schemas/vamsas.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!--
   3   Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   4   Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   5
   6   This program is free software; you can redistribute it and/or
   7   modify it under the terms of the GNU General Public License
   8   as published by the Free Software Foundation; either version 2
   9   of the License, or (at your option) any later version.
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  14   GNU General Public License for more details.
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  17   along with this program; if not, write to the Free Software
  18   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
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  20
  21 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
  22 <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">
  23         <xs:complexType name="VAMSAS">
  24                 <xs:sequence>
  25                         <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
  26                         <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
  27                 </xs:sequence>
  28         </xs:complexType>
  29         <xs:complexType name="mapListType">
  30                 <xs:annotation>
  31                         <xs:documentation>
  32                                 developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
  33                         </xs:documentation>
  34                         <xs:documentation>
  35                                 This effectively represents a java.util.MapList object
  36                         </xs:documentation>
  37                 </xs:annotation>
  38                 <xs:sequence>
  39                         <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
  40                                 <xs:annotation>
  41                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
  42                                 </xs:annotation>
  43                                 <xs:complexType>
  44                                         <xs:attribute name="start" type="xs:int" use="required"/>
  45                                         <xs:attribute name="end" type="xs:int" use="required"/>
  46                                 </xs:complexType>
  47                         </xs:element>
  48                         <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
  49                                 <xs:annotation>
  50                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
  51                                 </xs:annotation>
  52                                 <xs:complexType>
  53                                         <xs:attribute name="start" type="xs:int" use="required"/>
  54                                         <xs:attribute name="end" type="xs:int" use="required"/>
  55                                 </xs:complexType>
  56                         </xs:element>
  57                 </xs:sequence>
  58                 <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
  59                         <xs:annotation>
  60                                 <xs:documentation>number of dictionary symbol widths involved in each
  61                                         mapped position on this sequence (for example, 3 for a dna sequence exon
  62                                         region that is being mapped to a protein sequence). This is optional,
  63                                         since the unit can be usually be inferred from the dictionary type of
  64                                         each sequence involved in the mapping. </xs:documentation>
  65                         </xs:annotation>
  66                 </xs:attribute>
  67                 <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
  68                         <xs:annotation>
  69                                 <xs:documentation>number of dictionary symbol widths involved in each
  70                                         mapped position on this sequence (for example, 3 for a dna sequence exon
  71                                         region that is being mapped to a protein sequence). This is optional,
  72                                         since the unit can be usually be inferred from the dictionary type of
  73                                         each sequence involved in the mapping. </xs:documentation>
  74                         </xs:annotation>
  75                 </xs:attribute>
  76         </xs:complexType>
  77         <xs:element name="Mapping">
  78                 <xs:complexType>
  79                         <xs:annotation>
  80                                 <xs:documentation>
  81                                         Represent the jalview.datamodel.Mapping object - it also provides
  82                                         a way of storing sequences that are mapped 'to' without adding them
  83                                         to the sequence set (which will mean they are then added to the alignment too).
  84                                 </xs:documentation>
  85                         </xs:annotation>
  86                         <xs:complexContent>
  87                                 <xs:extension base="vamsas:mapListType">
  88                                         <xs:sequence>
  89                                                 <xs:choice minOccurs="0" maxOccurs="1">
  90                                                         <xs:element ref="vamsas:Sequence"/>
  91                                                         <xs:element name="dseqFor">
  92                                                                 <xs:simpleType>
  93                                                                         <xs:restriction base="xs:string">
  94                                                                                 <xs:annotation>
  95                                                                                         <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
  96                                                                                 </xs:annotation>
  97                                                                         </xs:restriction>
  98                                                                 </xs:simpleType>
  99                                                         </xs:element>
 100                                                 </xs:choice>
 101                                         </xs:sequence>
 102                                 </xs:extension>
 103                         </xs:complexContent>
 104                 </xs:complexType>
 105         </xs:element>
 106         <xs:element name="AlcodonFrame">
 107                 <xs:complexType>
 108                         <xs:sequence>
 109                                 <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
 110                                         <xs:complexType>
 111                                                 <xs:annotation>
 112                                                         <xs:documentation>
 113                                                                 specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
 114                                                                 Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
 115                                                         </xs:documentation>
 116                                                 </xs:annotation>
 117                                                 <xs:attribute name="pos1" type="xs:integer" use="optional"/>
 118                                                 <xs:attribute name="pos2" type="xs:integer" use="optional"/>
 119                                                 <xs:attribute name="pos3" type="xs:integer" use="optional"/>
 120                                         </xs:complexType>
 121                                 </xs:element>
 122                                 <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
 123                                         <xs:complexType>
 124                                                 <xs:sequence>
 125                                                         <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
 126                                                                 <xs:annotation>
 127                                                                         <xs:documentation>
 128                                                                                 a Mapping entry and an associated protein sequence
 129                                                                         </xs:documentation>
 130                                                                 </xs:annotation>
 131                                                         </xs:element>
 132                                                 </xs:sequence>
 133                                                 <xs:attribute name="dnasq" type="xs:string" use="required">
 134                                                         <xs:annotation>
 135                                                                 <xs:documentation>
 136                                                                         internal jalview id for the dnasq for this mapping.
