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"
  27         xmlns:vamsas="www.vamsas.ac.uk/jalview/version2"
  28         targetNamespace="www.vamsas.ac.uk/jalview/version2"
  29         elementFormDefault="qualified" attributeFormDefault="unqualified">
  30         <xs:complexType name="VAMSAS">
  31                 <xs:sequence>
  32                         <xs:element name="Tree" type="xs:string" minOccurs="0"
  33                                 maxOccurs="unbounded" />
  34                         <xs:element ref="vamsas:SequenceSet" minOccurs="0"
  35                                 maxOccurs="unbounded" />
  36                 </xs:sequence>
  37         </xs:complexType>
  38         <xs:complexType name="mapListType">
  39                 <xs:annotation>
  40                         <xs:documentation>
  41                                 developed after mapRangeType from
  42                                 http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
  43                         </xs:documentation>
  44                         <xs:documentation>
  45                                 This effectively represents a java.util.MapList
  46                                 object
  47                         </xs:documentation>
  48                 </xs:annotation>
  49                 <xs:sequence>
  50                         <xs:element name="mapListFrom" minOccurs="0"
  51                                 maxOccurs="unbounded">
  52                                 <xs:annotation>
  53                                         <xs:documentation> a region from start to end inclusive
  54                                         </xs:documentation>
  55                                 </xs:annotation>
  56                                 <xs:complexType>
  57                                         <xs:attribute name="start" type="xs:int"
  58                                                 use="required" />
  59                                         <xs:attribute name="end" type="xs:int" use="required" />
  60                                 </xs:complexType>
  61                         </xs:element>
  62                         <xs:element name="mapListTo" minOccurs="0"
  63                                 maxOccurs="unbounded">
  64                                 <xs:annotation>
  65                                         <xs:documentation> a region from start to end inclusive
  66                                         </xs:documentation>
  67                                 </xs:annotation>
  68                                 <xs:complexType>
  69                                         <xs:attribute name="start" type="xs:int"
  70                                                 use="required" />
  71                                         <xs:attribute name="end" type="xs:int" use="required" />
  72                                 </xs:complexType>
  73                         </xs:element>
  74                 </xs:sequence>
  75                 <xs:attribute name="mapFromUnit"
  76                         type="xs:positiveInteger" use="required">
  77                         <xs:annotation>
  78                                 <xs:documentation>number of dictionary symbol widths involved in
  79                                         each
  80                                         mapped position on this sequence (for example, 3 for a dna
  81                                         sequence exon
  82                                         region that is being mapped to a protein sequence).
  83                                         This is optional,
  84                                         since the unit can be usually be inferred from the
  85                                         dictionary type of
  86                                         each sequence involved in the mapping.
  87                                 </xs:documentation>
  88                         </xs:annotation>
  89                 </xs:attribute>
  90                 <xs:attribute name="mapToUnit" type="xs:positiveInteger"
  91                         use="required">
  92                         <xs:annotation>
  93                                 <xs:documentation>number of dictionary symbol widths involved in
  94                                         each
  95                                         mapped position on this sequence (for example, 3 for a dna
  96                                         sequence exon
  97                                         region that is being mapped to a protein sequence).
  98                                         This is optional,
  99                                         since the unit can be usually be inferred from the
 100                                         dictionary type of
 101                                         each sequence involved in the mapping.
 102                                 </xs:documentation>
 103                         </xs:annotation>
 104                 </xs:attribute>
 105         </xs:complexType>
 106         <xs:element name="Mapping">
 107                 <xs:complexType>
 108                         <xs:annotation>
 109                                 <xs:documentation>
 110                                         Represent the jalview.datamodel.Mapping object -
 111                                         it also provides
 112                                         a way of storing sequences that are mapped 'to'
 113                                         without adding them
 114                                         to the sequence set (which will mean they are
 115                                         then added to the alignment too).
