schemas/vamsas.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
   4  * Copyright (C) 2014 The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
  21 <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">
  22         <xs:complexType name="VAMSAS">
  23                 <xs:sequence>
  24                         <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
  25                         <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
  26                 </xs:sequence>
  27         </xs:complexType>
  28         <xs:complexType name="mapListType">
  29                 <xs:annotation>
  30                         <xs:documentation>
  31                                 developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
  32                         </xs:documentation>
  33                         <xs:documentation>
  34                                 This effectively represents a java.util.MapList object
  35                         </xs:documentation>
  36                 </xs:annotation>
  37                 <xs:sequence>
  38                         <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
  39                                 <xs:annotation>
  40                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
  41                                 </xs:annotation>
  42                                 <xs:complexType>
  43                                         <xs:attribute name="start" type="xs:int" use="required"/>
  44                                         <xs:attribute name="end" type="xs:int" use="required"/>
  45                                 </xs:complexType>
  46                         </xs:element>
  47                         <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
  48                                 <xs:annotation>
  49                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
  50                                 </xs:annotation>
  51                                 <xs:complexType>
  52                                         <xs:attribute name="start" type="xs:int" use="required"/>
  53                                         <xs:attribute name="end" type="xs:int" use="required"/>
  54                                 </xs:complexType>
  55                         </xs:element>
  56                 </xs:sequence>
  57                 <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
  58                         <xs:annotation>
  59                                 <xs:documentation>number of dictionary symbol widths involved in each
  60                                         mapped position on this sequence (for example, 3 for a dna sequence exon
  61                                         region that is being mapped to a protein sequence). This is optional,
  62                                         since the unit can be usually be inferred from the dictionary type of
  63                                         each sequence involved in the mapping. </xs:documentation>
  64                         </xs:annotation>
  65                 </xs:attribute>
  66                 <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
  67                         <xs:annotation>
  68                                 <xs:documentation>number of dictionary symbol widths involved in each
  69                                         mapped position on this sequence (for example, 3 for a dna sequence exon
  70                                         region that is being mapped to a protein sequence). This is optional,
  71                                         since the unit can be usually be inferred from the dictionary type of
  72                                         each sequence involved in the mapping. </xs:documentation>
  73                         </xs:annotation>
  74                 </xs:attribute>
  75         </xs:complexType>
  76         <xs:element name="Mapping">
  77                 <xs:complexType>
  78                         <xs:annotation>
  79                                 <xs:documentation>
  80                                         Represent the jalview.datamodel.Mapping object - it also provides
  81                                         a way of storing sequences that are mapped 'to' without adding them
  82                                         to the sequence set (which will mean they are then added to the alignment too).
  83                                 </xs:documentation>
  84                         </xs:annotation>
  85                         <xs:complexContent>
  86                                 <xs:extension base="vamsas:mapListType">
  87                                         <xs:sequence>
  88                                                 <xs:choice minOccurs="0" maxOccurs="1">
  89                                                         <xs:element ref="vamsas:Sequence"/>
  90                                                         <xs:element name="dseqFor">
  91                                                                 <xs:simpleType>
  92                                                                         <xs:restriction base="xs:string">
  93                                                                                 <xs:annotation>
  94                                                                                         <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
  95                                                                                 </xs:annotation>
  96                                                                         </xs:restriction>
  97                                                                 </xs:simpleType>
  98                                                         </xs:element>
  99                                                 </xs:choice>
 100                                         </xs:sequence>
 101                                 </xs:extension>
 102                         </xs:complexContent>
 103                 </xs:complexType>
 104         </xs:element>
 105         <xs:element name="AlcodonFrame">
 106                 <xs:complexType>
 107                         <xs:sequence>
 108                                 <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
 109                                         <xs:complexType>
 110                                                 <xs:annotation>
 111                                                         <xs:documentation>
 112                                                                 specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
 113                                                                 Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
 114                                                         </xs:documentation>
 115                                                 </xs:annotation>
 116                                                 <xs:attribute name="pos1" type="xs:integer" use="optional"/>
 117                                                 <xs:attribute name="pos2" type="xs:integer" use="optional"/>
 118                                                 <xs:attribute name="pos3" type="xs:integer" use="optional"/>
 119                                         </xs:complexType>
 120                                 </xs:element>
 121                                 <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
 122                                         <xs:complexType>
 123                                                 <xs:sequence>
 124                                                         <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
 125                                                                 <xs:annotation>
 126                                                                         <xs:documentation>
 127                                                                                 a Mapping entry and an associated protein sequence
 128                                                                         </xs:documentation>
 129                                                                 </xs:annotation>
 130                                                         </xs:element>
 131                                                 </xs:sequence>
 132                                                 <xs:attribute name="dnasq" type="xs:string" use="required">
 133                                                         <xs:annotation>
 134                                                                 <xs:documentation>
 135                                                                         internal jalview id for the dnasq for this mapping.
