schemas/jalview.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3         * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of
   4         Jalview. * * Jalview is free software: you can redistribute it and/or * modify
   5         it under the terms of the GNU General Public License * as published by the
   6         Free Software Foundation, either version 3 of the License, or (at your option)
   7         any later version. * * Jalview is distributed in the hope that it will be
   8         useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of
   9         MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General
  10         Public License for more details. * * You should have received a copy of the
  11         GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
  12         * The Jalview Authors are detailed in the 'AUTHORS' file. -->
  13 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
  14         xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours"
  15         xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset"
  16         targetNamespace="www.jalview.org" elementFormDefault="qualified"
  17         attributeFormDefault="unqualified">
  18         <xs:import namespace="www.vamsas.ac.uk/jalview/version2"
  19                 schemaLocation="vamsas.xsd" />
  20         <xs:import namespace="www.jalview.org/colours"
  21                 schemaLocation="JalviewUserColours.xsd" />
  22         <xs:import namespace="www.jalview.org/xml/wsparamset"
  23                 schemaLocation="JalviewWsParamSet.xsd" />
  24         <xs:element name="JalviewModel" type="jv:JalviewModel" />
  25         <xs:complexType name="JalviewModel">
  26                 <xs:sequence>
  27                         <xs:element name="creationDate" type="xs:dateTime" />
  28                         <xs:element name="version" type="xs:string" />
  29                         <xs:element name="vamsasModel" type="vamsas:VAMSAS" />
  30                         <xs:sequence>
  31                                 <xs:element name="JSeq" maxOccurs="unbounded" minOccurs="0">
  32                                         <xs:complexType>
  33                                                 <xs:sequence>
  34                                                         <xs:element name="features" type="jv:feature"
  35                                                                 minOccurs="0" maxOccurs="unbounded" />
  36                                                         <xs:element name="pdbids" minOccurs="0" maxOccurs="unbounded">
  37                                                                 <xs:complexType>
  38                                                                         <xs:complexContent>
  39                                                                                 <xs:extension base="jv:pdbentry">
  40                                                                                         <xs:sequence>
  41                                                                                                 <xs:element name="structureState" minOccurs="0"
  42                                                                                                         maxOccurs="unbounded">
  43                                                                                                         <xs:complexType>
  44                                                                                                                 <xs:simpleContent>
  45                                                                                                                         <xs:extension base="xs:string">
  46                                                                                                                                 <xs:attributeGroup ref="jv:swingwindow" />
  47                                                                                                                                 <xs:attribute name="visible" type="xs:boolean" />
  48                                                                                                                                 <xs:attribute name="viewId" type="xs:string"
  49                                                                                                                                         use="optional">
  50                                                                                                                                         <xs:annotation>
  51                                                                                                                                                 <xs:documentation>
  52                                                                                                                                                         additional
  53                                                                                                                                                         identifier
  54                                                                                                                                                         which
  55                                                                                                                                                         properly
  56                                                                                                                                                         disambiguates
  57                                                                                                                                                         the
  58                                                                                                                                                         structure
  59                                                                                                                                                         view
  60                                                                                                                                                         from
  61                                                                                                                                                         any
  62                                                                                                                                                         other
  63                                                                                                                                                         view
  64                                                                                                                                                         with
  65                                                                                                                                                         the
  66                                                                                                                                                         same
  67                                                                                                                                                         attributes.
  68                                                                                                                                                         This
  69                                                                                                                                                         is
  70                                                                                                                                                         not
  71                                                                                                                                                         an
  72                                                                                                                                                         ID,
  73                                                                                                                                                         because
  74                                                                                                                                                         it
  75                                                                                                                                                         is
  76                                                                                                                                                         possible
  77                                                                                                                                                         to
  78                                                                                                                                                         have
  79                                                                                                                                                         many
  80                                                                                                                                                         references
  81                                                                                                                                                         to
  82                                                                                                                                                         the
  83                                                                                                                                                         same
  84                                                                                                                                                         physical
  85                                                                                                                                                         structure
  86                                                                                                                                                         view
  87                                                                                                                                                         from
  88                                                                                                                                                         different
  89                                                                                                                                                         sequences
  90                                                                                                                                                         in
  91                                                                                                                                                         an
  92                                                                                                                                                         alignment.
