schemas/vamsas.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ 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 <!--
  22         Java JAXB binding classes are generated by running command line tool xjc:
  23             xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
  24         Note this also generates code for included schemas
  25 -->
  26 <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">
  27         <xs:complexType name="VAMSAS">
  28                 <xs:sequence>
  29                         <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
  30                         <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
  31                 </xs:sequence>
  32         </xs:complexType>
  33         <xs:complexType name="mapListType">
  34                 <xs:annotation>
  35                         <xs:documentation>
  36                                 developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
  37                         </xs:documentation>
  38                         <xs:documentation>
  39                                 This effectively represents a java.util.MapList object
  40                         </xs:documentation>
  41                 </xs:annotation>
  42                 <xs:sequence>
  43                         <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
  44                                 <xs:annotation>
  45                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
  46                                 </xs:annotation>
  47                                 <xs:complexType>
  48                                         <xs:attribute name="start" type="xs:int" use="required"/>
  49                                         <xs:attribute name="end" type="xs:int" use="required"/>
  50                                 </xs:complexType>
  51                         </xs:element>
  52                         <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
  53                                 <xs:annotation>
  54                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
  55                                 </xs:annotation>
  56                                 <xs:complexType>
  57                                         <xs:attribute name="start" type="xs:int" use="required"/>
  58                                         <xs:attribute name="end" type="xs:int" use="required"/>
  59                                 </xs:complexType>
  60                         </xs:element>
  61                 </xs:sequence>
  62                 <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
  63                         <xs:annotation>
  64                                 <xs:documentation>number of dictionary symbol widths involved in each
  65                                         mapped position on this sequence (for example, 3 for a dna sequence exon
  66                                         region that is being mapped to a protein sequence). This is optional,
  67                                         since the unit can be usually be inferred from the dictionary type of
  68                                         each sequence involved in the mapping. </xs:documentation>
  69                         </xs:annotation>
  70                 </xs:attribute>
  71                 <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
  72                         <xs:annotation>
  73                                 <xs:documentation>number of dictionary symbol widths involved in each
  74                                         mapped position on this sequence (for example, 3 for a dna sequence exon
  75                                         region that is being mapped to a protein sequence). This is optional,
  76                                         since the unit can be usually be inferred from the dictionary type of
  77                                         each sequence involved in the mapping. </xs:documentation>
  78                         </xs:annotation>
  79                 </xs:attribute>
  80         </xs:complexType>
  81         <xs:element name="Mapping">
  82                 <xs:complexType>
  83                         <xs:annotation>
  84                                 <xs:documentation>
  85                                         Represent the jalview.datamodel.Mapping object - it also provides
  86                                         a way of storing sequences that are mapped 'to' without adding them
  87                                         to the sequence set (which will mean they are then added to the alignment too).
  88                                 </xs:documentation>
  89                         </xs:annotation>
  90                         <xs:complexContent>
  91                                 <xs:extension base="vamsas:mapListType">
  92                                         <xs:sequence>
  93                                                 <xs:choice minOccurs="0" maxOccurs="1">
  94                                                         <xs:element ref="vamsas:Sequence"/>
  95                                                         <xs:element name="dseqFor">
  96                                                                 <xs:simpleType>
  97                                                                         <xs:restriction base="xs:string">
  98                                                                                 <xs:annotation>
  99                                                                                         <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
 100                                                                                 </xs:annotation>
 101                                                                         </xs:restriction>
 102                                                                 </xs:simpleType>
 103                                                         </xs:element>
 104                                                 </xs:choice>
 105                                         </xs:sequence>
 106                                         <xs:attribute name="mappingType" type="xs:string" use="optional">
 107                                                 <xs:annotation>
 108                                                         <xs:documentation>Biotype of the mapping e.g. CdsToPeptide</xs:documentation>
 109                                                 </xs:annotation>
 110                                         </xs:attribute>
 111                                 </xs:extension>
 112                         </xs:complexContent>
 113                 </xs:complexType>
 114         </xs:element>
 115         <xs:element name="AlcodonFrame">
 116                 <xs:complexType>
 117                         <xs:sequence>
 118                                 <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
 119                                         <xs:complexType>
 120                                                 <xs:annotation>
 121                                                         <xs:documentation>
 122                                                                 specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
 123                                                                 Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
 124                                                         </xs:documentation>
 125                                                 </xs:annotation>
 126                                                 <xs:attribute name="pos1" type="xs:integer" use="optional"/>
 127                                                 <xs:attribute name="pos2" type="xs:integer" use="optional"/>
 128                                                 <xs:attribute name="pos3" type="xs:integer" use="optional"/>
 129                                         </xs:complexType>
 130                                 </xs:element>
 131                                 <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
 132                                         <xs:complexType>
 133                                                 <xs:sequence>
 134                                                         <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
 135                                                                 <xs:annotation>
 136                                                                         <xs:documentation>
 137                                                                                 a Mapping entry and an associated protein sequence
 138                                                                         </xs:documentation>
 139                                                                 </xs:annotation>
 140                                                         </xs:element>
 141                                                 </xs:sequence>
 142                                                 <xs:attribute name="dnasq" type="xs:string" use="required">
 143                                                         <xs:annotation>
 144                                                                 <xs:documentation>
 145                                                                         internal jalview id for the dnasq for this mapping.
