schemas/jalview.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!--
   3   Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   4   Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   5
   6   This file is part of Jalview.
   7
   8   Jalview is free software: you can redistribute it and/or
   9   modify it under the terms of the GNU General Public License
  10   as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11
  12   Jalview is distributed in the hope that it will be useful, but
  13   WITHOUT ANY WARRANTY; without even the implied warranty
  14   of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15   PURPOSE.  See the GNU General Public License for more details.
  16
  17   You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18 -->
  19 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours" xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
  20                 <xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
  21         <xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
  22         <xs:import namespace="www.jalview.org/xml/wsparamset" schemaLocation="JalviewWsParamSet.xsd"/>
  23         <xs:complexType name="JalviewModel">
  24                 <xs:sequence>
  25                         <xs:element name="creationDate" type="xs:dateTime" />
  26                         <xs:element name="version" type="xs:string" />
  27                         <xs:element name="vamsasModel" type="vamsas:VAMSAS" />
  28                         <xs:sequence>
  29                                 <xs:element name="JSeq" maxOccurs="unbounded">
  30                                         <xs:complexType>
  31                                                 <xs:sequence>
  32                                                         <xs:element name="features"
  33                                                                 type="jv:feature" minOccurs="0" maxOccurs="unbounded" />
  34                                                         <xs:element name="pdbids" minOccurs="0"
  35                                                                 maxOccurs="unbounded">
  36                                                                 <xs:complexType>
  37                                                                         <xs:complexContent>
  38                                                                                 <xs:extension
  39                                                                                         base="jv:pdbentry">
  40                                                                                         <xs:sequence>
  41                                                                                                 <xs:element
  42                                                                                                         name="structureState" minOccurs="0"
  43                                                                                                         maxOccurs="unbounded">
  44                                                                                                         <xs:complexType>
  45                                                                                                                 <xs:simpleContent>
  46                                                                                                                         <xs:extension
  47                                                                                                                                 base="xs:string">
  48                                                                                                                                 <xs:attributeGroup
  49                                                                                                                                         ref="jv:swingwindow" />
  50                                                                                                                                 <xs:attribute
  51                                                                                                                                         name="visible" type="xs:boolean" />
  52                                                                                                                                 <xs:attribute
  53                                                                                                                                         name="viewId" type="xs:string" use="optional">
  54                                                                                                                                         <xs:annotation>
  55                                                                                                                                                 <xs:documentation>
  56                                                                                                                                                         additional
  57                                                                                                                                                         identifier
  58                                                                                                                                                         which
  59                                                                                                                                                         properly
  60                                                                                                                                                         disambiguates
  61                                                                                                                                                         the
  62                                                                                                                                                         structure
  63                                                                                                                                                         view
  64                                                                                                                                                         from
  65                                                                                                                                                         any
  66                                                                                                                                                         other
  67                                                                                                                                                         view
  68                                                                                                                                                         with
  69                                                                                                                                                         the
  70                                                                                                                                                         same
  71                                                                                                                                                         attributes.
  72                                                                                                                                                         This
  73                                                                                                                                                         is
  74                                                                                                                                                         not
  75                                                                                                                                                         an
  76                                                                                                                                                         ID,
  77                                                                                                                                                         because
  78                                                                                                                                                         it
  79                                                                                                                                                         is
  80                                                                                                                                                         possible
  81                                                                                                                                                         to
  82                                                                                                                                                         have
  83                                                                                                                                                         many
  84                                                                                                                                                         references
  85                                                                                                                                                         to
  86                                                                                                                                                         the
  87                                                                                                                                                         same
  88                                                                                                                                                         physical
  89                                                                                                                                                         structure
  90                                                                                                                                                         view
  91                                                                                                                                                         from
  92                                                                                                                                                         different
  93                                                                                                                                                         sequences
  94                                                                                                                                                         in
  95                                                                                                                                                         an
  96                                                                                                                                                         alignment.
  97                                                                                                                                                         A
  98                                                                                                                                                         structureState
  99                                                                                                                                                         element
 100                                                                                                                                                         citing
 101                                                                                                                                                         the
 102                                                                                                                                                         same
 103                                                                                                                                                         viewId
 104                                                                                                                                                         will
 105                                                                                                                                                         appear
 106                                                                                                                                                         for
 107                                                                                                                                                         each
 108                                                                                                                                                         instance.