  93                                                                                                                                                         A
  94                                                                                                                                                         structureState
  95                                                                                                                                                         element
  96                                                                                                                                                         citing
  97                                                                                                                                                         the
  98                                                                                                                                                         same
  99                                                                                                                                                         viewId
 100                                                                                                                                                         will
 101                                                                                                                                                         appear
 102                                                                                                                                                         for
 103                                                                                                                                                         each
 104                                                                                                                                                         instance.
 105                                                                                                                                                 </xs:documentation>
 106                                                                                                                                         </xs:annotation>
 107                                                                                                                                 </xs:attribute>
 108                                                                                                                                 <xs:attribute name="alignwithAlignPanel"
 109                                                                                                                                         type="xs:boolean" use="optional" default="true">
 110                                                                                                                                         <xs:annotation>
 111                                                                                                                                                 <xs:documentation>
 112                                                                                                                                                         Flag
 113                                                                                                                                                         set
 114                                                                                                                                                         if
 115                                                                                                                                                         the
 116                                                                                                                                                         alignment
 117                                                                                                                                                         panel
 118                                                                                                                                                         containing
 119                                                                                                                                                         this
 120                                                                                                                                                         JSeq
 121                                                                                                                                                         should
 122                                                                                                                                                         be
 123                                                                                                                                                         included
 124                                                                                                                                                         in
 125                                                                                                                                                         those
 126                                                                                                                                                         used
 127                                                                                                                                                         to
 128                                                                                                                                                         perform
 129                                                                                                                                                         a
 130                                                                                                                                                         structure
 131                                                                                                                                                         superposition
 132                                                                                                                                                         (since
 133                                                                                                                                                         Jalview
 134                                                                                                                                                         2.7).
 135                                                                                                                                                 </xs:documentation>
 136                                                                                                                                         </xs:annotation>
 137                                                                                                                                 </xs:attribute>
 138                                                                                                                                 <xs:attribute name="colourwithAlignPanel"
 139                                                                                                                                         type="xs:boolean" use="optional" default="false">
 140                                                                                                                                         <xs:annotation>
 141                                                                                                                                                 <xs:documentation>
 142                                                                                                                                                         Flag
 143                                                                                                                                                         set
 144                                                                                                                                                         if
 145                                                                                                                                                         the
 146                                                                                                                                                         alignment
 147                                                                                                                                                         panel
 148                                                                                                                                                         containing
 149                                                                                                                                                         this
 150                                                                                                                                                         JSeq
 151                                                                                                                                                         should
 152                                                                                                                                                         be
 153                                                                                                                                                         included
 154                                                                                                                                                         in
 155                                                                                                                                                         those
 156                                                                                                                                                         used
 157                                                                                                                                                         to
 158                                                                                                                                                         colour
 159                                                                                                                                                         its
 160                                                                                                                                                         associated
 161                                                                                                                                                         sequences
 162                                                                                                                                                         in
 163                                                                                                                                                         this
 164                                                                                                                                                         structureState(since
 165                                                                                                                                                         Jalview
 166                                                                                                                                                         2.7).