 146                                                                 </xs:documentation>
 147                                                         </xs:annotation>
 148                                                 </xs:attribute>
 149                                         </xs:complexType>
 150
 151                                 </xs:element>
 152
 153                         </xs:sequence>
 154                 </xs:complexType>
 155         </xs:element>
 156         <xs:element name="Sequence">
 157                 <xs:complexType>
 158                         <xs:complexContent>
 159                                 <xs:extension base="vamsas:SequenceType">
 160                                         <xs:sequence>
 161                                                 <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
 162                                                         <xs:complexType>
 163                                                                 <xs:sequence>
 164                                                                         <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
 165                                                                 </xs:sequence>
 166                                                                 <xs:attribute name="source" type="xs:string"/>
 167                                                                 <xs:attribute name="version" type="xs:string"/>
 168                                                                 <xs:attribute name="accessionId" type="xs:string"/>
 169                                                                 <xs:attribute name="locus" type="xs:boolean" default="false">
 170                                                                         <xs:annotation>
 171                                                                                 <xs:documentation>
 172                                                                                         true for gene locus mapping, source=species, version=assembly, accession=chromosome
 173                                                                                 </xs:documentation>
 174                                                                         </xs:annotation>
 175                                                                 </xs:attribute>
 176                                                                 <xs:attribute name="canonical" type="xs:boolean" default="false">
 177                                                                         <xs:annotation>
 178                                                                                 <xs:documentation>
 179                                                                                         true for the representative accession for databases where multiple accessions map to the same entry (eg. Uniprot)
 180                                                                                 </xs:documentation>
 181                                                                         </xs:annotation>
 182                                                                 </xs:attribute>
 183                                                         </xs:complexType>
 184                                                 </xs:element>
 185                                         </xs:sequence>
 186                                         <xs:attribute name="dsseqid" type="xs:string" use="optional">
 187                                                 <xs:annotation>
 188                                                         <xs:documentation>
 189                                                                 dataset sequence id for this sequence. Will be created as union of sequences.