 109                                                                                                                                                 </xs:documentation>
 110                                                                                                                                         </xs:annotation>
 111                                                                                                                                 </xs:attribute>
 112                                                                                                                                 <xs:attribute
 113                                                                                                                                         name="alignwithAlignPanel" type="xs:boolean"
 114                                                                                                                                         use="optional" default="true">
 115                                                                                                                                         <xs:annotation>
 116                                                                                                                                                 <xs:documentation>
 117                                                                                                                                                         Flag
 118                                                                                                                                                         set
 119                                                                                                                                                         if
 120                                                                                                                                                         the
 121                                                                                                                                                         alignment
 122                                                                                                                                                         panel
 123                                                                                                                                                         containing
 124                                                                                                                                                         this
 125                                                                                                                                                         JSeq
 126                                                                                                                                                         should
 127                                                                                                                                                         be
 128                                                                                                                                                         included
 129                                                                                                                                                         in
 130                                                                                                                                                         those
 131                                                                                                                                                         used
 132                                                                                                                                                         to
 133                                                                                                                                                         perform
 134                                                                                                                                                         a
 135                                                                                                                                                         structure
 136                                                                                                                                                         superposition
 137                                                                                                                                                         (since
 138                                                                                                                                                         Jalview
 139                                                                                                                                                         2.7).
 140                                                                                                                                                 </xs:documentation>
 141                                                                                                                                         </xs:annotation>
 142                                                                                                                                 </xs:attribute>
 143                                                                                                                                 <xs:attribute
 144                                                                                                                                         name="colourwithAlignPanel" type="xs:boolean"
 145                                                                                                                                         use="optional" default="false">
 146                                                                                                                                         <xs:annotation>
 147                                                                                                                                                 <xs:documentation>
 148                                                                                                                                                         Flag
 149                                                                                                                                                         set
 150                                                                                                                                                         if
 151                                                                                                                                                         the
 152                                                                                                                                                         alignment
 153                                                                                                                                                         panel
 154                                                                                                                                                         containing
 155                                                                                                                                                         this
 156                                                                                                                                                         JSeq
 157                                                                                                                                                         should
 158                                                                                                                                                         be
 159                                                                                                                                                         included
 160                                                                                                                                                         in
 161                                                                                                                                                         those
 162                                                                                                                                                         used
 163                                                                                                                                                         to
 164                                                                                                                                                         colour
 165                                                                                                                                                         its
 166                                                                                                                                                         associated
 167                                                                                                                                                         sequences
 168                                                                                                                                                         in
 169                                                                                                                                                         this
 170                                                                                                                                                         structureState(since
 171                                                                                                                                                         Jalview
 172                                                                                                                                                         2.7).
 173                                                                                                                                                 </xs:documentation>
 174                                                                                                                                         </xs:annotation>
 175                                                                                                                                 </xs:attribute>
 176                                                                                                                                 <xs:attribute
 177                                                                                                                                         name="colourByJmol" type="xs:boolean" use="optional"
 178                                                                                                                                         default="true">
 179                                                                                                                                         <xs:annotation>
 180                                                                                                                                                 <xs:documentation>
 181                                                                                                                                                         Flag
 182                                                                                                                                                         set
 183                                                                                                                                                         if
 184                                                                                                                                                         the
 185                                                                                                                                                         structure
 186                                                                                                                                                         display
 187                                                                                                                                                         is
 188                                                                                                                                                         coloured
 189                                                                                                                                                         by
 190                                                                                                                                                         the
 191                                                                                                                                                         Jmol
 192                                                                                                                                                         state,
 193                                                                                                                                                         rather
 194                                                                                                                                                         than
 195                                                                                                                                                         by
 196                                                                                                                                                         one
 197                                                                                                                                                         or
 198                                                                                                                                                         more
 199                                                                                                                                                         linked
 200                                                                                                                                                         alignment
 201                                                                                                                                                         views.