 167                                                                                                                                                 </xs:documentation>
 168                                                                                                                                         </xs:annotation>
 169                                                                                                                                 </xs:attribute>
 170                                                                                                                                 <xs:attribute name="colourByJmol" type="xs:boolean"
 171                                                                                                                                         use="optional" default="true">
 172                                                                                                                                         <xs:annotation>
 173                                                                                                                                                 <xs:documentation>
 174                                                                                                                                                         Flag
 175                                                                                                                                                         set
 176                                                                                                                                                         if
 177                                                                                                                                                         the
 178                                                                                                                                                         structure
 179                                                                                                                                                         display
 180                                                                                                                                                         is
 181                                                                                                                                                         coloured
 182                                                                                                                                                         by
 183                                                                                                                                                         the
 184                                                                                                                                                         Jmol
 185                                                                                                                                                         state,
 186                                                                                                                                                         rather
 187                                                                                                                                                         than
 188                                                                                                                                                         by
 189                                                                                                                                                         one
 190                                                                                                                                                         or
 191                                                                                                                                                         more
 192                                                                                                                                                         linked
 193                                                                                                                                                         alignment
 194                                                                                                                                                         views.
 195                                                                                                                                                 </xs:documentation>
 196                                                                                                                                         </xs:annotation>
 197                                                                                                                                 </xs:attribute>
 198                                                                                                                                 <xs:attribute name="type" type="xs:string"
 199                                                                                                                                         use="optional">
 200                                                                                                                                         <xs:annotation>
 201                                                                                                                                                 <xs:documentation>
 202                                                                                                                                                         An
 203                                                                                                                                                         identifier
 204                                                                                                                                                         for
 205                                                                                                                                                         the
 206                                                                                                                                                         viewer
 207                                                                                                                                                         type,
 208                                                                                                                                                         currently
 209                                                                                                                                                         either
 210                                                                                                                                                         JMOL
 211                                                                                                                                                         or
 212                                                                                                                                                         CHIMERA
 213                                                                                                                                                 </xs:documentation>
 214                                                                                                                                         </xs:annotation>
 215                                                                                                                                 </xs:attribute>
 216
 217                                                                                                                         </xs:extension>
 218                                                                                                                 </xs:simpleContent>
