schemas/jalview.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 <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">
  21                 <xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
  22         <xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
  23         <xs:import namespace="www.jalview.org/xml/wsparamset" schemaLocation="JalviewWsParamSet.xsd"/>
  24         <xs:complexType name="JalviewModel">
  25                 <xs:sequence>
  26                         <xs:element name="creationDate" type="xs:dateTime" />
  27                         <xs:element name="version" type="xs:string" />
  28                         <xs:element name="vamsasModel" type="vamsas:VAMSAS" />
  29                         <xs:sequence>
  30                                 <xs:element name="JSeq" maxOccurs="unbounded" minOccurs="0">
  31                                         <xs:complexType>
  32                                                 <xs:sequence>
  33                                                         <xs:element name="features"
  34                                                                 type="jv:feature" minOccurs="0" maxOccurs="unbounded" />
  35                                                         <xs:element name="pdbids" minOccurs="0"
  36                                                                 maxOccurs="unbounded">
  37                                                                 <xs:complexType>
  38                                                                         <xs:complexContent>
  39                                                                                 <xs:extension
  40                                                                                         base="jv:pdbentry">
  41                                                                                         <xs:sequence>
  42                                                                                                 <xs:element
  43                                                                                                         name="structureState" minOccurs="0"
  44                                                                                                         maxOccurs="unbounded">
  45                                                                                                         <xs:complexType>
  46                                                                                                                 <xs:simpleContent>
  47                                                                                                                         <xs:extension
  48                                                                                                                                 base="xs:string">
  49                                                                                                                                 <xs:attributeGroup
  50                                                                                                                                         ref="jv:swingwindow" />
  51                                                                                                                                 <xs:attribute
  52                                                                                                                                         name="visible" type="xs:boolean" />
  53                                                                                                                                 <xs:attribute
  54                                                                                                                                         name="viewId" type="xs:string" use="optional">
  55                                                                                                                                         <xs:annotation>
  56                                                                                                                                                 <xs:documentation>
  57                                                                                                                                                         additional
  58                                                                                                                                                         identifier
  59                                                                                                                                                         which
  60                                                                                                                                                         properly
  61                                                                                                                                                         disambiguates
  62                                                                                                                                                         the
  63                                                                                                                                                         structure
  64                                                                                                                                                         view
  65                                                                                                                                                         from
  66                                                                                                                                                         any
  67                                                                                                                                                         other
  68                                                                                                                                                         view
  69                                                                                                                                                         with
  70                                                                                                                                                         the
  71                                                                                                                                                         same
  72                                                                                                                                                         attributes.
  73                                                                                                                                                         This
  74                                                                                                                                                         is
  75                                                                                                                                                         not
  76                                                                                                                                                         an
  77                                                                                                                                                         ID,
  78                                                                                                                                                         because
  79                                                                                                                                                         it
  80                                                                                                                                                         is
  81                                                                                                                                                         possible
  82                                                                                                                                                         to
  83                                                                                                                                                         have
  84                                                                                                                                                         many
  85                                                                                                                                                         references
  86                                                                                                                                                         to
  87                                                                                                                                                         the
  88                                                                                                                                                         same
  89                                                                                                                                                         physical
  90                                                                                                                                                         structure
  91                                                                                                                                                         view
  92                                                                                                                                                         from
  93                                                                                                                                                         different
  94                                                                                                                                                         sequences
  95                                                                                                                                                         in
  96                                                                                                                                                         an
  97                                                                                                                                                         alignment.
  98                                                                                                                                                         A
  99                                                                                                                                                         structureState
 100                                                                                                                                                         element
 101                                                                                                                                                         citing
 102                                                                                                                                                         the
 103                                                                                                                                                         same
 104                                                                                                                                                         viewId
 105                                                                                                                                                         will
 106                                                                                                                                                         appear
 107                                                                                                                                                         for
 108                                                                                                                                                         each
 109                                                                                                                                                         instance.
