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:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
  28         xmlns:vamsas="www.vamsas.ac.uk/jalview/version2"
  29         targetNamespace="www.vamsas.ac.uk/jalview/version2"
  30         elementFormDefault="qualified" attributeFormDefault="unqualified">
  31         <xs:complexType name="VAMSAS">
  32                 <xs:sequence>
  33                         <xs:element name="Tree" type="xs:string" minOccurs="0"
  34                                 maxOccurs="unbounded" />
  35                         <xs:element ref="vamsas:SequenceSet" minOccurs="0"
  36                                 maxOccurs="unbounded" />
  37                 </xs:sequence>
  38         </xs:complexType>
  39         <xs:complexType name="mapListType">
  40                 <xs:annotation>
  41                         <xs:documentation>
  42                                 developed after mapRangeType from
  43                                 http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
  44                         </xs:documentation>
  45                         <xs:documentation>
  46                                 This effectively represents a java.util.MapList
  47                                 object
  48                         </xs:documentation>
  49                 </xs:annotation>
  50                 <xs:sequence>
  51                         <xs:element name="mapListFrom" minOccurs="0"
  52                                 maxOccurs="unbounded">
  53                                 <xs:annotation>
  54                                         <xs:documentation> a region from start to end inclusive
  55                                         </xs:documentation>
  56                                 </xs:annotation>
  57                                 <xs:complexType>
  58                                         <xs:attribute name="start" type="xs:int"
  59                                                 use="required" />
  60                                         <xs:attribute name="end" type="xs:int" use="required" />
  61                                 </xs:complexType>
  62                         </xs:element>
  63                         <xs:element name="mapListTo" minOccurs="0"
  64                                 maxOccurs="unbounded">
  65                                 <xs:annotation>
  66                                         <xs:documentation> a region from start to end inclusive
  67                                         </xs:documentation>
  68                                 </xs:annotation>
  69                                 <xs:complexType>
  70                                         <xs:attribute name="start" type="xs:int"
  71                                                 use="required" />
  72                                         <xs:attribute name="end" type="xs:int" use="required" />
  73                                 </xs:complexType>
  74                         </xs:element>
  75                 </xs:sequence>
  76                 <xs:attribute name="mapFromUnit"
  77                         type="xs:positiveInteger" use="required">
  78                         <xs:annotation>
  79                                 <xs:documentation>number of dictionary symbol widths involved in
  80                                         each
  81                                         mapped position on this sequence (for example, 3 for a dna
  82                                         sequence exon
  83                                         region that is being mapped to a protein sequence).
  84                                         This is optional,
  85                                         since the unit can be usually be inferred from the
  86                                         dictionary type of
  87                                         each sequence involved in the mapping.
  88                                 </xs:documentation>
  89                         </xs:annotation>
  90                 </xs:attribute>
  91                 <xs:attribute name="mapToUnit" type="xs:positiveInteger"
  92                         use="required">
  93                         <xs:annotation>
  94                                 <xs:documentation>number of dictionary symbol widths involved in
  95                                         each
  96                                         mapped position on this sequence (for example, 3 for a dna
  97                                         sequence exon
  98                                         region that is being mapped to a protein sequence).
  99                                         This is optional,
 100                                         since the unit can be usually be inferred from the
 101                                         dictionary type of
 102                                         each sequence involved in the mapping.
 103                                 </xs:documentation>
 104                         </xs:annotation>
 105                 </xs:attribute>
 106         </xs:complexType>
 107         <xs:element name="Mapping">
 108                 <xs:complexType>
 109                         <xs:annotation>
 110                                 <xs:documentation>
 111                                         Represent the jalview.datamodel.Mapping object -
 112                                         it also provides
 113                                         a way of storing sequences that are mapped 'to'
 114                                         without adding them
 115                                         to the sequence set (which will mean they are
 116                                         then added to the alignment too).