 136                                                                 </xs:documentation>
 137                                                         </xs:annotation>
 138                                                 </xs:attribute>
 139                                         </xs:complexType>
 140
 141                                 </xs:element>
 142
 143                         </xs:sequence>
 144                 </xs:complexType>
 145         </xs:element>
 146         <xs:element name="Sequence">
 147                 <xs:complexType>
 148                         <xs:complexContent>
 149                                 <xs:extension base="vamsas:SequenceType">
 150                                         <xs:sequence>
 151                                                 <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
 152                                                         <xs:complexType>
 153                                                                 <xs:sequence>
 154                                                                         <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
 155                                                                 </xs:sequence>
 156                                                                 <xs:attribute name="source" type="xs:string"/>
 157                                                                 <xs:attribute name="version" type="xs:string"/>
 158                                                                 <xs:attribute name="accessionId" type="xs:string"/>
 159                                                         </xs:complexType>
 160                                                 </xs:element>
 161                                         </xs:sequence>
 162                                         <xs:attribute name="dsseqid" type="xs:string" use="optional">
 163                                                 <xs:annotation>
 164                                                         <xs:documentation>
 165                                                                 dataset sequence id for this sequence. Will be created as union of sequences.
 166                                                         </xs:documentation>
 167                                                 </xs:annotation>
 168                                         </xs:attribute>
 169                                 </xs:extension>
 170                         </xs:complexContent>
 171                 </xs:complexType>
 172         </xs:element>
 173         <xs:element name="Annotation">
 174                 <xs:complexType>
 175                         <xs:sequence>
 176                                 <xs:element ref="vamsas:annotationElement" minOccurs="0"
 177                                         maxOccurs="unbounded" />
 178                                 <xs:element name="label" type="xs:string" />
 179                                 <xs:element name="description" type="xs:string"
 180                                         minOccurs="0" />
 181                                 <xs:element name="thresholdLine" minOccurs="0">
 182                                         <xs:complexType>
 183                                                 <xs:attribute name="label" type="xs:string" />
 184                                                 <xs:attribute name="value" type="xs:float" />
 185                                                 <xs:attribute name="colour" type="xs:int" />
 186                                         </xs:complexType>
 187                                 </xs:element>
 188                         </xs:sequence>
 189                         <xs:attribute name="graph" type="xs:boolean" use="required" />
 190                         <xs:attribute name="graphType" type="xs:int" use="optional" />
 191                         <xs:attribute name="sequenceRef" type="xs:string"
 192                                 use="optional" />
 193                         <xs:attribute name="groupRef" type="xs:string"
 194                                 use="optional" />
 195                         <xs:attribute name="graphColour" type="xs:int"
 196                                 use="optional" />
 197                         <xs:attribute name="graphGroup" type="xs:int"
 198                                 use="optional" />
 199                         <xs:attribute name="graphHeight" type="xs:int" use="optional">
 200                         <xs:annotation><xs:documentation>height in pixels for the graph if this is a graph-type annotation.</xs:documentation></xs:annotation></xs:attribute>
 201                         <xs:attribute name="id" type="xs:string" use="optional" />
 202                         <xs:attribute name="scoreOnly" type="xs:boolean"
 203                                 use="optional" default="false" />
 204                         <xs:attribute name="score" type="xs:double" use="optional" />