 137                                                                 </xs:documentation>
 138                                                         </xs:annotation>
 139                                                 </xs:attribute>
 140                                         </xs:complexType>
 141
 142                                 </xs:element>
 143
 144                         </xs:sequence>
 145                 </xs:complexType>
 146         </xs:element>
 147         <xs:element name="Sequence">
 148                 <xs:complexType>
 149                         <xs:complexContent>
 150                                 <xs:extension base="vamsas:SequenceType">
 151                                         <xs:sequence>
 152                                                 <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
 153                                                         <xs:complexType>
 154                                                                 <xs:sequence>
 155                                                                         <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
 156                                                                 </xs:sequence>
 157                                                                 <xs:attribute name="source" type="xs:string"/>
 158                                                                 <xs:attribute name="version" type="xs:string"/>
 159                                                                 <xs:attribute name="accessionId" type="xs:string"/>
 160                                                         </xs:complexType>
 161                                                 </xs:element>
 162                                         </xs:sequence>
 163                                         <xs:attribute name="dsseqid" type="xs:string" use="optional">
 164                                                 <xs:annotation>
 165                                                         <xs:documentation>
 166                                                                 dataset sequence id for this sequence. Will be created as union of sequences.
 167                                                         </xs:documentation>
 168                                                 </xs:annotation>
 169                                         </xs:attribute>
 170                                 </xs:extension>
 171                         </xs:complexContent>
 172                 </xs:complexType>
 173         </xs:element>
 174         <xs:element name="Annotation">
 175                 <xs:complexType>
 176                         <xs:sequence>
 177                                 <xs:element ref="vamsas:annotationElement" minOccurs="0"
 178                                         maxOccurs="unbounded" />
 179                                 <xs:element name="label" type="xs:string" />
 180                                 <xs:element name="description" type="xs:string"
 181                                         minOccurs="0" />
 182                                 <xs:element name="thresholdLine" minOccurs="0">
 183                                         <xs:complexType>
 184                                                 <xs:attribute name="label" type="xs:string" />
 185                                                 <xs:attribute name="value" type="xs:float" />
 186                                                 <xs:attribute name="colour" type="xs:int" />
 187                                         </xs:complexType>
 188                                 </xs:element>
 189                         </xs:sequence>
 190                         <xs:attribute name="graph" type="xs:boolean" use="required" />
 191                         <xs:attribute name="graphType" type="xs:int" use="optional" />
 192                         <xs:attribute name="sequenceRef" type="xs:string"
 193                                 use="optional" />
 194                         <xs:attribute name="groupRef" type="xs:string"
 195                                 use="optional" />
 196                         <xs:attribute name="graphColour" type="xs:int"
 197                                 use="optional" />
 198                         <xs:attribute name="graphGroup" type="xs:int"
 199                                 use="optional" />
 200                         <xs:attribute name="id" type="xs:string" use="optional" />
 201                         <xs:attribute name="scoreOnly" type="xs:boolean"
 202                                 use="optional" default="false" />
 203                         <xs:attribute name="score" type="xs:double" use="optional" />
 204                         <xs:attribute name="visible" type="xs:boolean"
 205                                 use="optional" />
 206                         <xs:attribute name="centreColLabels" type="xs:boolean"
 207                                 use="optional" />
 208                         <xs:attribute name="scaleColLabels" type="xs:boolean"
 209                                 use="optional" />
 210                         <xs:attribute name="showAllColLabels" type="xs:boolean"
 211                                 use="optional" />
 212
 213
 214                         <xs:attribute name="autoCalculated" type="xs:boolean" use="optional" default="false">
 215                         <xs:annotation><xs:documentation>is an autocalculated annotation row</xs:documentation>
 216                         </xs:annotation></xs:attribute>
 217                 </xs:complexType>
 218         </xs:element>
 219         <xs:element name="SequenceSet">
 220                 <xs:complexType>
 221                         <xs:sequence>
 222                                 <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
 223                                 <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
 224                                 <xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
 225                                         <xs:complexType>
 226                                                 <xs:attribute name="key" type="xs:string"/>
 227                                                 <xs:attribute name="value" type="xs:string"/>
 228                                         </xs:complexType>
 229                                 </xs:element>
 230                                 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
 231                         </xs:sequence>
 232                         <xs:attribute name="gapChar" type="xs:string" use="required"/>
 233                         <xs:attribute name="datasetId" type="xs:string" use="optional">
 234                                 <xs:annotation>
 235                                         <xs:documentation>
 236                                                 reference to set where jalview will gather the dataset sequences for all sequences in the set.
 237                                         </xs:documentation>
 238                                 </xs:annotation>
 239                         </xs:attribute>
 240                 </xs:complexType>
 241         </xs:element>
 242         <xs:element name="annotationElement">
 243                 <xs:complexType>
 244                         <xs:sequence>
 245                                 <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
 246                                 <xs:element name="description" type="xs:string" minOccurs="0"/>
 247                                 <xs:element name="secondaryStructure" minOccurs="0">
 248                                         <xs:simpleType>
 249                                                 <xs:restriction base="xs:string">
 250                                                         <xs:length value="1"/>
 251                                                 </xs:restriction>
 252                                         </xs:simpleType>
 253                                 </xs:element>
 254                                 <xs:element name="value" type="xs:float" minOccurs="0"/>
 255                         </xs:sequence>
 256                         <xs:attribute name="position" type="xs:int" use="required"/>
 257                         <xs:attribute name="colour" type="xs:int" use="optional"/>
 258                 </xs:complexType>
 259         </xs:element>
 260         <xs:complexType name="SequenceType">
 261                 <xs:sequence>
 262                         <xs:element name="sequence" type="xs:string" minOccurs="0"/>
 263                         <xs:element name="name" type="xs:string" minOccurs="0"/>
 264                 </xs:sequence>
 265                 <xs:attribute name="id" type="xs:string"/>
 266                 <xs:attribute name="description" type="xs:string"/>
 267         </xs:complexType>
 268 </xs:schema>