schemas/vamsas.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
   3 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">
   4         <xs:complexType name="VAMSAS">
   5                 <xs:sequence>
   6                         <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
   7                         <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
   8                 </xs:sequence>
   9         </xs:complexType>
  10         <xs:complexType name="mapListType">
  11                 <xs:annotation>
  12                         <xs:documentation>
  13                                 developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
  14                         </xs:documentation>
  15                         <xs:documentation>
  16                                 This effectively represents a java.util.MapList object
  17                         </xs:documentation>
  18                 </xs:annotation>
  19                 <xs:sequence>
  20                         <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
  21                                 <xs:annotation>
  22                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
  23                                 </xs:annotation>
  24                                 <xs:complexType>
  25                                         <xs:attribute name="start" type="xs:int" use="required"/>
  26                                         <xs:attribute name="end" type="xs:int" use="required"/>
  27                                 </xs:complexType>
  28                         </xs:element>
  29                         <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
  30                                 <xs:annotation>
  31                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
  32                                 </xs:annotation>
  33                                 <xs:complexType>
  34                                         <xs:attribute name="start" type="xs:int" use="required"/>
  35                                         <xs:attribute name="end" type="xs:int" use="required"/>
  36                                 </xs:complexType>
  37                         </xs:element>
  38                 </xs:sequence>
  39                 <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
  40                         <xs:annotation>
  41                                 <xs:documentation>number of dictionary symbol widths involved in each
  42                                         mapped position on this sequence (for example, 3 for a dna sequence exon
  43                                         region that is being mapped to a protein sequence). This is optional,
  44                                         since the unit can be usually be inferred from the dictionary type of
  45                                         each sequence involved in the mapping. </xs:documentation>
  46                         </xs:annotation>
  47                 </xs:attribute>
  48                 <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
  49                         <xs:annotation>
  50                                 <xs:documentation>number of dictionary symbol widths involved in each
  51                                         mapped position on this sequence (for example, 3 for a dna sequence exon
  52                                         region that is being mapped to a protein sequence). This is optional,
  53                                         since the unit can be usually be inferred from the dictionary type of
  54                                         each sequence involved in the mapping. </xs:documentation>
  55                         </xs:annotation>
  56                 </xs:attribute>
  57         </xs:complexType>
  58         <xs:element name="Mapping">
  59                 <xs:complexType>
  60                         <xs:annotation>
  61                                 <xs:documentation>
  62                                         Represent the jalview.datamodel.Mapping object - it also provides
  63                                         a way of storing sequences that are mapped 'to' without adding them
  64                                         to the sequence set (which will mean they are then added to the alignment too).
  65                                 </xs:documentation>
  66                         </xs:annotation>
  67                         <xs:complexContent>
  68                                 <xs:extension base="vamsas:mapListType">
  69                                         <xs:sequence>
  70                                                 <xs:choice minOccurs="0" maxOccurs="1">
  71                                                         <xs:element ref="vamsas:Sequence"/>
  72                                                         <xs:element name="dseqFor">
  73                                                                 <xs:simpleType>
  74                                                                         <xs:restriction base="xs:string">
  75                                                                                 <xs:annotation>
  76                                                                                         <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
  77                                                                                 </xs:annotation>
  78                                                                         </xs:restriction>
  79                                                                 </xs:simpleType>
  80                                                         </xs:element>
  81                                                 </xs:choice>
  82                                         </xs:sequence>
  83                                 </xs:extension>
  84                         </xs:complexContent>
  85                 </xs:complexType>
  86         </xs:element>
  87         <xs:element name="AlcodonFrame">
  88                 <xs:complexType>
  89                         <xs:sequence>
  90                                 <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
  91                                         <xs:complexType>
  92                                                 <xs:annotation>
  93                                                         <xs:documentation>
  94                                                                 specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
  95                                                                 Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
  96                                                         </xs:documentation>
  97                                                 </xs:annotation>
  98                                                 <xs:attribute name="pos1" type="xs:integer" use="optional"/>
  99                                                 <xs:attribute name="pos2" type="xs:integer" use="optional"/>
 100                                                 <xs:attribute name="pos3" type="xs:integer" use="optional"/>
 101                                         </xs:complexType>
 102                                 </xs:element>
 103                                 <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
 104                                         <xs:complexType>
 105                                                 <xs:sequence>
 106                                                         <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
 107                                                                 <xs:annotation>
 108                                                                         <xs:documentation>
 109                                                                                 a Mapping entry and an associated protein sequence
 110                                                                         </xs:documentation>
 111                                                                 </xs:annotation>
 112                                                         </xs:element>
 113                                                 </xs:sequence>
 114                                                 <xs:attribute name="dnasq" type="xs:string" use="required">
 115                                                         <xs:annotation>
 116                                                                 <xs:documentation>
 117                                                                         internal jalview id for the dnasq for this mapping.