 116                                 </xs:documentation>
 117                         </xs:annotation>
 118                         <xs:complexContent>
 119                                 <xs:extension base="vamsas:mapListType">
 120                                         <xs:sequence>
 121                                                 <xs:choice minOccurs="0" maxOccurs="1">
 122                                                         <xs:element ref="vamsas:Sequence" />
 123                                                         <xs:element name="dseqFor">
 124                                                                 <xs:simpleType>
 125                                                                         <xs:restriction base="xs:string">
 126                                                                                 <xs:annotation>
 127                                                                                         <xs:documentation>The sequence whose dataset sequence is to
 128                                                                                                 be referenced here
 129                                                                                         </xs:documentation>
 130                                                                                 </xs:annotation>
 131                                                                         </xs:restriction>
 132                                                                 </xs:simpleType>
 133                                                         </xs:element>
 134                                                 </xs:choice>
 135                                         </xs:sequence>
 136                                         <xs:attribute name="mappingType" type="xs:string"
 137                                                 use="optional">
 138                                                 <xs:annotation>
 139                                                         <xs:documentation>Biotype of the mapping e.g. CdsToPeptide
 140                                                         </xs:documentation>
 141                                                 </xs:annotation>
 142                                         </xs:attribute>
 143                                 </xs:extension>
 144                         </xs:complexContent>
 145                 </xs:complexType>
 146         </xs:element>
 147         <xs:element name="AlcodonFrame">
 148                 <xs:complexType>
 149                         <xs:sequence>
 150                                 <xs:element name="alcodon" minOccurs="0"
 151                                         maxOccurs="unbounded">
 152                                         <xs:complexType>
 153                                                 <xs:annotation>
 154                                                         <xs:documentation>
 155                                                                 specifies a series of aligned codons from an
 156                                                                 associated DNA sequence alignment that when translated
 157                                                                 correspond to columns of a peptide alignment.
 158                                                                 Element may have
 159                                                                 either all pos1,2,3 attributes specified, or none at all
 160                                                                 (indicating a gapped column with no translated peptide).
 161                                                         </xs:documentation>
 162                                                 </xs:annotation>
 163                                                 <xs:attribute name="pos1" type="xs:integer"
 164                                                         use="optional" />
 165                                                 <xs:attribute name="pos2" type="xs:integer"
 166                                                         use="optional" />
 167                                                 <xs:attribute name="pos3" type="xs:integer"
 168                                                         use="optional" />
 169                                         </xs:complexType>
 170                                 </xs:element>
 171                                 <xs:element name="alcodMap" minOccurs="0"
 172                                         maxOccurs="unbounded">
 173                                         <xs:complexType>
 174                                                 <xs:sequence>
 175                                                         <xs:element ref="vamsas:Mapping" maxOccurs="1"
 176                                                                 minOccurs="1">
 177                                                                 <xs:annotation>
 178                                                                         <xs:documentation>
 179                                                                                 a Mapping entry and an associated protein
 180                                                                                 sequence
 181                                                                         </xs:documentation>
 182                                                                 </xs:annotation>
 183                                                         </xs:element>
 184                                                 </xs:sequence>
 185                                                 <xs:attribute name="dnasq" type="xs:string"
 186                                                         use="required">
 187                                                         <xs:annotation>
 188                                                                 <xs:documentation>
 189                                                                         internal jalview id for the dnasq for this
 190                                                                         mapping.