 219                                                                                                         </xs:complexType>
 220                                                                                                 </xs:element>
 221                                                                                         </xs:sequence>
 222                                                                                 </xs:extension>
 223                                                                         </xs:complexContent>
 224                                                                 </xs:complexType>
 225                                                         </xs:element>
 226                                                         <xs:element name="hiddenSequences" type="xs:int"
 227                                                                 minOccurs="0" maxOccurs="unbounded" />
 228                                                         <xs:element name="rnaViewer" minOccurs="0" maxOccurs="unbounded">
 229                                                                 <xs:annotation>
 230                                                                         <xs:documentation>Reference to a viewer showing RNA structure
 231                                                                                 for this sequence. Schema supports one viewer showing multiple
 232                                                                                 annotations for multiple sequences, though currently only one
 233                                                                                 annotation for one sequence (gapped or trimmed) is used
 234                                                                         </xs:documentation>
 235                                                                 </xs:annotation>
 236                                                                 <xs:complexType>
 237                                                                         <xs:sequence>
 238                                                                                 <xs:element name="secondaryStructure" minOccurs="1"
 239                                                                                         maxOccurs="unbounded">
 240                                                                                         <xs:complexType>
 241                                                                                                 <xs:attribute name="title" type="xs:string" />
 242                                                                                                 <xs:attribute name="annotationId" type="xs:string"
 243                                                                                                         use="required">
 244                                                                                                         <xs:annotation>
 245                                                                                                                 <xs:documentation>id attribute of Annotation in
 246                                                                                                                         vamsasModel for
 247                                                                                                                         the secondary structure annotation shown
 248                                                                                                                         in the viewer
 249                                                                                                                 </xs:documentation>
 250                                                                                                         </xs:annotation>
 251                                                                                                 </xs:attribute>
 252                                                                                                 <xs:attribute name="gapped" type="xs:boolean">
 253                                                                                                         <xs:annotation>
 254                                                                                                                 <xs:documentation>if true the RNA structure is shown with gaps, if false without
 255                                                                                                                 </xs:documentation>
 256                                                                                                         </xs:annotation>
 257                                                                                                 </xs:attribute>
 258                                                                                                 <xs:attribute name="viewerState" type="xs:string">
 259                                                                                                         <xs:annotation>
 260                                                                                                                 <xs:documentation>name of the project jar entry that holds
 261                                                                                                                         the VARNA viewer state for the structure
 262                                                                                                                 </xs:documentation>
 263                                                                                                         </xs:annotation>
 264                                                                                                 </xs:attribute>
 265                                                                                         </xs:complexType>
 266                                                                                 </xs:element>
 267                                                                         </xs:sequence>
 268                                                                         <xs:attributeGroup ref="jv:swingwindow" />
 269                                                                         <xs:attribute name="title" type="xs:string" />
 270                                                                         <xs:attribute name="viewId" type="xs:string">
 271                                                                                 <xs:annotation>
 272                                                                                         <xs:documentation>An id unique to the RNA viewer panel
 273                                                                                         </xs:documentation>
 274                                                                                 </xs:annotation>
 275                                                                         </xs:attribute>
 276                                                                         <xs:attribute name="dividerLocation" type="xs:int">
 277                                                                                 <xs:annotation>
 278                                                                                         <xs:documentation>horizontal position of split pane divider
 279                                                                                         </xs:documentation>
 280                                                                                 </xs:annotation>
 281                                                                         </xs:attribute>
 282                                                                         <xs:attribute name="selectedRna" type="xs:int">
 283                                                                                 <xs:annotation>
 284                                                                                         <xs:documentation>Index of the selected structure in the
 285                                                                                                 viewer panel
