schemas/vamsas.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!--
   3   Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   4   Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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 -->
  19 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
  20 <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">
  21         <xs:complexType name="VAMSAS">
  22                 <xs:sequence>
  23                         <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
  24                         <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
  25                 </xs:sequence>
  26         </xs:complexType>
  27         <xs:complexType name="mapListType">
  28                 <xs:annotation>
  29                         <xs:documentation>
  30                                 developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
  31                         </xs:documentation>
  32                         <xs:documentation>
  33                                 This effectively represents a java.util.MapList object
  34                         </xs:documentation>
  35                 </xs:annotation>
  36                 <xs:sequence>
  37                         <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
  38                                 <xs:annotation>
  39                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
  40                                 </xs:annotation>
  41                                 <xs:complexType>
  42                                         <xs:attribute name="start" type="xs:int" use="required"/>
  43                                         <xs:attribute name="end" type="xs:int" use="required"/>
  44                                 </xs:complexType>
  45                         </xs:element>
  46                         <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
  47                                 <xs:annotation>
  48                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
  49                                 </xs:annotation>
  50                                 <xs:complexType>
  51                                         <xs:attribute name="start" type="xs:int" use="required"/>
  52                                         <xs:attribute name="end" type="xs:int" use="required"/>
  53                                 </xs:complexType>
  54                         </xs:element>
  55                 </xs:sequence>
  56                 <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
  57                         <xs:annotation>
  58                                 <xs:documentation>number of dictionary symbol widths involved in each
  59                                         mapped position on this sequence (for example, 3 for a dna sequence exon
  60                                         region that is being mapped to a protein sequence). This is optional,
  61                                         since the unit can be usually be inferred from the dictionary type of
  62                                         each sequence involved in the mapping. </xs:documentation>
  63                         </xs:annotation>
  64                 </xs:attribute>
  65                 <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
  66                         <xs:annotation>
  67                                 <xs:documentation>number of dictionary symbol widths involved in each
  68                                         mapped position on this sequence (for example, 3 for a dna sequence exon
  69                                         region that is being mapped to a protein sequence). This is optional,
  70                                         since the unit can be usually be inferred from the dictionary type of
  71                                         each sequence involved in the mapping. </xs:documentation>
  72                         </xs:annotation>
  73                 </xs:attribute>
  74         </xs:complexType>
  75         <xs:element name="Mapping">
  76                 <xs:complexType>
  77                         <xs:annotation>
  78                                 <xs:documentation>
  79                                         Represent the jalview.datamodel.Mapping object - it also provides
  80                                         a way of storing sequences that are mapped 'to' without adding them
  81                                         to the sequence set (which will mean they are then added to the alignment too).
  82                                 </xs:documentation>
  83                         </xs:annotation>
  84                         <xs:complexContent>
  85                                 <xs:extension base="vamsas:mapListType">
  86                                         <xs:sequence>
  87                                                 <xs:choice minOccurs="0" maxOccurs="1">
  88                                                         <xs:element ref="vamsas:Sequence"/>
  89                                                         <xs:element name="dseqFor">
  90                                                                 <xs:simpleType>
  91                                                                         <xs:restriction base="xs:string">
  92                                                                                 <xs:annotation>
  93                                                                                         <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
  94                                                                                 </xs:annotation>
  95                                                                         </xs:restriction>
  96                                                                 </xs:simpleType>
  97                                                         </xs:element>
  98                                                 </xs:choice>
  99                                         </xs:sequence>
 100                                 </xs:extension>
 101                         </xs:complexContent>
 102                 </xs:complexType>
 103         </xs:element>
 104         <xs:element name="AlcodonFrame">
 105                 <xs:complexType>
 106                         <xs:sequence>
 107                                 <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
 108                                         <xs:complexType>
 109                                                 <xs:annotation>
 110                                                         <xs:documentation>
 111                                                                 specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
 112                                                                 Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
 113                                                         </xs:documentation>
 114                                                 </xs:annotation>
 115                                                 <xs:attribute name="pos1" type="xs:integer" use="optional"/>
 116                                                 <xs:attribute name="pos2" type="xs:integer" use="optional"/>
 117                                                 <xs:attribute name="pos3" type="xs:integer" use="optional"/>
 118                                         </xs:complexType>
 119                                 </xs:element>
 120                                 <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
 121                                         <xs:complexType>
 122                                                 <xs:sequence>
 123                                                         <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
 124                                                                 <xs:annotation>
 125                                                                         <xs:documentation>
 126                                                                                 a Mapping entry and an associated protein sequence
 127                                                                         </xs:documentation>
 128                                                                 </xs:annotation>
 129                                                         </xs:element>
 130                                                 </xs:sequence>
 131                                                 <xs:attribute name="dnasq" type="xs:string" use="required">
 132                                                         <xs:annotation>
 133                                                                 <xs:documentation>
 134                                                                         internal jalview id for the dnasq for this mapping.