 110                                                                                                                                                 </xs:documentation>
 111                                                                                                                                         </xs:annotation>
 112                                                                                                                                 </xs:attribute>
 113                                                                                                                                 <xs:attribute
 114                                                                                                                                         name="alignwithAlignPanel" type="xs:boolean"
 115                                                                                                                                         use="optional" default="true">
 116                                                                                                                                         <xs:annotation>
 117                                                                                                                                                 <xs:documentation>
 118                                                                                                                                                         Flag
 119                                                                                                                                                         set
 120                                                                                                                                                         if
 121                                                                                                                                                         the
 122                                                                                                                                                         alignment
 123                                                                                                                                                         panel
 124                                                                                                                                                         containing
 125                                                                                                                                                         this
 126                                                                                                                                                         JSeq
 127                                                                                                                                                         should
 128                                                                                                                                                         be
 129                                                                                                                                                         included
 130                                                                                                                                                         in
 131                                                                                                                                                         those
 132                                                                                                                                                         used
 133                                                                                                                                                         to
 134                                                                                                                                                         perform
 135                                                                                                                                                         a
 136                                                                                                                                                         structure
 137                                                                                                                                                         superposition
 138                                                                                                                                                         (since
 139                                                                                                                                                         Jalview
 140                                                                                                                                                         2.7).
 141                                                                                                                                                 </xs:documentation>
 142                                                                                                                                         </xs:annotation>
 143                                                                                                                                 </xs:attribute>
 144                                                                                                                                 <xs:attribute
 145                                                                                                                                         name="colourwithAlignPanel" type="xs:boolean"
 146                                                                                                                                         use="optional" default="false">
 147                                                                                                                                         <xs:annotation>
 148                                                                                                                                                 <xs:documentation>
 149                                                                                                                                                         Flag
 150                                                                                                                                                         set
 151                                                                                                                                                         if
 152                                                                                                                                                         the
 153                                                                                                                                                         alignment
 154                                                                                                                                                         panel
 155                                                                                                                                                         containing
 156                                                                                                                                                         this
 157                                                                                                                                                         JSeq
 158                                                                                                                                                         should
 159                                                                                                                                                         be
 160                                                                                                                                                         included
 161                                                                                                                                                         in
 162                                                                                                                                                         those
 163                                                                                                                                                         used
 164                                                                                                                                                         to
 165                                                                                                                                                         colour
 166                                                                                                                                                         its
 167                                                                                                                                                         associated
 168                                                                                                                                                         sequences
 169                                                                                                                                                         in
 170                                                                                                                                                         this
 171                                                                                                                                                         structureState(since
 172                                                                                                                                                         Jalview
 173                                                                                                                                                         2.7).
 174                                                                                                                                                 </xs:documentation>
 175                                                                                                                                         </xs:annotation>
 176                                                                                                                                 </xs:attribute>
 177                                                                                                                                 <xs:attribute
 178                                                                                                                                         name="colourByJmol" type="xs:boolean" use="optional"
 179                                                                                                                                         default="true">
 180                                                                                                                                         <xs:annotation>
 181                                                                                                                                                 <xs:documentation>
 182                                                                                                                                                         Flag
 183                                                                                                                                                         set
 184                                                                                                                                                         if
 185                                                                                                                                                         the
 186                                                                                                                                                         structure
 187                                                                                                                                                         display
 188                                                                                                                                                         is
 189                                                                                                                                                         coloured
 190                                                                                                                                                         by
 191                                                                                                                                                         the
 192                                                                                                                                                         Jmol
 193                                                                                                                                                         state,
 194                                                                                                                                                         rather
 195                                                                                                                                                         than
 196                                                                                                                                                         by
 197                                                                                                                                                         one
 198                                                                                                                                                         or
 199                                                                                                                                                         more
 200                                                                                                                                                         linked
 201                                                                                                                                                         alignment
 202                                                                                                                                                         views.