 286                                                                                         </xs:documentation>
 287                                                                                 </xs:annotation>
 288                                                                         </xs:attribute>
 289                                                                 </xs:complexType>
 290                                                         </xs:element>
 291                                                 </xs:sequence>
 292                                                 <xs:attribute name="colour" type="xs:int" use="optional" />
 293                                                 <xs:attribute name="start" type="xs:int" use="required" />
 294                                                 <xs:attribute name="end" type="xs:int" use="required" />
 295                                                 <xs:attribute name="id" type="xs:string" use="required" />
 296                                                 <xs:attribute name="hidden" type="xs:boolean" />
 297                                                 <xs:attribute name="viewreference" type="xs:boolean" use="optional"/>
 298                                         </xs:complexType>
 299                                 </xs:element>
 300                                 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
 301                                         <xs:complexType>
 302                                                 <xs:sequence>
 303                                                         <xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
 304                                                         <xs:element name="annotationColours" type="jv:AnnotationColourScheme"
 305                                                                 minOccurs="0" maxOccurs="1" />
 306                                                 </xs:sequence>
 307                                                 <xs:attribute name="start" type="xs:int" />
 308                                                 <xs:attribute name="end" type="xs:int" />
 309                                                 <xs:attribute name="name" type="xs:string" />
 310                                                 <xs:attribute name="colour" type="xs:string" />
 311                                                 <xs:attribute name="consThreshold" type="xs:int" />
 312                                                 <xs:attribute name="pidThreshold" type="xs:int" />
 313                                                 <xs:attribute name="outlineColour" type="xs:int" />
 314                                                 <xs:attribute name="displayBoxes" type="xs:boolean" />
 315                                                 <xs:attribute name="displayText" type="xs:boolean" />
 316                                                 <xs:attribute name="colourText" type="xs:boolean" />
 317                                                 <xs:attribute name="textCol1" type="xs:int" />
 318                                                 <xs:attribute name="textCol2" type="xs:int" />
 319                                                 <xs:attribute name="textColThreshold" type="xs:int" />
 320                                                 <xs:attribute name="showUnconserved" type="xs:boolean"
 321                                                         use="optional" />
 322                                                 <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
 323                                                         use="optional" default="true" />
 324                                                 <xs:attribute name="showConsensusHistogram" type="xs:boolean"
 325                                                         use="optional" default="true" />
 326                                                 <xs:attribute name="showSequenceLogo" type="xs:boolean"
 327                                                         use="optional" default="false" />
 328                                                 <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
 329                                                         use="optional" default="false" />
 330                                                 <xs:attribute name="id" type="xs:string" use="optional">
 331                                                         <xs:annotation>
 332                                                                 <xs:documentation>
 333                                                                         Optional sequence group ID (only
 334                                                                         needs to be
 335                                                                         unique for this
 336                                                                         alignment)
 337                                                                 </xs:documentation>
 338                                                         </xs:annotation>
 339                                                 </xs:attribute>
 340                                         </xs:complexType>
 341                                 </xs:element>
 342                                 <xs:element name="Viewport" maxOccurs="unbounded"
 343                                         minOccurs="0">
 344                                         <xs:complexType>
 345                                                 <xs:sequence>
 346                                                         <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
 347                                                                 minOccurs="0" maxOccurs="1">
 348                                                         </xs:element>
 349                                                         <xs:element name="hiddenColumns" minOccurs="0"
 350                                                                 maxOccurs="unbounded">
 351                                                                 <xs:complexType>
 352                                                                         <xs:attribute name="start" type="xs:int" />
 353                                                                         <xs:attribute name="end" type="xs:int" />
 354                                                                 </xs:complexType>
 355                                                         </xs:element>
 356                                                         <xs:element name="calcIdParam" minOccurs="0"
 357                                                                 maxOccurs="unbounded">
 358                                                                 <xs:complexType>
 359                                                                         <xs:complexContent>
 360                                                                                 <xs:extension base="jvws:WebServiceParameterSet">
 361                                                                                         <xs:attribute name="calcId" type="xs:string"
 362                                                                                                 use="required">
 363                                                                                                 <xs:annotation>
 364                                                                                                         <xs:documentation>handle for the calculation which uses
 365                                                                                                                 this parameter set
 366                                                                                                         </xs:documentation>
 367                                                                                                 </xs:annotation>
 368                                                                                         </xs:attribute>
 369                                                                                         <xs:attribute name="needsUpdate" type="xs:boolean"