 205                         <xs:attribute name="visible" type="xs:boolean"
 206                                 use="optional" />
 207                         <xs:attribute name="centreColLabels" type="xs:boolean"
 208                                 use="optional" />
 209                         <xs:attribute name="scaleColLabels" type="xs:boolean"
 210                                 use="optional" />
 211                         <xs:attribute name="showAllColLabels" type="xs:boolean"
 212                                 use="optional" />
 213
 214
 215                         <xs:attribute name="autoCalculated" type="xs:boolean" use="optional" default="false">
 216                         <xs:annotation><xs:documentation>is an autocalculated annotation row</xs:documentation>
 217                         </xs:annotation></xs:attribute>
 218                         <xs:attribute name="belowAlignment" type="xs:boolean" use="optional" default="true">
 219                         <xs:annotation><xs:documentation>is to be shown below the alignment - introduced in Jalview 2.8 for visualizing T-COFFEE alignment scores</xs:documentation></xs:annotation></xs:attribute>
 220                         <xs:attribute name="calcId" type="xs:string" use="optional">
 221                         <xs:annotation><xs:documentation>Optional string identifier used to group sets of annotation produced by a particular calculation. Values are opaque strings but have semantic meaning to Jalview's renderer, data importer and calculation system.</xs:documentation></xs:annotation>
 222                         </xs:attribute>
 223                 </xs:complexType>
 224         </xs:element>
 225         <xs:element name="SequenceSet">
 226                 <xs:complexType>
 227                         <xs:sequence>
 228                                 <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
 229                                 <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
 230                                 <xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
 231                                         <xs:complexType>
 232                                                 <xs:attribute name="key" type="xs:string"/>
 233                                                 <xs:attribute name="value" type="xs:string"/>
 234                                         </xs:complexType>
 235                                 </xs:element>
 236                                 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
 237                         </xs:sequence>
 238                         <xs:attribute name="gapChar" type="xs:string" use="required"/>
 239                         <xs:attribute name="datasetId" type="xs:string" use="optional">
 240                                 <xs:annotation>
 241                                         <xs:documentation>
 242                                                 reference to set where jalview will gather the dataset sequences for all sequences in the set.
 243                                         </xs:documentation>
 244                                 </xs:annotation>
 245                         </xs:attribute>
 246                 </xs:complexType>
 247         </xs:element>
 248         <xs:element name="annotationElement">
 249                 <xs:complexType>
 250                         <xs:sequence>
 251                                 <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
 252                                 <xs:element name="description" type="xs:string" minOccurs="0"/>
 253                                 <xs:element name="secondaryStructure" minOccurs="0">
 254                                         <xs:simpleType>
 255                                                 <xs:restriction base="xs:string">
 256                                                         <xs:length value="1"/>
 257                                                 </xs:restriction>
 258                                         </xs:simpleType>
 259                                 </xs:element>
 260                                 <xs:element name="value" type="xs:float" minOccurs="0"/>
 261                         </xs:sequence>
 262                         <xs:attribute name="position" type="xs:int" use="required"/>
 263                         <xs:attribute name="colour" type="xs:int" use="optional"/>
 264                 </xs:complexType>
 265         </xs:element>
 266         <xs:complexType name="SequenceType">
 267                 <xs:sequence>
 268                         <xs:element name="sequence" type="xs:string" minOccurs="0"/>
 269                         <xs:element name="name" type="xs:string" minOccurs="0"/>
 270                 </xs:sequence>
 271                 <xs:attribute name="id" type="xs:string"/>
 272                 <xs:attribute name="description" type="xs:string"/>
 273         </xs:complexType>
 274 </xs:schema>