 202                                                                                                                                                 </xs:documentation>
 203                                                                                                                                         </xs:annotation>
 204                                                                                                                                 </xs:attribute>
 205
 206                                                                                                                         </xs:extension>
 207                                                                                                                 </xs:simpleContent>
 208                                                                                                         </xs:complexType>
 209                                                                                                 </xs:element>
 210                                                                                         </xs:sequence>
 211                                                                                 </xs:extension>
 212                                                                         </xs:complexContent>
 213                                                                 </xs:complexType>
 214                                                         </xs:element>
 215                                                         <xs:element name="hiddenSequences"
 216                                                                 type="xs:int" minOccurs="0" maxOccurs="unbounded" />
 217                                                 </xs:sequence>
 218                                                 <xs:attribute name="colour" type="xs:int"
 219                                                         use="optional" />
 220                                                 <xs:attribute name="start" type="xs:int"
 221                                                         use="required" />
 222                                                 <xs:attribute name="end" type="xs:int"
 223                                                         use="required" />
 224                                                 <xs:attribute name="id" type="xs:string"
 225                                                         use="required" />
 226                                                 <xs:attribute name="hidden" type="xs:boolean" />
 227                                         </xs:complexType>
 228                                 </xs:element>
 229                                 <xs:element name="JGroup" minOccurs="0"
 230                                         maxOccurs="unbounded">
 231                                         <xs:complexType>
 232                                                 <xs:sequence>
 233                                                         <xs:element name="seq" type="xs:string"
 234                                                                 maxOccurs="unbounded" />
 235                                                 </xs:sequence>
 236                                                 <xs:attribute name="start" type="xs:int" />
 237                                                 <xs:attribute name="end" type="xs:int" />
 238                                                 <xs:attribute name="name" type="xs:string" />
 239                                                 <xs:attribute name="colour" type="xs:string" />
 240                                                 <xs:attribute name="consThreshold"
 241                                                         type="xs:int" />
 242                                                 <xs:attribute name="pidThreshold" type="xs:int" />
 243                                                 <xs:attribute name="outlineColour"
 244                                                         type="xs:int" />
 245                                                 <xs:attribute name="displayBoxes"
 246                                                         type="xs:boolean" />
 247                                                 <xs:attribute name="displayText"
 248                                                         type="xs:boolean" />
 249                                                 <xs:attribute name="colourText"
 250                                                         type="xs:boolean" />
 251                                                 <xs:attribute name="textCol1" type="xs:int" />
 252                                                 <xs:attribute name="textCol2" type="xs:int" />
 253                                                 <xs:attribute name="textColThreshold"
 254                                                         type="xs:int" />
 255                                                 <xs:attribute name="showUnconserved"
 256                                                         type="xs:boolean" use="optional" />
 257                                                 <xs:attribute name="ignoreGapsinConsensus"
 258                                                         type="xs:boolean" use="optional" default="true" />
 259                                                 <xs:attribute name="showConsensusHistogram"
 260                                                         type="xs:boolean" use="optional" default="true" />
 261                                                 <xs:attribute name="showSequenceLogo"
 262                                                         type="xs:boolean" use="optional" default="false" />
 263                                                 <xs:attribute name="normaliseSequenceLogo"
 264               type="xs:boolean" use="optional" default="false" />
 265             <xs:attribute name="id" type="xs:string"
 266                                                         use="optional">
 267                                                         <xs:annotation>
 268                                                                 <xs:documentation>
 269                                                                         Optional sequence group ID (only
 270                                                                         needs to be unique for this
 271                                                                         alignment)
 272                                                                 </xs:documentation>
 273                                                         </xs:annotation>
 274                                                 </xs:attribute>
 275                                         </xs:complexType>
 276                                 </xs:element>
 277                                 <xs:element name="Viewport" maxOccurs="unbounded">
 278                                         <xs:complexType>
 279                                                 <xs:sequence>
 280                                                         <xs:element name="AnnotationColours"
 281                                                                 minOccurs="0">
 282                                                                 <xs:complexType>
 283                                                                         <xs:attribute name="aboveThreshold"
 284                                                                                 type="xs:int" />
 285                                                                         <xs:attribute name="annotation"
 286                                                                                 type="xs:string" />
 287                                                                         <xs:attribute name="minColour"
 288                                                                                 type="xs:int" />
 289                                                                         <xs:attribute name="maxColour"