 191                                                                 </xs:documentation>
 192                                                         </xs:annotation>
 193                                                 </xs:attribute>
 194                                         </xs:complexType>
 195
 196                                 </xs:element>
 197
 198                         </xs:sequence>
 199                 </xs:complexType>
 200         </xs:element>
 201         <xs:element name="Sequence">
 202                 <xs:complexType>
 203                         <xs:complexContent>
 204                                 <xs:extension base="vamsas:SequenceType">
 205                                         <xs:sequence>
 206                                                 <xs:element name="DBRef" minOccurs="0"
 207                                                         maxOccurs="unbounded">
 208                                                         <xs:complexType>
 209                                                                 <xs:sequence>
 210                                                                         <xs:element ref="vamsas:Mapping" minOccurs="0"
 211                                                                                 maxOccurs="1" />
 212                                                                 </xs:sequence>
 213                                                                 <xs:attribute name="source" type="xs:string" />
 214                                                                 <xs:attribute name="version" type="xs:string" />
 215                                                                 <xs:attribute name="accessionId" type="xs:string" />
 216                                                                 <xs:attribute name="locus" type="xs:boolean"
 217                                                                         default="false">
 218                                                                         <xs:annotation>
 219                                                                                 <xs:documentation>
 220                                                                                         true for gene locus mapping, source=species,
 221                                                                                         version=assembly, accession=chromosome
 222                                                                                 </xs:documentation>
 223                                                                         </xs:annotation>
 224                                                                 </xs:attribute>
 225                                                                 <xs:attribute name="canonical" type="xs:boolean"
 226                                                                         default="false">
 227                                                                         <xs:annotation>
 228                                                                                 <xs:documentation>
 229                                                                                         true for the representative accession for
 230                                                                                         databases where multiple accessions map to the same entry
 231                                                                                         (eg. Uniprot)
 232                                                                                 </xs:documentation>
 233                                                                         </xs:annotation>
 234                                                                 </xs:attribute>
 235                                                         </xs:complexType>
 236                                                 </xs:element>
 237                                         </xs:sequence>
 238                                         <xs:attribute name="dsseqid" type="xs:string"
 239                                                 use="optional">
 240                                                 <xs:annotation>
 241                                                         <xs:documentation>
 242                                                                 dataset sequence id for this sequence. Will be
 243                                                                 created as union of sequences.
 244                                                         </xs:documentation>
 245                                                 </xs:annotation>
 246                                         </xs:attribute>
 247                                         <xs:attribute name="biotype" type="xs:string"
 248                                                 use="optional">
 249                                                 <xs:annotation>
 250                                                         <xs:documentation>
 251                                                                 Biotype of the sequence (if known)
 252                                                         </xs:documentation>
 253                                                 </xs:annotation>
 254                                         </xs:attribute>
 255                                 </xs:extension>
 256                         </xs:complexContent>
 257                 </xs:complexType>
 258         </xs:element>
 259         <xs:element name="Annotation">
 260                 <xs:complexType>
 261                         <xs:sequence>
 262                                 <xs:element ref="vamsas:annotationElement" minOccurs="0"
 263                                         maxOccurs="unbounded" />
 264                                 <xs:element name="label" type="xs:string" />
 265                                 <xs:element name="description" type="xs:string"
 266                                         minOccurs="0" />
 267                                 <xs:element name="thresholdLine" minOccurs="0">
 268                                         <xs:complexType>
 269                                                 <xs:attribute name="label" type="xs:string" />
 270                                                 <xs:attribute name="value" type="xs:float" />
 271                                                 <xs:attribute name="colour" type="xs:int" />
 272                                         </xs:complexType>
 273                                 </xs:element>
 274                                 <xs:element name="contactmatrix"
 275                                         type="vamsas:MapOnAMatrixType" maxOccurs="unbounded" minOccurs="0">
 276                                 </xs:element>
 277                                 <xs:element name="property" type="vamsas:property"
 278                                         minOccurs="0" maxOccurs="unbounded" />
 279                         </xs:sequence>
 280                         <xs:attribute name="graph" type="xs:boolean"
 281                                 use="required" />
 282                         <xs:attribute name="graphType" type="xs:int"
 283                                 use="optional" />
 284                         <xs:attribute name="sequenceRef" type="xs:string"
 285                                 use="optional" />
 286                         <xs:attribute name="groupRef" type="xs:string"
 287                                 use="optional" />
 288                         <xs:attribute name="graphColour" type="xs:int"
 289                                 use="optional" />
 290                         <xs:attribute name="graphGroup" type="xs:int"
 291                                 use="optional" />
 292                         <xs:attribute name="graphHeight" type="xs:int"
 293                                 use="optional">
 294                                 <xs:annotation>
 295                                         <xs:documentation>height in pixels for the graph if this is a
 296                                                 graph-type annotation.