 190                                                         </xs:documentation>
 191                                                 </xs:annotation>
 192                                         </xs:attribute>
 193                                         <xs:attribute name="biotype" type="xs:string" use="optional">
 194                                                 <xs:annotation>
 195                                                         <xs:documentation>
 196                                                                 Biotype of the sequence (if known)
 197                                                         </xs:documentation>
 198                                                 </xs:annotation>
 199                                         </xs:attribute>
 200                                 </xs:extension>
 201                         </xs:complexContent>
 202                 </xs:complexType>
 203         </xs:element>
 204         <xs:element name="Annotation">
 205                 <xs:complexType>
 206                         <xs:sequence>
 207                                 <xs:element ref="vamsas:annotationElement" minOccurs="0"
 208                                         maxOccurs="unbounded" />
 209                                 <xs:element name="label" type="xs:string" />
 210                                 <xs:element name="description" type="xs:string"
 211                                         minOccurs="0" />
 212                                 <xs:element name="thresholdLine" minOccurs="0">
 213                                         <xs:complexType>
 214                                                 <xs:attribute name="label" type="xs:string" />
 215                                                 <xs:attribute name="value" type="xs:float" />
 216                                                 <xs:attribute name="colour" type="xs:int" />
 217                                         </xs:complexType>
 218                                 </xs:element>
 219                                 <xs:element name="contactmatrix" type="vamsas:MatrixType"
 220                                         maxOccurs="unbounded" minOccurs="0">
 221                                 </xs:element>
 222                                 <xs:element name="property" type="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
 223                         </xs:sequence>
 224                         <xs:attribute name="graph" type="xs:boolean" use="required" />
 225                         <xs:attribute name="graphType" type="xs:int" use="optional" />
 226                         <xs:attribute name="sequenceRef" type="xs:string"
 227                                 use="optional" />
 228                         <xs:attribute name="groupRef" type="xs:string"
 229                                 use="optional" />
 230                         <xs:attribute name="graphColour" type="xs:int"
 231                                 use="optional" />
 232                         <xs:attribute name="graphGroup" type="xs:int"
 233                                 use="optional" />
 234                         <xs:attribute name="graphHeight" type="xs:int" use="optional">
 235                         <xs:annotation><xs:documentation>height in pixels for the graph if this is a graph-type annotation.</xs:documentation></xs:annotation></xs:attribute>
 236                         <xs:attribute name="id" type="xs:string" use="optional" />
 237                         <xs:attribute name="scoreOnly" type="xs:boolean"
 238                                 use="optional" default="false" />
 239                         <xs:attribute name="score" type="xs:double" use="optional" />
 240                         <xs:attribute name="visible" type="xs:boolean"
 241                                 use="optional" />
 242                         <xs:attribute name="centreColLabels" type="xs:boolean"
 243                                 use="optional" />
 244                         <xs:attribute name="scaleColLabels" type="xs:boolean"
 245                                 use="optional" />
 246                         <xs:attribute name="showAllColLabels" type="xs:boolean"
 247                                 use="optional" />
 248
 249
 250                         <xs:attribute name="autoCalculated" type="xs:boolean" use="optional" default="false">
 251                         <xs:annotation><xs:documentation>is an autocalculated annotation row</xs:documentation>
 252                         </xs:annotation></xs:attribute>
 253                         <xs:attribute name="belowAlignment" type="xs:boolean" use="optional" default="true">
 254                         <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>
 255                         <xs:attribute name="calcId" type="xs:string" use="optional">
 256                         <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>
 257                         </xs:attribute>
 258                 </xs:complexType>
 259         </xs:element>
 260         <xs:element name="SequenceSet">
 261                 <xs:complexType>
 262                         <xs:sequence>
 263                                 <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
 264                                 <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
 265                                 <xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
 266                                         <xs:complexType>
 267                                                 <xs:attribute name="key" type="xs:string"/>
 268                                                 <xs:attribute name="value" type="xs:string"/>
 269                                         </xs:complexType>
 270                                 </xs:element>
 271                                 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
 272                                 <xs:element name="Matrices" type="vamsas:MatrixType" minOccurs="0" maxOccurs="unbounded"/>
 273                         </xs:sequence>
 274                         <xs:attribute name="gapChar" type="xs:string" use="required"/>
 275                         <xs:attribute name="datasetId" type="xs:string" use="optional">
 276                                 <xs:annotation>
 277                                         <xs:documentation>
 278                                                 reference to set where jalview will gather the dataset sequences for all sequences in the set.