 370                                                                                                 use="optional" default="false">
 371                                                                                                 <xs:annotation>
 372                                                                                                         <xs:documentation>should the calculation be performed
 373                                                                                                                 immediately after loading in order to refresh results
 374                                                                                                         </xs:documentation>
 375                                                                                                 </xs:annotation>
 376                                                                                         </xs:attribute>
 377                                                                                         <xs:attribute name="autoUpdate" type="xs:boolean"
 378                                                                                                 use="required">
 379                                                                                                 <xs:annotation>
 380                                                                                                         <xs:documentation>should the calculation be automatically
 381                                                                                                                 performed on edits
 382                                                                                                         </xs:documentation>
 383                                                                                                 </xs:annotation>
 384                                                                                         </xs:attribute>
 385                                                                                 </xs:extension>
 386                                                                         </xs:complexContent>
 387                                                                 </xs:complexType>
 388                                                         </xs:element>
 389                                                 </xs:sequence>
 390                                                 <xs:attributeGroup ref="jv:swingwindow" />
 391                                                 <xs:attribute name="conservationSelected" type="xs:boolean" />
 392                                                 <xs:attribute name="pidSelected" type="xs:boolean" />
 393                                                 <xs:attribute name="bgColour" type="xs:string" />
 394                                                 <xs:attribute name="consThreshold" type="xs:int" />
 395                                                 <xs:attribute name="pidThreshold" type="xs:int" />
 396                                                 <xs:attribute name="title" type="xs:string" />
 397                                                 <xs:attribute name="showFullId" type="xs:boolean" />
 398                                                 <xs:attribute name="rightAlignIds" type="xs:boolean" />
 399                                                 <xs:attribute name="showText" type="xs:boolean" />
 400                                                 <xs:attribute name="showColourText" type="xs:boolean" />
 401                                                 <xs:attribute name="showUnconserved" type="xs:boolean"
 402                                                         use="optional" default="false" />
 403                                                 <xs:attribute name="showBoxes" type="xs:boolean" />
 404                                                 <xs:attribute name="wrapAlignment" type="xs:boolean" />
 405                                                 <xs:attribute name="renderGaps" type="xs:boolean" />
 406                                                 <xs:attribute name="showSequenceFeatures" type="xs:boolean" />
 407                                                 <xs:attribute name="showNPfeatureTooltip" type="xs:boolean"
 408                                                         use="optional" />
 409                                                 <xs:attribute name="showDbRefTooltip" type="xs:boolean"
 410                                                         use="optional" />
 411                                                 <xs:attribute name="followHighlight" type="xs:boolean"
 412                                                         use="optional" default="true" />
 413                                                 <xs:attribute name="followSelection" type="xs:boolean"
 414                                                         use="optional" default="true" />
 415                                                 <xs:attribute name="showAnnotation" type="xs:boolean" />
 416                                                 <xs:attribute name="centreColumnLabels" type="xs:boolean"
 417                                                         use="optional" default="false" />
 418                                                 <xs:attribute name="showGroupConservation" type="xs:boolean"
 419                                                         use="optional" default="false" />
 420                                                 <xs:attribute name="showGroupConsensus" type="xs:boolean"
 421                                                         use="optional" default="false" />
 422                                                 <xs:attribute name="showConsensusHistogram" type="xs:boolean"
 423                                                         use="optional" default="true" />
 424                                                 <xs:attribute name="showSequenceLogo" type="xs:boolean"
 425                                                         use="optional" default="false" />
 426                                                 <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
 427                                                         use="optional" default="false" />
 428                                                 <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
 429                                                         use="optional" default="true" />
 430                                                 <xs:attribute name="startRes" type="xs:int" />
 431                                                 <xs:attribute name="startSeq" type="xs:int" />
 432                                                 <xs:attribute name="fontName" type="xs:string" />
 433                                                 <xs:attribute name="fontSize" type="xs:int" />
 434                                                 <xs:attribute name="fontStyle" type="xs:int" />
 435                                                 <xs:attribute name="scaleProteinAsCdna" type="xs:boolean" use="optional" default="true" />
 436                                                 <xs:attribute name="viewName" type="xs:string" />
 437                                                 <xs:attribute name="sequenceSetId" type="xs:string" />
 438                                                 <xs:attribute name="gatheredViews" type="xs:boolean" />
 439                                                 <xs:attribute name="textCol1" type="xs:int" />
 440                                                 <xs:attribute name="textCol2" type="xs:int" />
 441                                                 <xs:attribute name="textColThreshold" type="xs:int" />
 442                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 443                                                         <xs:annotation>
 444                                                                 <xs:documentation>
 445                                                                         unique id used by jalview to
 446                                                                         synchronize