 117                                 </xs:documentation>
 118                         </xs:annotation>
 119                         <xs:complexContent>
 120                                 <xs:extension base="vamsas:mapListType">
 121                                         <xs:sequence>
 122                                                 <xs:choice minOccurs="0" maxOccurs="1">
 123                                                         <xs:element ref="vamsas:Sequence" />
 124                                                         <xs:element name="dseqFor">
 125                                                                 <xs:simpleType>
 126                                                                         <xs:restriction base="xs:string">
 127                                                                                 <xs:annotation>
 128                                                                                         <xs:documentation>The sequence whose dataset sequence is to
 129                                                                                                 be referenced here
 130                                                                                         </xs:documentation>
 131                                                                                 </xs:annotation>
 132                                                                         </xs:restriction>
 133                                                                 </xs:simpleType>
 134                                                         </xs:element>
 135                                                 </xs:choice>
 136                                         </xs:sequence>
 137                                         <xs:attribute name="mappingType" type="xs:string"
 138                                                 use="optional">
 139                                                 <xs:annotation>
 140                                                         <xs:documentation>Biotype of the mapping e.g. CdsToPeptide
 141                                                         </xs:documentation>
 142                                                 </xs:annotation>
 143                                         </xs:attribute>
 144                                 </xs:extension>
 145                         </xs:complexContent>
 146                 </xs:complexType>
 147         </xs:element>
 148         <xs:element name="AlcodonFrame">
 149                 <xs:complexType>
 150                         <xs:sequence>
 151                                 <xs:element name="alcodon" minOccurs="0"
 152                                         maxOccurs="unbounded">
 153                                         <xs:complexType>
 154                                                 <xs:annotation>
 155                                                         <xs:documentation>
 156                                                                 specifies a series of aligned codons from an
 157                                                                 associated DNA sequence alignment that when translated
 158                                                                 correspond to columns of a peptide alignment.
 159                                                                 Element may have
 160                                                                 either all pos1,2,3 attributes specified, or none at all
 161                                                                 (indicating a gapped column with no translated peptide).
 162                                                         </xs:documentation>
 163                                                 </xs:annotation>
 164                                                 <xs:attribute name="pos1" type="xs:integer"
 165                                                         use="optional" />
 166                                                 <xs:attribute name="pos2" type="xs:integer"
 167                                                         use="optional" />
 168                                                 <xs:attribute name="pos3" type="xs:integer"
 169                                                         use="optional" />
 170                                         </xs:complexType>
 171                                 </xs:element>
 172                                 <xs:element name="alcodMap" minOccurs="0"
 173                                         maxOccurs="unbounded">
 174                                         <xs:complexType>
 175                                                 <xs:sequence>
 176                                                         <xs:element ref="vamsas:Mapping" maxOccurs="1"
 177                                                                 minOccurs="1">
 178                                                                 <xs:annotation>
 179                                                                         <xs:documentation>
 180                                                                                 a Mapping entry and an associated protein
 181                                                                                 sequence
 182                                                                         </xs:documentation>
 183                                                                 </xs:annotation>
 184                                                         </xs:element>
 185                                                 </xs:sequence>
 186                                                 <xs:attribute name="dnasq" type="xs:string"
 187                                                         use="required">
 188                                                         <xs:annotation>
 189                                                                 <xs:documentation>
 190                                                                         internal jalview id for the dnasq for this
 191                                                                         mapping.