 279                                         </xs:documentation>
 280                                 </xs:annotation>
 281                         </xs:attribute>
 282                 </xs:complexType>
 283         </xs:element>
 284         <xs:element name="annotationElement">
 285                 <xs:complexType>
 286                         <xs:sequence>
 287                                 <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
 288                                 <xs:element name="description" type="xs:string" minOccurs="0"/>
 289                                 <xs:element name="secondaryStructure" minOccurs="0">
 290                                         <xs:simpleType>
 291                                                 <xs:restriction base="xs:string">
 292                                                         <xs:length value="1"/>
 293                                                 </xs:restriction>
 294                                         </xs:simpleType>
 295                                 </xs:element>
 296                                 <xs:element name="value" type="xs:float" minOccurs="0"/>
 297                         </xs:sequence>
 298                         <xs:attribute name="position" type="xs:int" use="required"/>
 299                         <xs:attribute name="colour" type="xs:int" use="optional"/>
 300                 </xs:complexType>
 301         </xs:element>
 302         <xs:complexType name="SequenceType">
 303                 <xs:sequence>
 304                         <xs:element name="sequence" type="xs:string" minOccurs="0"/>
 305                         <xs:element name="name" type="xs:string" minOccurs="0"/>
 306                 </xs:sequence>
 307                 <xs:attribute name="id" type="xs:string"/>
 308                 <xs:attribute name="description" type="xs:string"/>
 309         </xs:complexType>
 310         <xs:complexType name="MatrixType">
 311                 <xs:sequence>
 312                         <xs:element name="elements" type="xs:string" minOccurs="1"
 313                                 maxOccurs="1">
 314                                 <xs:annotation>
 315                                         <xs:documentation>serialised representation of matrix as one or
 316                                                 more sets of comma separated values</xs:documentation>
 317                                 </xs:annotation>
 318                         </xs:element>
 319                         <xs:element name="groups" type="xs:string" minOccurs="0"
 320                                 maxOccurs="unbounded">
 321                                 <xs:annotation>
 322                                         <xs:documentation>Comma separated series of longs formed from
 323                                                 bitsets defining partitions on the rows/columns of the matrix
 324                                         </xs:documentation>
 325                                 </xs:annotation>
 326                         </xs:element>
 327                         <xs:element name="newick" type="xs:string" minOccurs="0"
 328                                 maxOccurs="unbounded">
 329                                 <xs:annotation>
 330                                         <xs:documentation>tree computed for this</xs:documentation>
 331                                 </xs:annotation>
 332                         </xs:element>
 333                         <xs:element name="property" type="vamsas:property"
 334                                 minOccurs="0" maxOccurs="unbounded" />
 335                         <xs:element name="mapping" type="vamsas:mapListType"
 336                                 minOccurs="0" maxOccurs="1">
 337                         <xs:annotation>
 338                                 <xs:documentation>mapping from the matrix row and column positions to
 339                                         associated reference frame</xs:documentation>
 340                                 </xs:annotation>
 341                         </xs:element>
 342                 </xs:sequence>
 343
 344                 <xs:attribute name="type" type="xs:string" use="required" />
 345                 <xs:attribute name="rows" type="xs:integer"
 346                         use="required" />
 347                 <xs:attribute name="cols" type="xs:integer"
 348                         use="required" />
 349                 <xs:attribute name="treeMethod" type="xs:string"
 350                         use="optional" />
 351                 <xs:attribute name="cutHeight" type="xs:double"
 352                         use="optional" />
 353                 <xs:attribute name="id" type="xs:string" use="required" />
 354
 355         </xs:complexType>
 356         <xs:complexType name="MapOnAMatrixType">
 357                 <xs:sequence>
 358                         <xs:element name="property" type="vamsas:property"
 359                                 minOccurs="0" maxOccurs="unbounded" />
 360                         <xs:element name="mapping" type="vamsas:mapListType"
 361                                 minOccurs="0" maxOccurs="1">
 362                                 <xs:annotation>
 363                                         <xs:documentation>mapping from the matrix row and column positions
 364                                                 to
 365                                                 associated reference frame
 366                                         </xs:documentation>
 367                                 </xs:annotation>
 368                         </xs:element>
 369                 </xs:sequence>
 370
 371                 <xs:attribute name="matrix" type="xs:string"
 372                         use="required">
 373
 374                         <xs:annotation>
 375                                 <xs:documentation>reference to the matrix type this Map refers to
 376                                 </xs:documentation>
 377                         </xs:annotation>
 378                 </xs:attribute>
 379                 <xs:attribute name="id" type="xs:string" use="optional" />
 380         </xs:complexType>
 381         <xs:complexType name="property">
 382                 <xs:attribute name="name" type="xs:string" />
 383                 <xs:attribute name="value" type="xs:string" />
 384         </xs:complexType>
 385
 386
 387 </xs:schema>