 447                                                                         between stored and
 448                                                                         instantiated views
 449                                                                 </xs:documentation>
 450                                                         </xs:annotation>
 451                                                 </xs:attribute>
 452                                                 <xs:attribute name="complementId" type="xs:string"
 453                                                         use="optional">
 454                                                         <xs:annotation>
 455                                                                 <xs:documentation>
 456                                                                         The viewport id of this viewport's
 457                                                                         (cdna/protein) coding complement, if any
 458                                                                 </xs:documentation>
 459                                                         </xs:annotation>
 460                                                 </xs:attribute>
 461                                         </xs:complexType>
 462                                 </xs:element>
 463                                 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
 464                                         <xs:complexType>
 465                                                 <xs:sequence>
 466                                                         <xs:element name="UserColourScheme" type="jalview:JalviewUserColours" />
 467                                                 </xs:sequence>
 468                                                 <xs:attribute name="id" type="xs:string" />
 469                                         </xs:complexType>
 470                                 </xs:element>
 471                                 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
 472                                         <xs:complexType>
 473                                                 <xs:sequence minOccurs="0">
 474                                                         <xs:element name="title" type="xs:string" />
 475                                                         <xs:element name="newick" type="xs:string" />
 476                                                 </xs:sequence>
 477                                                 <xs:attribute name="fontName" type="xs:string" />
 478                                                 <xs:attribute name="fontSize" type="xs:int" />
 479                                                 <xs:attribute name="fontStyle" type="xs:int" />
 480                                                 <xs:attribute name="threshold" type="xs:float" />
 481                                                 <xs:attribute name="showBootstrap" type="xs:boolean" />
 482                                                 <xs:attribute name="showDistances" type="xs:boolean" />
 483                                                 <xs:attribute name="markUnlinked" type="xs:boolean" />
 484                                                 <xs:attribute name="fitToWindow" type="xs:boolean" />
 485                                                 <xs:attribute name="currentTree" type="xs:boolean" />
 486                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 487                                                         <xs:annotation>
 488                                                                 <xs:documentation>
 489                                                                         Tree ID added for binding tree
 490                                                                         visualization
 491                                                                         settings to vamsas
 492                                                                         document trees in jalview 2.4.1
 493                                                                 </xs:documentation>
 494                                                         </xs:annotation>
 495                                                 </xs:attribute>
 496                                                 <xs:attributeGroup ref="jv:swingwindow" />
 497                                         </xs:complexType>
 498                                 </xs:element>
 499                                 <xs:element name="FeatureSettings" minOccurs="0">
 500                                         <xs:complexType>
 501                                                 <xs:sequence>
 502                                                         <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
 503                                                                 <xs:complexType>
 504                                                                         <xs:sequence>
 505                                                                             <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
 506                                                                                         <xs:annotation>
 507                                                                                                 <xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
 508                                                                                         </xs:annotation>
 509                                                                             </xs:element>
 510                                                                                 <xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
 511                                                                                         <xs:annotation>
 512                                                                                                 <xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
 513                                                                                         </xs:annotation>
 514                                                                                 </xs:element>
 515                                                                         </xs:sequence>
 516                                                                         <xs:attribute name="type" type="xs:string" use="required" />
 517                                                                         <xs:attribute name="colour" type="xs:int" use="required" />
 518                                                                         <xs:attribute name="display" type="xs:boolean"
 519                                                                                 use="required" />
 520                                                                         <xs:attribute name="order" type="xs:float" use="optional" />
 521                                                                         <xs:attribute name="mincolour" type="xs:int" use="optional">
 522                                                                                 <xs:annotation>
 523                                                                                         <xs:documentation>
 524                                                                                                 Optional minimum colour
 525                                                                                                 for graduated
 526                                                                                                 feature
 527                                                                                                 colour
 528                                                                                         </xs:documentation>
 529                                                                                 </xs:annotation>
 530                                                                         </xs:attribute>
 531                                                                         <xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