 203                                                                                                                                                 </xs:documentation>
 204                                                                                                                                         </xs:annotation>
 205                                                                                                                                 </xs:attribute>
 206                                                                                                                                 <xs:attribute name="type" type="xs:string"
 207                                                                                                                                         use="optional">
 208                                                                                                                                         <xs:annotation>
 209                                                                                                                                                 <xs:documentation>
 210                                                                                                                                                         An identifier for the viewer type, currently either
 211                                                                                                                                                         JMOL or CHIMERA
 212                                                                                                                                                 </xs:documentation>
 213                                                                                                                                         </xs:annotation>
 214                                                                                                                                 </xs:attribute>
 215
 216                                                                                                                         </xs:extension>
 217                                                                                                                 </xs:simpleContent>
 218                                                                                                         </xs:complexType>
 219                                                                                                 </xs:element>
 220                                                                                         </xs:sequence>
 221                                                                                 </xs:extension>
 222                                                                         </xs:complexContent>
 223                                                                 </xs:complexType>
 224                                                         </xs:element>
 225                                                         <xs:element name="hiddenSequences"
 226                                                                 type="xs:int" minOccurs="0" maxOccurs="unbounded" />
 227                                                 </xs:sequence>
 228                                                 <xs:attribute name="colour" type="xs:int"
 229                                                         use="optional" />
 230                                                 <xs:attribute name="start" type="xs:int"
 231                                                         use="required" />
 232                                                 <xs:attribute name="end" type="xs:int"
 233                                                         use="required" />
 234                                                 <xs:attribute name="id" type="xs:string"
 235                                                         use="required" />
 236                                                 <xs:attribute name="hidden" type="xs:boolean" />
 237                                         </xs:complexType>
 238                                 </xs:element>
 239                                 <xs:element name="JGroup" minOccurs="0"
 240                                         maxOccurs="unbounded">
 241                                         <xs:complexType>
 242             <xs:sequence>
 243                                                         <xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
 244                                                         <xs:element name="annotationColours" type="jv:AnnotationColourScheme"
 245                                                                 minOccurs="0" maxOccurs="1" />
 246                                                 </xs:sequence>
 247                                                 <xs:attribute name="start" type="xs:int" />
 248                                                 <xs:attribute name="end" type="xs:int" />
 249                                                 <xs:attribute name="name" type="xs:string" />
 250                                                 <xs:attribute name="colour" type="xs:string" />
 251                                                 <xs:attribute name="consThreshold"
 252                                                         type="xs:int" />
 253                                                 <xs:attribute name="pidThreshold" type="xs:int" />
 254                                                 <xs:attribute name="outlineColour"
 255                                                         type="xs:int" />
 256                                                 <xs:attribute name="displayBoxes"
 257                                                         type="xs:boolean" />
 258                                                 <xs:attribute name="displayText"
 259                                                         type="xs:boolean" />
 260                                                 <xs:attribute name="colourText"
 261                                                         type="xs:boolean" />
 262                                                 <xs:attribute name="textCol1" type="xs:int" />
 263                                                 <xs:attribute name="textCol2" type="xs:int" />
 264                                                 <xs:attribute name="textColThreshold"
 265                                                         type="xs:int" />
 266                                                 <xs:attribute name="showUnconserved"
 267                                                         type="xs:boolean" use="optional" />
 268                                                 <xs:attribute name="ignoreGapsinConsensus"