 290                                                                                 type="xs:int" />
 291                                                                         <xs:attribute name="colourScheme"
 292                                                                                 type="xs:string" />
 293                                                                         <xs:attribute name="threshold"
 294                                                                                 type="xs:float" />
 295                                                                 </xs:complexType>
 296                                                         </xs:element>
 297                                                         <xs:element name="hiddenColumns"
 298                                                                 minOccurs="0" maxOccurs="unbounded">
 299                                                                 <xs:complexType>
 300                                                                         <xs:attribute name="start"
 301                                                                                 type="xs:int" />
 302                                                                         <xs:attribute name="end"
 303                                                                                 type="xs:int" />
 304                                                                 </xs:complexType>
 305                                                         </xs:element>
 306                                                         <xs:element name="calcIdParam"
 307
 308                                                         minOccurs="0" maxOccurs="unbounded">
 309                                                         <xs:complexType>
 310                                                         <xs:complexContent>
 311                                                         <xs:extension base="jvws:WebServiceParameterSet">
 312                                                         <xs:attribute name="calcId" type="xs:string" use="required">
 313                                                         <xs:annotation>
 314                                                         <xs:documentation>handle for the calculation which uses this parameter set</xs:documentation></xs:annotation>
 315                                                         </xs:attribute>
 316                                                         <xs:attribute name="needsUpdate" type="xs:boolean" use="optional" default="false">
 317                                                         <xs:annotation><xs:documentation>should the calculation be performed immediately after loading in order to refresh results</xs:documentation></xs:annotation>
 318                                                         </xs:attribute>
 319                                                         <xs:attribute name="autoUpdate" type="xs:boolean" use="required">
 320                                                         <xs:annotation><xs:documentation>should the calculation be automatically performed on edits</xs:documentation></xs:annotation>
 321                                                         </xs:attribute>
 322                                                         </xs:extension>
 323                                                         </xs:complexContent>
 324                                                         </xs:complexType>
 325                                                         </xs:element>
 326                                                 </xs:sequence>
 327                                                 <xs:attributeGroup ref="jv:swingwindow" />
 328                                                 <xs:attribute name="conservationSelected"
 329                                                         type="xs:boolean" />
 330                                                 <xs:attribute name="pidSelected"
 331                                                         type="xs:boolean" />
 332                                                 <xs:attribute name="bgColour" type="xs:string" />
 333                                                 <xs:attribute name="consThreshold"
 334                                                         type="xs:int" />
 335                                                 <xs:attribute name="pidThreshold" type="xs:int" />
 336                                                 <xs:attribute name="title" type="xs:string" />
 337                                                 <xs:attribute name="showFullId"
 338                                                         type="xs:boolean" />
 339                                                 <xs:attribute name="rightAlignIds"
 340                                                         type="xs:boolean" />
 341                                                 <xs:attribute name="showText" type="xs:boolean" />
 342                                                 <xs:attribute name="showColourText"
 343                                                         type="xs:boolean" />
 344                                                 <xs:attribute name="showUnconserved"
 345                                                         type="xs:boolean" use="optional" default="false" />
 346                                                 <xs:attribute name="showBoxes"
 347                                                         type="xs:boolean" />
 348                                                 <xs:attribute name="wrapAlignment"
 349                                                         type="xs:boolean" />
 350                                                 <xs:attribute name="renderGaps"
 351                                                         type="xs:boolean" />
 352                                                 <xs:attribute name="showSequenceFeatures"
 353                                                         type="xs:boolean" />
 354                                                 <xs:attribute name="showNPfeatureTooltip"
 355                                                         type="xs:boolean" use="optional" />
 356                                                 <xs:attribute name="showDbRefTooltip"
 357                                                         type="xs:boolean" use="optional" />
 358                                                 <xs:attribute name="followHighlight"
 359                                                         type="xs:boolean" use="optional" default="true" />
 360                                                 <xs:attribute name="followSelection"
 361                                                         type="xs:boolean" use="optional" default="true" />
 362                                                 <xs:attribute name="showAnnotation"
 363                                                         type="xs:boolean" />
 364                                                 <xs:attribute name="centreColumnLabels"
 365                                                         type="xs:boolean" use="optional" default="false" />
 366                                                 <xs:attribute name="showGroupConservation"
 367                                                         type="xs:boolean" use="optional" default="false" />
 368                                                 <xs:attribute name="showGroupConsensus"
 369                                                         type="xs:boolean" use="optional" default="false" />
 370                                                 <xs:attribute name="showConsensusHistogram"
 371                                                         type="xs:boolean" use="optional" default="true" />
 372                                                 <xs:attribute name="showSequenceLogo"
 373                                                         type="xs:boolean" use="optional" default="false" />