 532                                                                         <xs:attribute name="threshold" type="xs:float"
 533                                                                                 use="optional">
 534                                                                                 <xs:annotation>
 535                                                                                         <xs:documentation>
 536                                                                                                 threshold value for
 537                                                                                                 graduated feature colour
 538                                                                                         </xs:documentation>
 539                                                                                 </xs:annotation>
 540                                                                         </xs:attribute>
 541                                                                         <xs:attribute name="threshstate" type="xs:int"
 542                                                                                 use="optional">
 543                                                                                 <xs:annotation>
 544                                                                                         <xs:documentation>
 545                                                                                                 threshold type for
 546                                                                                                 graduated feature colour
 547                                                                                         </xs:documentation>
 548                                                                                 </xs:annotation>
 549                                                                         </xs:attribute>
 550                                                                         <xs:attribute name="max" type="xs:float" use="optional" />
 551                                                                         <xs:attribute name="min" type="xs:float" use="optional" />
 552                                                                         <xs:attribute name="colourByLabel" type="xs:boolean"
 553                                                                                 use="optional" />
 554                                                                         <xs:attribute name="autoScale" type="xs:boolean"
 555                                                                                 use="optional" />
 556                                                                 </xs:complexType>
 557                                                         </xs:element>
 558                                                         <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
 559                                                                 <xs:complexType>
 560                                                                         <xs:attribute name="name" type="xs:string" use="required" />
 561                                                                         <xs:attribute name="display" type="xs:boolean"
 562                                                                                 use="required" />
 563                                                                 </xs:complexType>
 564                                                         </xs:element>
 565                                                 </xs:sequence>
 566                                         </xs:complexType>
 567                                 </xs:element>
 568                         </xs:sequence>
 569                 </xs:sequence>
 570         </xs:complexType>
 571         <xs:complexType name="feature">
 572                 <xs:sequence>
 573                         <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 574                                 <xs:complexType>
 575                                         <xs:attribute name="key" type="xs:string" use="required" />
 576                                         <xs:attribute name="key2" type="xs:string" use="optional">
 577                                                 <xs:annotation>
 578                                                         <xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
 579                                                 </xs:annotation>
 580                                         </xs:attribute>
 581                                         <xs:attribute name="value" type="xs:string" use="required" />
 582                                 </xs:complexType>
 583                         </xs:element>
 584                 </xs:sequence>
 585                 <xs:attribute name="begin" type="xs:int" use="required" />
 586                 <xs:attribute name="end" type="xs:int" use="required" />
 587                 <xs:attribute name="type" type="xs:string" use="required" />
 588                 <xs:attribute name="description" type="xs:string" use="optional" />
 589                 <xs:attribute name="status" type="xs:string" use="optional" />
 590                 <xs:attribute name="featureGroup" type="xs:string" use="optional" />
 591                 <xs:attribute name="score" type="xs:float" use="optional" />
 592         </xs:complexType>
 593         <xs:complexType name="pdbentry">
 594                 <xs:sequence minOccurs="0" maxOccurs="unbounded">
 595                         <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
 596                                 <xs:complexType>
 597                                         <xs:attribute name="name" type="xs:string" use="required" />
 598                                         <xs:attribute name="value" type="xs:string" use="required" />
 599                                 </xs:complexType>
 600                         </xs:element>
 601                 </xs:sequence>
 602                 <xs:attribute name="id" type="xs:string" use="required" />
 603                 <xs:attribute name="type" type="xs:string" use="optional" />
 604                 <xs:attribute name="file" type="xs:string" />
 605         </xs:complexType>
 606         <!-- <xs:complexType name="reportWindow"> <xs:annotation> <xs:documentation>Generic
 607                 type for windows containing mime-typed data associated with other jalview
 608                 windows</xs:documentation> </xs:annotation> <xs:sequence> </xs:sequence>
 609                 <xs:attribute name="id" type="xs:string" use="required"/> <xs:attribute name="type"
 610                 type="xs:string" use="optional"/> <xs:attribute name="file" type="xs:string"
 611                 use="optional"/> </xs:complexType> -->
 612         <xs:attributeGroup name="swingwindow">
 613                 <xs:annotation>
 614                         <xs:documentation>
 615                                 base attributes for windows displayed in Jalview
 616                                 desktop.
 617                         </xs:documentation>
 618                 </xs:annotation>
 619                 <xs:attribute name="width" type="xs:int" />
 620                 <xs:attribute name="height" type="xs:int" />
 621                 <xs:attribute name="xpos" type="xs:int" />
 622                 <xs:attribute name="ypos" type="xs:int" />
 623         </xs:attributeGroup>
 624         <xs:complexType name="AnnotationColourScheme">
 625                 <xs:attribute name="aboveThreshold" type="xs:int" />
 626                 <xs:attribute name="annotation" type="xs:string" />
 627                 <xs:attribute name="minColour" type="xs:int" />
 628                 <xs:attribute name="maxColour" type="xs:int" />
 629                 <xs:attribute name="colourScheme" type="xs:string" />
 630                 <xs:attribute name="threshold" type="xs:float" />
 631                 <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
 632                 <xs:attribute name="predefinedColours" type="xs:boolean"
 633                         use="optional" />
 634         </xs:complexType>
 635
 636 </xs:schema>