 269                                                         type="xs:boolean" use="optional" default="true" />
 270                                                 <xs:attribute name="showConsensusHistogram"
 271                                                         type="xs:boolean" use="optional" default="true" />
 272                                                 <xs:attribute name="showSequenceLogo"
 273                                                         type="xs:boolean" use="optional" default="false" />
 274                                                 <xs:attribute name="normaliseSequenceLogo"
 275               type="xs:boolean" use="optional" default="false" />
 276             <xs:attribute name="id" type="xs:string"
 277                                                         use="optional">
 278                                                         <xs:annotation>
 279                                                                 <xs:documentation>
 280                                                                         Optional sequence group ID (only
 281                                                                         needs to be unique for this
 282                                                                         alignment)
 283                                                                 </xs:documentation>
 284                                                         </xs:annotation>
 285                                                 </xs:attribute>
 286                                         </xs:complexType>
 287                                 </xs:element>
 288                                 <xs:element name="Viewport" maxOccurs="unbounded" minOccurs="0">
 289                                         <xs:complexType>
 290                                                 <xs:sequence>
 291                                                         <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
 292                                                                 minOccurs="0" maxOccurs="1">
 293                                                         </xs:element>
 294                                                         <xs:element name="hiddenColumns"
 295                                                                 minOccurs="0" maxOccurs="unbounded">
 296                                                                 <xs:complexType>
 297                                                                         <xs:attribute name="start"
 298                                                                                 type="xs:int" />
 299                                                                         <xs:attribute name="end"
 300                                                                                 type="xs:int" />
 301                                                                 </xs:complexType>
 302                                                         </xs:element>
 303                                                         <xs:element name="calcIdParam"
 304
 305                                                         minOccurs="0" maxOccurs="unbounded">
 306                                                         <xs:complexType>
 307                                                         <xs:complexContent>
 308                                                         <xs:extension base="jvws:WebServiceParameterSet">
 309                                                         <xs:attribute name="calcId" type="xs:string" use="required">
 310                                                         <xs:annotation>
 311                                                         <xs:documentation>handle for the calculation which uses this parameter set</xs:documentation></xs:annotation>
 312                                                         </xs:attribute>
 313                                                         <xs:attribute name="needsUpdate" type="xs:boolean" use="optional" default="false">
 314                                                         <xs:annotation><xs:documentation>should the calculation be performed immediately after loading in order to refresh results</xs:documentation></xs:annotation>
 315                                                         </xs:attribute>
 316                                                         <xs:attribute name="autoUpdate" type="xs:boolean" use="required">
 317                                                         <xs:annotation><xs:documentation>should the calculation be automatically performed on edits</xs:documentation></xs:annotation>
 318                                                         </xs:attribute>
 319                                                         </xs:extension>
 320                                                         </xs:complexContent>
 321                                                         </xs:complexType>
 322                                                         </xs:element>
 323                                                 </xs:sequence>
 324                                                 <xs:attributeGroup ref="jv:swingwindow" />
 325                                                 <xs:attribute name="conservationSelected"
 326                                                         type="xs:boolean" />
 327                                                 <xs:attribute name="pidSelected"
 328                                                         type="xs:boolean" />
 329                                                 <xs:attribute name="bgColour" type="xs:string" />
 330                                                 <xs:attribute name="consThreshold"
 331                                                         type="xs:int" />
 332                                                 <xs:attribute name="pidThreshold" type="xs:int" />
 333                                                 <xs:attribute name="title" type="xs:string" />
 334                                                 <xs:attribute name="showFullId"
 335                                                         type="xs:boolean" />
 336                                                 <xs:attribute name="rightAlignIds"
 337                                                         type="xs:boolean" />
 338                                                 <xs:attribute name="showText" type="xs:boolean" />
 339                                                 <xs:attribute name="showColourText"
 340                                                         type="xs:boolean" />
 341                                                 <xs:attribute name="showUnconserved"