 118                                                                 </xs:documentation>
 119                                                         </xs:annotation>
 120                                                 </xs:attribute>
 121                                         </xs:complexType>
 122
 123                                 </xs:element>
 124
 125                         </xs:sequence>
 126                 </xs:complexType>
 127         </xs:element>
 128         <xs:element name="Sequence">
 129                 <xs:complexType>
 130                         <xs:complexContent>
 131                                 <xs:extension base="vamsas:SequenceType">
 132                                         <xs:sequence>
 133                                                 <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
 134                                                         <xs:complexType>
 135                                                                 <xs:sequence>
 136                                                                         <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
 137                                                                 </xs:sequence>
 138                                                                 <xs:attribute name="source" type="xs:string"/>
 139                                                                 <xs:attribute name="version" type="xs:string"/>
 140                                                                 <xs:attribute name="accessionId" type="xs:string"/>
 141                                                         </xs:complexType>
 142                                                 </xs:element>
 143                                         </xs:sequence>
 144                                         <xs:attribute name="dsseqid" type="xs:string" use="optional">
 145                                                 <xs:annotation>
 146                                                         <xs:documentation>
 147                                                                 dataset sequence id for this sequence. Will be created as union of sequences.
 148                                                         </xs:documentation>
 149                                                 </xs:annotation>
 150                                         </xs:attribute>
 151                                 </xs:extension>
 152                         </xs:complexContent>
 153                 </xs:complexType>
 154         </xs:element>
 155         <xs:element name="Annotation">
 156                 <xs:complexType>
 157                         <xs:sequence>
 158                                 <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
 159                                 <xs:element name="label" type="xs:string"/>
 160                                 <xs:element name="description" type="xs:string" minOccurs="0"/>
 161                                 <xs:element name="thresholdLine" minOccurs="0">
 162                                         <xs:complexType>
 163                                                 <xs:attribute name="label" type="xs:string"/>
 164                                                 <xs:attribute name="value" type="xs:float"/>
 165                                                 <xs:attribute name="colour" type="xs:int"/>
 166                                         </xs:complexType>
 167                                 </xs:element>
 168                         </xs:sequence>
 169                         <xs:attribute name="graph" type="xs:boolean" use="required"/>
 170                         <xs:attribute name="graphType" type="xs:int" use="optional"/>
 171                         <xs:attribute name="sequenceRef" type="xs:string" use="optional"/>
 172                         <xs:attribute name="graphColour" type="xs:int" use="optional"/>
 173                         <xs:attribute name="graphGroup" type="xs:int" use="optional"/>
 174                         <xs:attribute name="id" type="xs:string" use="optional"/>
 175                         <xs:attribute name="scoreOnly" type="xs:boolean" use="optional" default="false"/>
 176                         <xs:attribute name="score" type="xs:double" use="optional"/>
 177                         <xs:attribute name="visible" type="xs:boolean" use="optional"/>
 178                 </xs:complexType>
 179         </xs:element>
 180         <xs:element name="SequenceSet">
 181                 <xs:complexType>
 182                         <xs:sequence>
 183                                 <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
 184                                 <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
 185                                 <xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
 186                                         <xs:complexType>
 187                                                 <xs:attribute name="key" type="xs:string"/>
 188                                                 <xs:attribute name="value" type="xs:string"/>
 189                                         </xs:complexType>
 190                                 </xs:element>
 191                                 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
 192                         </xs:sequence>
 193                         <xs:attribute name="gapChar" type="xs:string" use="required"/>
 194                         <xs:attribute name="datasetId" type="xs:string" use="optional">
 195                                 <xs:annotation>
 196                                         <xs:documentation>
 197                                                 reference to set where jalview will gather the dataset sequences for all sequences in the set.
 198                                         </xs:documentation>
 199                                 </xs:annotation>
 200                         </xs:attribute>
 201                 </xs:complexType>
 202         </xs:element>
 203         <xs:element name="annotationElement">
 204                 <xs:complexType>
 205                         <xs:sequence>
 206                                 <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
 207                                 <xs:element name="description" type="xs:string" minOccurs="0"/>
 208                                 <xs:element name="secondaryStructure" minOccurs="0">
 209                                         <xs:simpleType>
 210                                                 <xs:restriction base="xs:string">
 211                                                         <xs:length value="1"/>
 212                                                 </xs:restriction>
 213                                         </xs:simpleType>
 214                                 </xs:element>
 215                                 <xs:element name="value" type="xs:float" minOccurs="0"/>
 216                         </xs:sequence>
 217                         <xs:attribute name="position" type="xs:int" use="required"/>
 218                         <xs:attribute name="colour" type="xs:int" use="optional"/>
 219                 </xs:complexType>
 220         </xs:element>
 221         <xs:complexType name="SequenceType">
 222                 <xs:sequence>
 223                         <xs:element name="sequence" type="xs:string" minOccurs="0"/>
 224                         <xs:element name="name" type="xs:string" minOccurs="0"/>
 225                 </xs:sequence>
 226                 <xs:attribute name="id" type="xs:string"/>
 227                 <xs:attribute name="description" type="xs:string"/>
 228         </xs:complexType>
 229 </xs:schema>