 192                                                                 </xs:documentation>
 193                                                         </xs:annotation>
 194                                                 </xs:attribute>
 195                                         </xs:complexType>
 196
 197                                 </xs:element>
 198
 199                         </xs:sequence>
 200                 </xs:complexType>
 201         </xs:element>
 202         <xs:element name="Sequence">
 203                 <xs:complexType>
 204                         <xs:complexContent>
 205                                 <xs:extension base="vamsas:SequenceType">
 206                                         <xs:sequence>
 207                                                 <xs:element name="DBRef" minOccurs="0"
 208                                                         maxOccurs="unbounded">
 209                                                         <xs:complexType>
 210                                                                 <xs:sequence>
 211                                                                         <xs:element ref="vamsas:Mapping" minOccurs="0"
 212                                                                                 maxOccurs="1" />
 213                                                                 </xs:sequence>
 214                                                                 <xs:attribute name="source" type="xs:string" />
 215                                                                 <xs:attribute name="version" type="xs:string" />
 216                                                                 <xs:attribute name="accessionId" type="xs:string" />
 217                                                                 <xs:attribute name="locus" type="xs:boolean"
 218                                                                         default="false">
 219                                                                         <xs:annotation>
 220                                                                                 <xs:documentation>
 221                                                                                         true for gene locus mapping, source=species,
 222                                                                                         version=assembly, accession=chromosome
 223                                                                                 </xs:documentation>
 224                                                                         </xs:annotation>
 225                                                                 </xs:attribute>
 226                                                                 <xs:attribute name="canonical" type="xs:boolean"
 227                                                                         default="false">
 228                                                                         <xs:annotation>
 229                                                                                 <xs:documentation>
 230                                                                                         true for the representative accession for
 231                                                                                         databases where multiple accessions map to the same entry
 232                                                                                         (eg. Uniprot)
 233                                                                                 </xs:documentation>
 234                                                                         </xs:annotation>
 235                                                                 </xs:attribute>
 236                                                         </xs:complexType>
 237                                                 </xs:element>
 238                                         </xs:sequence>
 239                                         <xs:attribute name="dsseqid" type="xs:string"
 240                                                 use="optional">
 241                                                 <xs:annotation>
 242                                                         <xs:documentation>
 243                                                                 dataset sequence id for this sequence. Will be
 244                                                                 created as union of sequences.
 245                                                         </xs:documentation>
 246                                                 </xs:annotation>
 247                                         </xs:attribute>
 248                                         <xs:attribute name="biotype" type="xs:string"
 249                                                 use="optional">
 250                                                 <xs:annotation>
 251                                                         <xs:documentation>
 252                                                                 Biotype of the sequence (if known)
 253                                                         </xs:documentation>
 254                                                 </xs:annotation>
 255                                         </xs:attribute>
 256                                 </xs:extension>
 257                         </xs:complexContent>
 258                 </xs:complexType>
 259         </xs:element>
 260         <xs:element name="Annotation">
 261                 <xs:complexType>
 262                         <xs:sequence>
 263                                 <xs:element ref="vamsas:annotationElement" minOccurs="0"
 264                                         maxOccurs="unbounded" />
 265                                 <xs:element name="label" type="xs:string" />
 266                                 <xs:element name="description" type="xs:string"
 267                                         minOccurs="0" />
 268                                 <xs:element name="thresholdLine" minOccurs="0">
 269                                         <xs:complexType>
 270                                                 <xs:attribute name="label" type="xs:string" />
 271                                                 <xs:attribute name="value" type="xs:float" />
 272                                                 <xs:attribute name="colour" type="xs:int" />
 273                                         </xs:complexType>
 274                                 </xs:element>
 275                                 <xs:element name="contactmatrix"
 276                                         type="vamsas:MapOnAMatrixType" maxOccurs="unbounded" minOccurs="0">
 277                                 </xs:element>
 278                                 <xs:element name="property" type="vamsas:property"
 279                                         minOccurs="0" maxOccurs="unbounded" />
 280                         </xs:sequence>
 281                         <xs:attribute name="graph" type="xs:boolean"
 282                                 use="required" />
 283                         <xs:attribute name="graphType" type="xs:int"
 284                                 use="optional" />
 285                         <xs:attribute name="sequenceRef" type="xs:string"
 286                                 use="optional" />
 287                         <xs:attribute name="groupRef" type="xs:string"
 288                                 use="optional" />
 289                         <xs:attribute name="graphColour" type="xs:int"
 290                                 use="optional" />
 291                         <xs:attribute name="graphGroup" type="xs:int"
 292                                 use="optional" />
 293                         <xs:attribute name="graphHeight" type="xs:int"
 294                                 use="optional">
 295                                 <xs:annotation>
 296                                         <xs:documentation>height in pixels for the graph if this is a
 297                                                 graph-type annotation.