 374             <xs:attribute name="normaliseSequenceLogo"
 375               type="xs:boolean" use="optional" default="false" />
 376                                                 <xs:attribute name="ignoreGapsinConsensus"
 377                                                         type="xs:boolean" use="optional" default="true" />
 378
 379                                                 <xs:attribute name="startRes" type="xs:int" />
 380                                                 <xs:attribute name="startSeq" type="xs:int" />
 381                                                 <xs:attribute name="fontName" type="xs:string" />
 382                                                 <xs:attribute name="fontSize" type="xs:int" />
 383                                                 <xs:attribute name="fontStyle" type="xs:int" />
 384                                                 <xs:attribute name="viewName" type="xs:string" />
 385                                                 <xs:attribute name="sequenceSetId"
 386                                                         type="xs:string" />
 387                                                 <xs:attribute name="gatheredViews"
 388                                                         type="xs:boolean" />
 389                                                 <xs:attribute name="textCol1" type="xs:int" />
 390                                                 <xs:attribute name="textCol2" type="xs:int" />
 391                                                 <xs:attribute name="textColThreshold"
 392                                                         type="xs:int" />
 393                                                 <xs:attribute name="id" type="xs:ID"
 394                                                         use="optional">
 395                                                         <xs:annotation>
 396                                                                 <xs:documentation>
 397                                                                         unique id used by jalview to
 398                                                                         synchronize between stored and
 399                                                                         instantiated views
 400                                                                 </xs:documentation>
 401                                                         </xs:annotation>
 402                                                 </xs:attribute>
 403                                         </xs:complexType>
 404                                 </xs:element>
 405                                 <xs:element name="UserColours" minOccurs="0"
 406                                         maxOccurs="unbounded">
 407                                         <xs:complexType>
 408                                                 <xs:sequence>
 409                                                         <xs:element name="UserColourScheme"
 410                                                                 type="jalview:JalviewUserColours" />
 411                                                 </xs:sequence>
 412                                                 <xs:attribute name="id" type="xs:string" />
 413                                         </xs:complexType>
 414                                 </xs:element>
 415                                 <xs:element name="tree" minOccurs="0"
 416                                         maxOccurs="unbounded">
 417                                         <xs:complexType>
 418                                                 <xs:sequence minOccurs="0">
 419                                                         <xs:element name="title" type="xs:string" />
 420                                                         <xs:element name="newick" type="xs:string" />
 421                                                 </xs:sequence>
 422                                                 <xs:attribute name="fontName" type="xs:string" />
 423                                                 <xs:attribute name="fontSize" type="xs:int" />
 424                                                 <xs:attribute name="fontStyle" type="xs:int" />
 425                                                 <xs:attribute name="threshold" type="xs:float" />
 426                                                 <xs:attribute name="showBootstrap"
 427                                                         type="xs:boolean" />
 428                                                 <xs:attribute name="showDistances"
 429                                                         type="xs:boolean" />
 430                                                 <xs:attribute name="markUnlinked"
 431                                                         type="xs:boolean" />
 432                                                 <xs:attribute name="fitToWindow"
 433                                                         type="xs:boolean" />
 434                                                 <xs:attribute name="currentTree"
 435                                                         type="xs:boolean" />
 436                                                 <xs:attribute name="id" type="xs:ID"
 437                                                         use="optional">
 438                                                         <xs:annotation>
 439                                                                 <xs:documentation>
 440                                                                         Tree ID added for binding tree
 441                                                                         visualization settings to vamsas
 442                                                                         document trees in jalview 2.4.1
 443                                                                 </xs:documentation>
 444                                                         </xs:annotation>
 445                                                 </xs:attribute>
 446                                                 <xs:attributeGroup ref="jv:swingwindow" />
 447                                         </xs:complexType>
 448                                 </xs:element>
 449                                 <xs:element name="FeatureSettings" minOccurs="0">
 450                                         <xs:complexType>
 451                                                 <xs:sequence>
 452                                                         <xs:element name="setting" minOccurs="0"
 453                                                                 maxOccurs="unbounded">
 454                                                                 <xs:complexType>
 455                                                                         <xs:attribute name="type"
 456                                                                                 type="xs:string" use="required" />
 457                                                                         <xs:attribute name="colour"
 458                                                                                 type="xs:int" use="required" />
 459                                                                         <xs:attribute name="display"
 460                                                                                 type="xs:boolean" use="required" />
 461                                                                         <xs:attribute name="order"
 462                                                                                 type="xs:float" use="optional" />
 463                                                                         <xs:attribute name="mincolour"
 464                                                                                 type="xs:int" use="optional">
 465                                                                                 <xs:annotation>