 342                                                         type="xs:boolean" use="optional" default="false" />
 343                                                 <xs:attribute name="showBoxes"
 344                                                         type="xs:boolean" />
 345                                                 <xs:attribute name="wrapAlignment"
 346                                                         type="xs:boolean" />
 347                                                 <xs:attribute name="renderGaps"
 348                                                         type="xs:boolean" />
 349                                                 <xs:attribute name="showSequenceFeatures"
 350                                                         type="xs:boolean" />
 351                                                 <xs:attribute name="showNPfeatureTooltip"
 352                                                         type="xs:boolean" use="optional" />
 353                                                 <xs:attribute name="showDbRefTooltip"
 354                                                         type="xs:boolean" use="optional" />
 355                                                 <xs:attribute name="followHighlight"
 356                                                         type="xs:boolean" use="optional" default="true" />
 357                                                 <xs:attribute name="followSelection"
 358                                                         type="xs:boolean" use="optional" default="true" />
 359                                                 <xs:attribute name="showAnnotation"
 360                                                         type="xs:boolean" />
 361                                                 <xs:attribute name="centreColumnLabels"
 362                                                         type="xs:boolean" use="optional" default="false" />
 363                                                 <xs:attribute name="showGroupConservation"
 364                                                         type="xs:boolean" use="optional" default="false" />
 365                                                 <xs:attribute name="showGroupConsensus"
 366                                                         type="xs:boolean" use="optional" default="false" />
 367                                                 <xs:attribute name="showConsensusHistogram"
 368                                                         type="xs:boolean" use="optional" default="true" />
 369                                                 <xs:attribute name="showSequenceLogo"
 370                                                         type="xs:boolean" use="optional" default="false" />
 371                                     <xs:attribute name="normaliseSequenceLogo"
 372                                       type="xs:boolean" use="optional" default="false" />
 373                                                 <xs:attribute name="ignoreGapsinConsensus"
 374                                                         type="xs:boolean" use="optional" default="true" />
 375                                                         <xs:attribute name="startRes" type="xs:int" />
 376                                                 <xs:attribute name="startSeq" type="xs:int" />
 377                                                 <xs:attribute name="fontName" type="xs:string" />
 378                                                 <xs:attribute name="fontSize" type="xs:int" />
 379                                                 <xs:attribute name="fontStyle" type="xs:int" />
 380                                                 <xs:attribute name="viewName" type="xs:string" />
 381                                                 <xs:attribute name="sequenceSetId"
 382                                                         type="xs:string" />
 383                                                 <xs:attribute name="gatheredViews"
 384                                                         type="xs:boolean" />
 385                                                 <xs:attribute name="textCol1" type="xs:int" />
 386                                                 <xs:attribute name="textCol2" type="xs:int" />
 387                                                 <xs:attribute name="textColThreshold"
 388                                                         type="xs:int" />
 389                                                 <xs:attribute name="id" type="xs:ID"
 390                                                         use="optional">
 391                                                         <xs:annotation>
 392                                                                 <xs:documentation>
 393                                                                         unique id used by jalview to
 394                                                                         synchronize between stored and
 395                                                                         instantiated views
 396                                                                 </xs:documentation>
 397                                                         </xs:annotation>
 398                                                 </xs:attribute>
 399                                                 <xs:attribute name="complementId" type="xs:string"
 400                                                         use="optional">
 401                                                         <xs:annotation>
 402                                                                 <xs:documentation>
 403                                                                         The viewport id of this viewport's (cdna/protein) coding complement, if any
 404                                                                 </xs:documentation>
 405                                                         </xs:annotation>
 406                                                 </xs:attribute>
 407                                         </xs:complexType>
 408                                 </xs:element>
 409                                 <xs:element name="UserColours" minOccurs="0"
 410                                         maxOccurs="unbounded">
 411                                         <xs:complexType>
 412                                                 <xs:sequence>
 413                                                         <xs:element name="UserColourScheme"
 414                                                                 type="jalview:JalviewUserColours" />
 415                                                 </xs:sequence>
