                                         </xs:complexType>
  31                                 </xs:element>
  32                         </xs:sequence>
  33                 </xs:complexType>
  34         </xs:element>
  35         <xs:element name="SequenceSet">
  36                 <xs:complexType>
  37                         <xs:sequence>
  38                                 <xs:element name="Sequence" maxOccurs="unbounded">
  39                                         <xs:complexType>
  40                                                 <xs:complexContent>
  41                                                         <xs:extension base="vamsas:SequenceType">
  42                                                                 <xs:attribute name="dictionary" type="xs:string"/>
  43                                                         </xs:extension>
  44                                                 </xs:complexContent>
  45                                         </xs:complexType>
  46                                 </xs:element>
  47                                 <xs:element name="SequenceSetAnnotations" minOccurs="0" maxOccurs="unbounded">
  48                                         <xs:complexType>
  49                                                 <xs:sequence>
  50                                                         <xs:element name="description" type="xs:string" minOccurs="0"/>
  51                                                         <xs:element name="status" type="xs:string" minOccurs="0"/>
  52                                                         <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
  53                                                         <xs:element ref="vamsas:Provenance"/>
  54                                                 </xs:sequence>
  55                                                 <xs:attribute name="type" type="xs:string" use="required"/>
  56                                                 <xs:attribute name="end" type="xs:string" use="required"/>
  57                                                 <xs:attribute name="begin" type="xs:string" use="required"/>
  58                                                 <xs:attribute name="seqRef" type="xs:IDREF" use="required"/>
  59                                                 <xs:attribute name="id" type="xs:ID"/>
  60                                         </xs:complexType>
  61                                 </xs:element>
  62                                 <xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
  63                                         <xs:complexType>
  64                                                 <xs:sequence>
  65                                                         <xs:element name="AlignmentAnnotations" minOccurs="0">
  66                                                                 <xs:complexType>
  67                                                                         <xs:sequence>
  68                                                                                 <xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/>
  69                                                                                 <xs:element name="label" type="xs:string"/>
  70                                                                                 <xs:element name="description" type="xs:string"/>
  71                                                                                 <xs:element ref="vamsas:Provenance"/>
  72                                                                         </xs:sequence>
  73                                                                         <xs:attribute name="graph" type="xs:boolean" use="required"/>
  74                                                                         <xs:attribute name="id" type="xs:ID"/>
  75                                                                 </xs:complexType>
  76                                                         </xs:element>
  77                                                         <xs:element name="tree" type="vamsas:TreeType" minOccurs="0" maxOccurs="unbounded"/>
  78                                                         <xs:element name="alignmentSequence" minOccurs="2" maxOccurs="unbounded">
  79                                                                 <xs:complexType>
  80                                                                         <xs:complexContent>
  81                                                                                 <xs:extension base="vamsas:SequenceType">
  82                                                                                         <xs:attribute name="refid" type="xs:IDREF" use="required"/>
  83                                                                                 </xs:extension>
  84                                                                         </xs:complexContent>
  85                                                                 </xs:complexType>
  86                                                         </xs:element>
  87                                                         <xs:element ref="vamsas:Provenance"/>
  88                                                 </xs:sequence>
  89                                         </xs:complexType>
  90                                 </xs:element>
  91                                 <xs:element name="tree" type="vamsas:TreeType"/>
  92                                 <xs:element ref="vamsas:Provenance"/>
  93                         </xs:sequence>
  94                         <xs:attribute name="gapChar" type="xs:string" use="required"/>
  95                         <xs:attribute name="aligned" type="xs:boolean" use="optional"/>
  96                         <xs:attribute name="id" type="xs:ID"/>
  97                 </xs:complexType>
  98         </xs:element>
  99         <xs:element name="annotationElement">
 100                 <xs:complexType>
 101                         <xs:sequence>
 102                                 <xs:element name="displayCharacter" type="xs:string"/>
 103                                 <xs:element name="description" type="xs:string"/>
 104                                 <xs:element name="secondaryStructure">
 105                                         <xs:simpleType>
 106                                                 <xs:restriction base="xs:string">
 107                                                         <xs:length value="1"/>
 108                                                 </xs:restriction>
 109                                         </xs:simpleType>
 110                                 </xs:element>
 111                                 <xs:element name="value" type="xs:float"/>
 112                         </xs:sequence>
 113                         <xs:attribute name="position" type="xs:int" use="required"/>
 114                         <xs:attribute name="id" type="xs:ID"/>
 115                 </xs:complexType>
 116         </xs:element>
 117     <xs:complexType name="SequenceType">
 118                 <xs:sequence>
 119                         <xs:element name="sequence" type="xs:string"/>
 120                         <xs:element name="name" type="xs:string"/>
 121                         <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
 122                                 <xs:complexType>
 123                                         <xs:attribute name="source"/>
 124                                         <xs:attribute name="version"/>
 125                                         <xs:attribute name="accessionId"/>
 126                                         <xs:attribute name="id" type="xs:ID"/>
 127                                 </xs:complexType>
 128                         </xs:element>
 129                 </xs:sequence>
 130                 <xs:attribute name="start" type="xs:int" use="required"/>
 131                 <xs:attribute name="end" type="xs:int" use="required"/>
 132                 <xs:attribute name="id" type="xs:ID"/>
 133         </xs:complexType>
 134
 135     <xs:complexType name="TreeType">
 136         <xs:sequence>
 137           <xs:element name="newickFormat" type="xs:string" minOccurs="1" maxOccurs="unbounded"/>
 138           <xs:element ref="vamsas:Provenance" minOccurs="1" maxOccurs="1"/>
 139         </xs:sequence>
 140         <xs:attribute name="id" type="xs:ID"/>
 141     </xs:complexType>
 142     <xs:complexType name="ApplicationData">
 143                 <xs:sequence>
 144                         <xs:element name="Application">
 145                                 <xs:complexType>
 146                                         <xs:attribute name="version" type="xs:string"/>
 147                                         <xs:attribute name="name" type="xs:string"/>
 148                                         <xs:attribute name="session" type="xs:string"/>
 149                                         <xs:attribute name="data" type="xs:string"/>
 150                                 </xs:complexType>
 151                         </xs:element>
 152                 </xs:sequence>
 153         </xs:complexType>
 154 </xs:schema>