 297                                         </xs:documentation>
 298                                 </xs:annotation>
 299                         </xs:attribute>
 300                         <xs:attribute name="id" type="xs:string" use="optional" />
 301                         <xs:attribute name="scoreOnly" type="xs:boolean"
 302                                 use="optional" default="false" />
 303                         <xs:attribute name="score" type="xs:double"
 304                                 use="optional" />
 305                         <xs:attribute name="visible" type="xs:boolean"
 306                                 use="optional" />
 307                         <xs:attribute name="centreColLabels" type="xs:boolean"
 308                                 use="optional" />
 309                         <xs:attribute name="scaleColLabels" type="xs:boolean"
 310                                 use="optional" />
 311                         <xs:attribute name="showAllColLabels" type="xs:boolean"
 312                                 use="optional" />
 313
 314
 315                         <xs:attribute name="autoCalculated" type="xs:boolean"
 316                                 use="optional" default="false">
 317                                 <xs:annotation>
 318                                         <xs:documentation>is an autocalculated annotation row
 319                                         </xs:documentation>
 320                                 </xs:annotation>
 321                         </xs:attribute>
 322                         <xs:attribute name="belowAlignment" type="xs:boolean"
 323                                 use="optional" default="true">
 324                                 <xs:annotation>
 325                                         <xs:documentation>is to be shown below the alignment - introduced
 326                                                 in Jalview 2.8 for visualizing T-COFFEE alignment scores
 327                                         </xs:documentation>
 328                                 </xs:annotation>
 329                         </xs:attribute>
 330                         <xs:attribute name="calcId" type="xs:string"
 331                                 use="optional">
 332                                 <xs:annotation>
 333                                         <xs:documentation>Optional string identifier used to group sets of
 334                                                 annotation produced by a particular calculation. Values are opaque
 335                                                 strings but have semantic meaning to Jalview's renderer, data
 336                                                 importer and calculation system.
 337                                         </xs:documentation>
 338                                 </xs:annotation>
 339                         </xs:attribute>
 340                 </xs:complexType>
 341         </xs:element>
 342         <xs:element name="SequenceSet">
 343                 <xs:complexType>
 344                         <xs:sequence>
 345                                 <xs:element ref="vamsas:Sequence" minOccurs="0"
 346                                         maxOccurs="unbounded" />
 347                                 <xs:element ref="vamsas:Annotation" minOccurs="0"
 348                                         maxOccurs="unbounded" />
 349                                 <xs:element name="sequenceSetProperties" minOccurs="0"
 350                                         maxOccurs="unbounded">
 351                                         <xs:complexType>
 352                                                 <xs:attribute name="key" type="xs:string" />
 353                                                 <xs:attribute name="value" type="xs:string" />
 354                                         </xs:complexType>
 355                                 </xs:element>
 356                                 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0"
 357                                         maxOccurs="unbounded" />
 358                                 <xs:element name="Matrix" type="vamsas:MatrixType"
 359                                         minOccurs="0" maxOccurs="unbounded">
 360                                         <xs:annotation>
 361                                                 <xs:documentation>Matrices referred to by this set of sequences.
 362                                                 </xs:documentation>
 363                                         </xs:annotation>
 364                                 </xs:element>
 365                         </xs:sequence>
 366                         <xs:attribute name="gapChar" type="xs:string"
 367                                 use="required" />
 368                         <xs:attribute name="datasetId" type="xs:string"
 369                                 use="optional">
 370                                 <xs:annotation>
 371                                         <xs:documentation>
 372                                                 reference to set where jalview will gather the
 373                                                 dataset sequences for all sequences in the set.
 374                                         </xs:documentation>
 375                                 </xs:annotation>
 376                         </xs:attribute>
 377                 </xs:complexType>
 378         </xs:element>
 379         <xs:element name="annotationElement">
 380                 <xs:complexType>
 381                         <xs:sequence>
 382                                 <xs:element name="displayCharacter" type="xs:string"
 383                                         minOccurs="0" />
 384                                 <xs:element name="description" type="xs:string"
 385                                         minOccurs="0" />
 386                                 <xs:element name="secondaryStructure" minOccurs="0">
 387                                         <xs:simpleType>
 388                                                 <xs:restriction base="xs:string">
 389                                                         <xs:length value="1" />
 390                                                 </xs:restriction>
 391                                         </xs:simpleType>
 392                                 </xs:element>
 393                                 <xs:element name="value" type="xs:float" minOccurs="0" />
 394                         </xs:sequence>
 395                         <xs:attribute name="position" type="xs:int"
 396                                 use="required" />
 397                         <xs:attribute name="colour" type="xs:int" use="optional" />
 398                 </xs:complexType>
 399         </xs:element>
 400         <xs:complexType name="SequenceType">
 401                 <xs:sequence>
 402                         <xs:element name="sequence" type="xs:string" minOccurs="0" />
 403                         <xs:element name="name" type="xs:string" minOccurs="0" />
 404                 </xs:sequence>
 405                 <xs:attribute name="id" type="xs:string" />
 406                 <xs:attribute name="description" type="xs:string" />
 407         </xs:complexType>
 408         <xs:complexType name="MatrixType">
 409                 <xs:annotation>
 410                         <xs:documentation>Represents matrix data imported to Jalview, and the
 411                                 results of any derived calculations (independent of a particular
 412                                 view
 413                                 on the matrix).