 298                                         </xs:documentation>
 299                                 </xs:annotation>
 300                         </xs:attribute>
 301                         <xs:attribute name="id" type="xs:string" use="optional" />
 302                         <xs:attribute name="scoreOnly" type="xs:boolean"
 303                                 use="optional" default="false" />
 304                         <xs:attribute name="score" type="xs:double"
 305                                 use="optional" />
 306                         <xs:attribute name="visible" type="xs:boolean"
 307                                 use="optional" />
 308                         <xs:attribute name="centreColLabels" type="xs:boolean"
 309                                 use="optional" />
 310                         <xs:attribute name="scaleColLabels" type="xs:boolean"
 311                                 use="optional" />
 312                         <xs:attribute name="showAllColLabels" type="xs:boolean"
 313                                 use="optional" />
 314
 315
 316                         <xs:attribute name="autoCalculated" type="xs:boolean"
 317                                 use="optional" default="false">
 318                                 <xs:annotation>
 319                                         <xs:documentation>is an autocalculated annotation row
 320                                         </xs:documentation>
 321                                 </xs:annotation>
 322                         </xs:attribute>
 323                         <xs:attribute name="belowAlignment" type="xs:boolean"
 324                                 use="optional" default="true">
 325                                 <xs:annotation>
 326                                         <xs:documentation>is to be shown below the alignment - introduced
 327                                                 in Jalview 2.8 for visualizing T-COFFEE alignment scores
 328                                         </xs:documentation>
 329                                 </xs:annotation>
 330                         </xs:attribute>
 331                         <xs:attribute name="calcId" type="xs:string"
 332                                 use="optional">
 333                                 <xs:annotation>
 334                                         <xs:documentation>Optional string identifier used to group sets of
 335                                                 annotation produced by a particular calculation. Values are opaque
 336                                                 strings but have semantic meaning to Jalview's renderer, data
 337                                                 importer and calculation system.
 338                                         </xs:documentation>
 339                                 </xs:annotation>
 340                         </xs:attribute>
 341                 </xs:complexType>
 342         </xs:element>
 343         <xs:element name="SequenceSet">
 344                 <xs:complexType>
 345                         <xs:sequence>
 346                                 <xs:element ref="vamsas:Sequence" minOccurs="0"
 347                                         maxOccurs="unbounded" />
 348                                 <xs:element ref="vamsas:Annotation" minOccurs="0"
 349                                         maxOccurs="unbounded" />
 350                                 <xs:element name="sequenceSetProperties" minOccurs="0"
 351                                         maxOccurs="unbounded">
 352                                         <xs:complexType>
 353                                                 <xs:attribute name="key" type="xs:string" />
 354                                                 <xs:attribute name="value" type="xs:string" />
 355                                         </xs:complexType>
 356                                 </xs:element>
 357                                 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0"
 358                                         maxOccurs="unbounded" />
 359                                 <xs:element name="Matrices" type="vamsas:MatrixType"
 360                                         minOccurs="0" maxOccurs="unbounded">
 361                                         <xs:annotation>
 362                                                 <xs:documentation>Matrices referred to by this set of sequences.
 363                                                 </xs:documentation>
 364                                         </xs:annotation>
 365                                 </xs:element>
 366                         </xs:sequence>
 367                         <xs:attribute name="gapChar" type="xs:string"
 368                                 use="required" />
 369                         <xs:attribute name="datasetId" type="xs:string"
 370                                 use="optional">
 371                                 <xs:annotation>
 372                                         <xs:documentation>
 373                                                 reference to set where jalview will gather the
 374                                                 dataset sequences for all sequences in the set.
 375                                         </xs:documentation>
 376                                 </xs:annotation>
 377                         </xs:attribute>
 378                 </xs:complexType>
 379         </xs:element>
 380         <xs:element name="annotationElement">
 381                 <xs:complexType>
 382                         <xs:sequence>
 383                                 <xs:element name="displayCharacter" type="xs:string"
 384                                         minOccurs="0" />
 385                                 <xs:element name="description" type="xs:string"
 386                                         minOccurs="0" />
 387                                 <xs:element name="secondaryStructure" minOccurs="0">
 388                                         <xs:simpleType>
 389                                                 <xs:restriction base="xs:string">
 390                                                         <xs:length value="1" />
 391                                                 </xs:restriction>
 392                                         </xs:simpleType>
 393                                 </xs:element>
 394                                 <xs:element name="value" type="xs:float" minOccurs="0" />
 395                         </xs:sequence>
 396                         <xs:attribute name="position" type="xs:int"
 397                                 use="required" />
 398                         <xs:attribute name="colour" type="xs:int" use="optional" />
 399                 </xs:complexType>
 400         </xs:element>
 401         <xs:complexType name="SequenceType">
 402                 <xs:sequence>
 403                         <xs:element name="sequence" type="xs:string" minOccurs="0" />
 404                         <xs:element name="name" type="xs:string" minOccurs="0" />
 405                 </xs:sequence>
 406                 <xs:attribute name="id" type="xs:string" />
 407                 <xs:attribute name="description" type="xs:string" />
 408         </xs:complexType>
 409         <xs:complexType name="MatrixType">
 410                 <xs:annotation>
 411                         <xs:documentation>Represents matrix data imported to Jalview, and the
 412                                 results of any derived calculations (independent of a particular
 413                                 view
 414                                 on the matrix).