 416                                                 <xs:attribute name="id" type="xs:string" />
 417                                         </xs:complexType>
 418                                 </xs:element>
 419                                 <xs:element name="tree" minOccurs="0"
 420                                         maxOccurs="unbounded">
 421                                         <xs:complexType>
 422                                                 <xs:sequence minOccurs="0">
 423                                                         <xs:element name="title" type="xs:string" />
 424                                                         <xs:element name="newick" type="xs:string" />
 425                                                 </xs:sequence>
 426                                                 <xs:attribute name="fontName" type="xs:string" />
 427                                                 <xs:attribute name="fontSize" type="xs:int" />
 428                                                 <xs:attribute name="fontStyle" type="xs:int" />
 429                                                 <xs:attribute name="threshold" type="xs:float" />
 430                                                 <xs:attribute name="showBootstrap"
 431                                                         type="xs:boolean" />
 432                                                 <xs:attribute name="showDistances"
 433                                                         type="xs:boolean" />
 434                                                 <xs:attribute name="markUnlinked"
 435                                                         type="xs:boolean" />
 436                                                 <xs:attribute name="fitToWindow"
 437                                                         type="xs:boolean" />
 438                                                 <xs:attribute name="currentTree"
 439                                                         type="xs:boolean" />
 440                                                 <xs:attribute name="id" type="xs:ID"
 441                                                         use="optional">
 442                                                         <xs:annotation>
 443                                                                 <xs:documentation>
 444                                                                         Tree ID added for binding tree
 445                                                                         visualization settings to vamsas
 446                                                                         document trees in jalview 2.4.1
 447                                                                 </xs:documentation>
 448                                                         </xs:annotation>
 449                                                 </xs:attribute>
 450                                                 <xs:attributeGroup ref="jv:swingwindow" />
 451                                         </xs:complexType>
 452                                 </xs:element>
 453                                 <xs:element name="FeatureSettings" minOccurs="0">
 454                                         <xs:complexType>
 455                                                 <xs:sequence>
 456                                                         <xs:element name="setting" minOccurs="0"
 457                                                                 maxOccurs="unbounded">
 458                                                                 <xs:complexType>
 459                                                                         <xs:attribute name="type"
 460                                                                                 type="xs:string" use="required" />
 461                                                                         <xs:attribute name="colour"
 462                                                                                 type="xs:int" use="required" />
 463                                                                         <xs:attribute name="display"
 464                                                                                 type="xs:boolean" use="required" />
 465                                                                         <xs:attribute name="order"
 466                                                                                 type="xs:float" use="optional" />
 467                                                                         <xs:attribute name="mincolour"
 468                                                                                 type="xs:int" use="optional">
 469                                                                                 <xs:annotation>
 470                                                                                         <xs:documentation>
 471                                                                                                 Optional minimum colour
 472                                                                                                 for graduated feature
 473                                                                                                 colour
 474                                                                                         </xs:documentation>
 475                                                                                 </xs:annotation>
 476                                                                         </xs:attribute>
 477                                                                         <xs:attribute name="threshold"
 478                                                                                 type="xs:float" use="optional">
 479                                                                                 <xs:annotation>
 480                                                                                         <xs:documentation>
 481                                                                                                 threshold value for
 482                                                                                                 graduated feature colour
 483                                                                                         </xs:documentation>
 484                                                                                 </xs:annotation>
 485                                                                         </xs:attribute>
 486                                                                         <xs:attribute name="threshstate"
 487                                                                                 type="xs:int" use="optional">