 466                                                                                         <xs:documentation>
 467                                                                                                 Optional minimum colour
 468                                                                                                 for graduated feature
 469                                                                                                 colour
 470                                                                                         </xs:documentation>
 471                                                                                 </xs:annotation>
 472                                                                         </xs:attribute>
 473                                                                         <xs:attribute name="threshold"
 474                                                                                 type="xs:float" use="optional">
 475                                                                                 <xs:annotation>
 476                                                                                         <xs:documentation>
 477                                                                                                 threshold value for
 478                                                                                                 graduated feature colour
 479                                                                                         </xs:documentation>
 480                                                                                 </xs:annotation>
 481                                                                         </xs:attribute>
 482                                                                         <xs:attribute name="threshstate"
 483                                                                                 type="xs:int" use="optional">
 484                                                                                 <xs:annotation>
 485                                                                                         <xs:documentation>
 486                                                                                                 threshold type for
 487                                                                                                 graduated feature colour
 488                                                                                         </xs:documentation>
 489                                                                                 </xs:annotation>
 490                                                                         </xs:attribute>
 491                                                                         <xs:attribute name="max"
 492                                                                                 type="xs:float" use="optional" />
 493                                                                         <xs:attribute name="min"
 494                                                                                 type="xs:float" use="optional" />
 495                                                                         <xs:attribute name="colourByLabel"
 496                                                                                 type="xs:boolean" use="optional" />
 497                                                                         <xs:attribute name="autoScale"
 498                                                                                 type="xs:boolean" use="optional" />
 499                                                                 </xs:complexType>
 500                                                         </xs:element>
 501                                                         <xs:element name="group" minOccurs="0"
 502                                                                 maxOccurs="unbounded">
 503                                                                 <xs:complexType>
 504                                                                         <xs:attribute name="name"
 505                                                                                 type="xs:string" use="required" />
 506                                                                         <xs:attribute name="display"
 507                                                                                 type="xs:boolean" use="required" />
 508                                                                 </xs:complexType>
 509                                                         </xs:element>
 510                                                 </xs:sequence>
 511                                         </xs:complexType>
 512                                 </xs:element>
 513                         </xs:sequence>
 514                 </xs:sequence>
 515         </xs:complexType>
 516         <xs:complexType name="feature">
 517                 <xs:sequence>
 518                         <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 519                                 <xs:complexType>
 520                                         <xs:attribute name="key" type="xs:string" use="required"/>
 521                                         <xs:attribute name="value" type="xs:string" use="required"/>
 522                                 </xs:complexType>
 523                         </xs:element>
 524                 </xs:sequence>
 525                 <xs:attribute name="begin" type="xs:int" use="required"/>
 526                 <xs:attribute name="end" type="xs:int" use="required"/>
 527                 <xs:attribute name="type" type="xs:string" use="required"/>
 528                 <xs:attribute name="description" type="xs:string" use="optional"/>
 529                 <xs:attribute name="status" type="xs:string" use="optional"/>
 530                 <xs:attribute name="featureGroup" type="xs:string" use="optional"/>
 531                 <xs:attribute name="score" type="xs:float" use="optional"/>
 532         </xs:complexType>
 533         <xs:complexType name="pdbentry">
 534                 <xs:sequence minOccurs="0" maxOccurs="unbounded">
 535                         <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
 536                                 <xs:complexType>
 537                                         <xs:attribute name="name" type="xs:string" use="required"/>
 538                                         <xs:attribute name="value" type="xs:string" use="required"/>
 539                                 </xs:complexType>
 540                         </xs:element>
 541                 </xs:sequence>
 542                 <xs:attribute name="id" type="xs:string" use="required"/>
 543                 <xs:attribute name="type" type="xs:string" use="optional"/>
 544                 <xs:attribute name="file" type="xs:string"/>
 545         </xs:complexType>
 546         <!--
 547         <xs:complexType name="reportWindow">
 548         <xs:annotation>
 549         <xs:documentation>Generic type for windows containing mime-typed data associated with other jalview windows</xs:documentation>
 550         </xs:annotation>
 551         <xs:sequence>
 552         </xs:sequence>
 553     <xs:attribute name="id" type="xs:string" use="required"/>
 554     <xs:attribute name="type" type="xs:string" use="optional"/>
 555     <xs:attribute name="file" type="xs:string" use="optional"/>
 556         </xs:complexType>
 557  -->
 558     <xs:attributeGroup name="swingwindow">
 559     <xs:annotation>
 560     <xs:documentation>
 561       base attributes for windows displayed in Jalview desktop.
 562     </xs:documentation>
 563     </xs:annotation>
 564       <xs:attribute name="width" type="xs:int"/>
 565       <xs:attribute name="height" type="xs:int"/>
 566       <xs:attribute name="xpos" type="xs:int"/>
 567       <xs:attribute name="ypos" type="xs:int"/>
 568     </xs:attributeGroup>
 569 </xs:schema>