 415                         </xs:documentation>
 416                 </xs:annotation>
 417                 <xs:sequence>
 418                         <xs:element name="elements" type="xs:string" minOccurs="1"
 419                                 maxOccurs="1">
 420                                 <xs:annotation>
 421                                         <xs:documentation>serialised representation of matrix as one or
 422                                                 more sets of comma separated values
 423                                         </xs:documentation>
 424                                 </xs:annotation>
 425                         </xs:element>
 426                         <xs:element name="groups" type="xs:string" minOccurs="0"
 427                                 maxOccurs="unbounded">
 428                                 <xs:annotation>
 429                                         <xs:documentation>Comma separated series of longs formed from
 430                                                 bitsets defining partitions on the rows/columns of the matrix
 431                                         </xs:documentation>
 432                                 </xs:annotation>
 433                         </xs:element>
 434                         <xs:element name="newick" type="xs:string" minOccurs="0"
 435                                 maxOccurs="unbounded">
 436                                 <xs:annotation>
 437                                         <xs:documentation>tree computed for this</xs:documentation>
 438                                 </xs:annotation>
 439                         </xs:element>
 440                         <xs:element name="property" type="vamsas:property"
 441                                 minOccurs="0" maxOccurs="unbounded" />
 442                 </xs:sequence>
 443
 444                 <xs:attribute name="type" type="xs:string" use="required" />
 445                 <xs:attribute name="rows" type="xs:integer"
 446                         use="required" />
 447                 <xs:attribute name="cols" type="xs:integer"
 448                         use="required" />
 449                 <xs:attribute name="treeMethod" type="xs:string"
 450                         use="optional" />
 451                 <xs:attribute name="cutHeight" type="xs:double"
 452                         use="optional" />
 453                 <xs:attribute name="id" type="xs:string" use="required" />
 454
 455         </xs:complexType>
 456         <xs:complexType name="MapOnAMatrixType">
 457                 <xs:annotation>
 458                         <xs:documentation>Defines a mapping from the local frame to a matrix
 459                                 and its associated data specified by MatrixType
 460                         </xs:documentation>
 461                 </xs:annotation>
 462                 <xs:sequence>
 463                         <xs:element name="property" type="vamsas:property"
 464                                 minOccurs="0" maxOccurs="unbounded" />
 465                         <xs:element name="mapping" type="vamsas:mapListType"
 466                                 minOccurs="0" maxOccurs="1">
 467                                 <xs:annotation>
 468                                         <xs:documentation>mapping from the matrix row and column positions
 469                                                 to
 470                                                 associated reference frame
 471                                         </xs:documentation>
 472                                 </xs:annotation>
 473                         </xs:element>
 474                 </xs:sequence>
 475
 476                 <xs:attribute name="matrix" type="xs:string"
 477                         use="required">
 478
 479                         <xs:annotation>
 480                                 <xs:documentation>reference to the matrix type this Map refers to
 481                                 </xs:documentation>
 482                         </xs:annotation>
 483                 </xs:attribute>
 484                 <xs:attribute name="id" type="xs:string" use="optional" />
 485         </xs:complexType>
 486         <xs:complexType name="property">
 487                 <xs:attribute name="name" type="xs:string" />
 488                 <xs:attribute name="value" type="xs:string" />
 489         </xs:complexType>
 490
 491
 492 </xs:schema>