 414                         </xs:documentation>
 415                 </xs:annotation>
 416                 <xs:sequence>
 417                         <xs:element name="elements" type="xs:string" minOccurs="1"
 418                                 maxOccurs="1">
 419                                 <xs:annotation>
 420                                         <xs:documentation>serialised representation of matrix as one or
 421                                                 more sets of comma separated values
 422                                         </xs:documentation>
 423                                 </xs:annotation>
 424                         </xs:element>
 425                         <xs:element name="groups" type="xs:string" minOccurs="0"
 426                                 maxOccurs="unbounded">
 427                                 <xs:annotation>
 428                                         <xs:documentation>Comma separated series of longs formed from
 429                                                 bitsets defining partitions on the rows/columns of the matrix
 430                                         </xs:documentation>
 431                                 </xs:annotation>
 432                         </xs:element>
 433                         <xs:element name="newick" type="xs:string" minOccurs="0"
 434                                 maxOccurs="unbounded">
 435                                 <xs:annotation>
 436                                         <xs:documentation>tree computed for this</xs:documentation>
 437                                 </xs:annotation>
 438                         </xs:element>
 439                         <xs:element name="property" type="vamsas:property"
 440                                 minOccurs="0" maxOccurs="unbounded" />
 441                 </xs:sequence>
 442
 443                 <xs:attribute name="type" type="xs:string" use="required" />
 444                 <xs:attribute name="rows" type="xs:integer"
 445                         use="required" />
 446                 <xs:attribute name="cols" type="xs:integer"
 447                         use="required" />
 448                 <xs:attribute name="treeMethod" type="xs:string"
 449                         use="optional" />
 450                 <xs:attribute name="cutHeight" type="xs:double"
 451                         use="optional" />
 452                 <xs:attribute name="id" type="xs:string" use="required" />
 453
 454         </xs:complexType>
 455         <xs:complexType name="MapOnAMatrixType">
 456                 <xs:annotation>
 457                         <xs:documentation>Defines a mapping from the local frame to a matrix
 458                                 and its associated data specified by MatrixType
 459                         </xs:documentation>
 460                 </xs:annotation>
 461                 <xs:sequence>
 462                         <xs:element name="property" type="vamsas:property"
 463                                 minOccurs="0" maxOccurs="unbounded" />
 464                         <xs:element name="mapping" type="vamsas:mapListType"
 465                                 minOccurs="0" maxOccurs="1">
 466                                 <xs:annotation>
 467                                         <xs:documentation>mapping from the matrix row and column positions
 468                                                 to
 469                                                 associated reference frame
 470                                         </xs:documentation>
 471                                 </xs:annotation>
 472                         </xs:element>
 473                 </xs:sequence>
 474
 475                 <xs:attribute name="matrix" type="xs:string"
 476                         use="required">
 477
 478                         <xs:annotation>
 479                                 <xs:documentation>reference to the matrix type this Map refers to
 480                                 </xs:documentation>
 481                         </xs:annotation>
 482                 </xs:attribute>
 483                 <xs:attribute name="id" type="xs:string" use="optional" />
 484         </xs:complexType>
 485         <xs:complexType name="property">
 486                 <xs:attribute name="name" type="xs:string" />
 487                 <xs:attribute name="value" type="xs:string" />
 488         </xs:complexType>
 489
 490
 491 </xs:schema>