 488                                                                                 <xs:annotation>
 489                                                                                         <xs:documentation>
 490                                                                                                 threshold type for
 491                                                                                                 graduated feature colour
 492                                                                                         </xs:documentation>
 493                                                                                 </xs:annotation>
 494                                                                         </xs:attribute>
 495                                                                         <xs:attribute name="max"
 496                                                                                 type="xs:float" use="optional" />
 497                                                                         <xs:attribute name="min"
 498                                                                                 type="xs:float" use="optional" />
 499                                                                         <xs:attribute name="colourByLabel"
 500                                                                                 type="xs:boolean" use="optional" />
 501                                                                         <xs:attribute name="autoScale"
 502                                                                                 type="xs:boolean" use="optional" />
 503                                                                 </xs:complexType>
 504                                                         </xs:element>
 505                                                         <xs:element name="group" minOccurs="0"
 506                                                                 maxOccurs="unbounded">
 507                                                                 <xs:complexType>
 508                                                                         <xs:attribute name="name"
 509                                                                                 type="xs:string" use="required" />
 510                                                                         <xs:attribute name="display"
 511                                                                                 type="xs:boolean" use="required" />
 512                                                                 </xs:complexType>
 513                                                         </xs:element>
 514                                                 </xs:sequence>
 515                                         </xs:complexType>
 516                                 </xs:element>
 517                         </xs:sequence>
 518                 </xs:sequence>
 519         </xs:complexType>
 520         <xs:complexType name="feature">
 521                 <xs:sequence>
 522                         <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 523                                 <xs:complexType>
 524                                         <xs:attribute name="key" type="xs:string" use="required"/>
 525                                         <xs:attribute name="value" type="xs:string" use="required"/>
 526                                 </xs:complexType>
 527                         </xs:element>
 528                 </xs:sequence>
 529                 <xs:attribute name="begin" type="xs:int" use="required"/>
 530                 <xs:attribute name="end" type="xs:int" use="required"/>
 531                 <xs:attribute name="type" type="xs:string" use="required"/>
 532                 <xs:attribute name="description" type="xs:string" use="optional"/>
 533                 <xs:attribute name="status" type="xs:string" use="optional"/>
 534                 <xs:attribute name="featureGroup" type="xs:string" use="optional"/>
 535                 <xs:attribute name="score" type="xs:float" use="optional"/>
 536         </xs:complexType>
 537         <xs:complexType name="pdbentry">
 538                 <xs:sequence minOccurs="0" maxOccurs="unbounded">
 539                         <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
 540                                 <xs:complexType>
 541                                         <xs:attribute name="name" type="xs:string" use="required"/>
 542                                         <xs:attribute name="value" type="xs:string" use="required"/>
 543                                 </xs:complexType>
 544                         </xs:element>
 545                 </xs:sequence>
 546                 <xs:attribute name="id" type="xs:string" use="required"/>
 547                 <xs:attribute name="type" type="xs:string" use="optional"/>
 548                 <xs:attribute name="file" type="xs:string"/>
 549         </xs:complexType>
 550         <!--
 551         <xs:complexType name="reportWindow">
 552         <xs:annotation>
 553         <xs:documentation>Generic type for windows containing mime-typed data associated with other jalview windows</xs:documentation>
 554         </xs:annotation>
 555         <xs:sequence>
 556         </xs:sequence>
 557     <xs:attribute name="id" type="xs:string" use="required"/>
 558     <xs:attribute name="type" type="xs:string" use="optional"/>
 559     <xs:attribute name="file" type="xs:string" use="optional"/>
 560         </xs:complexType>
 561  -->
 562     <xs:attributeGroup name="swingwindow">
 563     <xs:annotation>
 564     <xs:documentation>
 565       base attributes for windows displayed in Jalview desktop.
 566     </xs:documentation>
 567     </xs:annotation>
 568       <xs:attribute name="width" type="xs:int"/>
 569       <xs:attribute name="height" type="xs:int"/>
 570       <xs:attribute name="xpos" type="xs:int"/>
 571       <xs:attribute name="ypos" type="xs:int"/>
 572     </xs:attributeGroup>
 573   <xs:complexType name="AnnotationColourScheme">
 574         <xs:attribute name="aboveThreshold" type="xs:int" />
 575         <xs:attribute name="annotation" type="xs:string" />
 576         <xs:attribute name="minColour" type="xs:int" />
 577         <xs:attribute name="maxColour" type="xs:int" />
 578         <xs:attribute name="colourScheme" type="xs:string" />
 579         <xs:attribute name="threshold" type="xs:float" />
 580         <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
 581         <xs:attribute name="predefinedColours" type="xs:boolean"
 582                 use="optional" />
 583   </xs:complexType>
 584
 585 </xs:schema>