 135                                                                 </xs:documentation>
 136                                                         </xs:annotation>
 137                                                 </xs:attribute>
 138                                         </xs:complexType>
 139
 140                                 </xs:element>
 141
 142                         </xs:sequence>
 143                 </xs:complexType>
 144         </xs:element>
 145         <xs:element name="Sequence">
 146                 <xs:complexType>
 147                         <xs:complexContent>
 148                                 <xs:extension base="vamsas:SequenceType">
 149                                         <xs:sequence>
 150                                                 <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
 151                                                         <xs:complexType>
 152                                                                 <xs:sequence>
 153                                                                         <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
 154                                                                 </xs:sequence>
 155                                                                 <xs:attribute name="source" type="xs:string"/>
 156                                                                 <xs:attribute name="version" type="xs:string"/>
 157                                                                 <xs:attribute name="accessionId" type="xs:string"/>
 158                                                         </xs:complexType>
 159                                                 </xs:element>
 160                                         </xs:sequence>
 161                                         <xs:attribute name="dsseqid" type="xs:string" use="optional">
 162                                                 <xs:annotation>
 163                                                         <xs:documentation>
 164                                                                 dataset sequence id for this sequence. Will be created as union of sequences.
 165                                                         </xs:documentation>
 166                                                 </xs:annotation>
 167                                         </xs:attribute>
 168                                 </xs:extension>
 169                         </xs:complexContent>
 170                 </xs:complexType>
 171         </xs:element>
 172         <xs:element name="Annotation">
 173                 <xs:complexType>
 174                         <xs:sequence>
 175                                 <xs:element ref="vamsas:annotationElement" minOccurs="0"
 176                                         maxOccurs="unbounded" />
 177                                 <xs:element name="label" type="xs:string" />
 178                                 <xs:element name="description" type="xs:string"
 179                                         minOccurs="0" />
 180                                 <xs:element name="thresholdLine" minOccurs="0">
 181                                         <xs:complexType>
 182                                                 <xs:attribute name="label" type="xs:string" />
 183                                                 <xs:attribute name="value" type="xs:float" />
 184                                                 <xs:attribute name="colour" type="xs:int" />
 185                                         </xs:complexType>
 186                                 </xs:element>
 187                         </xs:sequence>
 188                         <xs:attribute name="graph" type="xs:boolean" use="required" />
 189                         <xs:attribute name="graphType" type="xs:int" use="optional" />
 190                         <xs:attribute name="sequenceRef" type="xs:string"
 191                                 use="optional" />
 192                         <xs:attribute name="groupRef" type="xs:string"
 193                                 use="optional" />
 194                         <xs:attribute name="graphColour" type="xs:int"
 195                                 use="optional" />
 196                         <xs:attribute name="graphGroup" type="xs:int"
 197                                 use="optional" />
 198                         <xs:attribute name="graphHeight" type="xs:int" use="optional">
 199                         <xs:annotation><xs:documentation>height in pixels for the graph if this is a graph-type annotation.</xs:documentation></xs:annotation></xs:attribute>
 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:attribute name="belowAlignment" type="xs:boolean" use="optional" default="true">
 218                         <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>
 219                         <xs:attribute name="calcId" type="xs:string" use="optional">
 220                         <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>
 221                         </xs:attribute>
 222                 </xs:complexType>
 223         </xs:element>
 224         <xs:element name="SequenceSet">
 225                 <xs:complexType>
 226                         <xs:sequence>
 227                                 <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
 228                                 <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
 229                                 <xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
 230                                         <xs:complexType>
 231                                                 <xs:attribute name="key" type="xs:string"/>
 232                                                 <xs:attribute name="value" type="xs:string"/>
 233                                         </xs:complexType>
 234                                 </xs:element>
 235                                 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
 236                         </xs:sequence>
 237                         <xs:attribute name="gapChar" type="xs:string" use="required"/>
 238                         <xs:attribute name="datasetId" type="xs:string" use="optional">
 239                                 <xs:annotation>
 240                                         <xs:documentation>
 241                                                 reference to set where jalview will gather the dataset sequences for all sequences in the set.
 242                                         </xs:documentation>
 243                                 </xs:annotation>
 244                         </xs:attribute>
 245                 </xs:complexType>
 246         </xs:element>
 247         <xs:element name="annotationElement">
 248                 <xs:complexType>
 249                         <xs:sequence>
 250                                 <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
 251                                 <xs:element name="description" type="xs:string" minOccurs="0"/>
 252                                 <xs:element name="secondaryStructure" minOccurs="0">
 253                                         <xs:simpleType>
 254                                                 <xs:restriction base="xs:string">
 255                                                         <xs:length value="1"/>
 256                                                 </xs:restriction>
 257                                         </xs:simpleType>
 258                                 </xs:element>
 259                                 <xs:element name="value" type="xs:float" minOccurs="0"/>
 260                         </xs:sequence>
 261                         <xs:attribute name="position" type="xs:int" use="required"/>
 262                         <xs:attribute name="colour" type="xs:int" use="optional"/>
 263                 </xs:complexType>
 264         </xs:element>
 265         <xs:complexType name="SequenceType">
 266                 <xs:sequence>
 267                         <xs:element name="sequence" type="xs:string" minOccurs="0"/>
 268                         <xs:element name="name" type="xs:string" minOccurs="0"/>
 269                 </xs:sequence>
 270                 <xs:attribute name="id" type="xs:string"/>
 271                 <xs:attribute name="description" type="xs:string"/>
 272         </xs:complexType>
 273 </xs:schema>