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: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" type="jv:feature"
  34                                                                 minOccurs="0" maxOccurs="unbounded" />
  35                                                         <xs:element name="pdbids" minOccurs="0" maxOccurs="unbounded">
  36                                                                 <xs:complexType>
  37                                                                         <xs:complexContent>
  38                                                                                 <xs:extension base="jv:pdbentry">
  39                                                                                         <xs:sequence>
  40                                                                                                 <xs:element name="structureState" minOccurs="0"
  41                                                                                                         maxOccurs="unbounded">
  42                                                                                                         <xs:complexType>
  43                                                                                                                 <xs:simpleContent>
  44                                                                                                                         <xs:extension base="xs:string">
  45                                                                                                                                 <xs:attributeGroup ref="jv:swingwindow" />
  46                                                                                                                                 <xs:attribute name="visible" type="xs:boolean" />
  47                                                                                                                                 <xs:attribute name="viewId" type="xs:string"
  48                                                                                                                                         use="optional">
  49                                                                                                                                         <xs:annotation>
  50                                                                                                                                                 <xs:documentation>
  51                                                                                                                                                         additional
  52                                                                                                                                                         identifier
  53                                                                                                                                                         which
  54                                                                                                                                                         properly
  55                                                                                                                                                         disambiguates
  56                                                                                                                                                         the
  57                                                                                                                                                         structure
  58                                                                                                                                                         view
  59                                                                                                                                                         from
  60                                                                                                                                                         any
  61                                                                                                                                                         other
  62                                                                                                                                                         view
  63                                                                                                                                                         with
  64                                                                                                                                                         the
  65                                                                                                                                                         same
  66                                                                                                                                                         attributes.
  67                                                                                                                                                         This
  68                                                                                                                                                         is
  69                                                                                                                                                         not
  70                                                                                                                                                         an
  71                                                                                                                                                         ID,
  72                                                                                                                                                         because
  73                                                                                                                                                         it
  74                                                                                                                                                         is
  75                                                                                                                                                         possible
  76                                                                                                                                                         to
  77                                                                                                                                                         have
  78                                                                                                                                                         many
  79                                                                                                                                                         references
  80                                                                                                                                                         to
  81                                                                                                                                                         the
  82                                                                                                                                                         same
  83                                                                                                                                                         physical
  84                                                                                                                                                         structure
  85                                                                                                                                                         view
  86                                                                                                                                                         from
  87                                                                                                                                                         different
  88                                                                                                                                                         sequences
  89                                                                                                                                                         in
  90                                                                                                                                                         an
  91                                                                                                                                                         alignment.
  92                                                                                                                                                         A
  93                                                                                                                                                         structureState
  94                                                                                                                                                         element
  95                                                                                                                                                         citing
  96                                                                                                                                                         the
  97                                                                                                                                                         same
  98                                                                                                                                                         viewId
  99                                                                                                                                                         will
 100                                                                                                                                                         appear
 101                                                                                                                                                         for
 102                                                                                                                                                         each
 103                                                                                                                                                         instance.
 104                                                                                                                                                 </xs:documentation>
 105                                                                                                                                         </xs:annotation>
 106                                                                                                                                 </xs:attribute>
 107                                                                                                                                 <xs:attribute name="alignwithAlignPanel"
 108                                                                                                                                         type="xs:boolean" use="optional" default="true">
 109                                                                                                                                         <xs:annotation>
 110                                                                                                                                                 <xs:documentation>
 111                                                                                                                                                         Flag
 112                                                                                                                                                         set
 113                                                                                                                                                         if
 114                                                                                                                                                         the
 115                                                                                                                                                         alignment
 116                                                                                                                                                         panel
 117                                                                                                                                                         containing
 118                                                                                                                                                         this
 119                                                                                                                                                         JSeq
 120                                                                                                                                                         should
 121                                                                                                                                                         be
 122                                                                                                                                                         included
 123                                                                                                                                                         in
 124                                                                                                                                                         those
 125                                                                                                                                                         used
 126                                                                                                                                                         to
 127                                                                                                                                                         perform
 128                                                                                                                                                         a
 129                                                                                                                                                         structure
 130                                                                                                                                                         superposition
 131                                                                                                                                                         (since
 132                                                                                                                                                         Jalview
 133                                                                                                                                                         2.7).
 134                                                                                                                                                 </xs:documentation>
 135                                                                                                                                         </xs:annotation>
 136                                                                                                                                 </xs:attribute>
 137                                                                                                                                 <xs:attribute name="colourwithAlignPanel"
 138                                                                                                                                         type="xs:boolean" use="optional" default="false">
 139                                                                                                                                         <xs:annotation>
 140                                                                                                                                                 <xs:documentation>
 141                                                                                                                                                         Flag
 142                                                                                                                                                         set
 143                                                                                                                                                         if
 144                                                                                                                                                         the
 145                                                                                                                                                         alignment
 146                                                                                                                                                         panel
 147                                                                                                                                                         containing
 148                                                                                                                                                         this
 149                                                                                                                                                         JSeq
 150                                                                                                                                                         should
 151                                                                                                                                                         be
 152                                                                                                                                                         included
 153                                                                                                                                                         in
 154                                                                                                                                                         those
 155                                                                                                                                                         used
 156                                                                                                                                                         to
 157                                                                                                                                                         colour
 158                                                                                                                                                         its
 159                                                                                                                                                         associated
 160                                                                                                                                                         sequences
 161                                                                                                                                                         in
 162                                                                                                                                                         this
 163                                                                                                                                                         structureState(since
 164                                                                                                                                                         Jalview
 165                                                                                                                                                         2.7).
 166                                                                                                                                                 </xs:documentation>
 167                                                                                                                                         </xs:annotation>
 168                                                                                                                                 </xs:attribute>
 169                                                                                                                                 <xs:attribute name="colourByJmol" type="xs:boolean"
 170                                                                                                                                         use="optional" default="true">
 171                                                                                                                                         <xs:annotation>
 172                                                                                                                                                 <xs:documentation>
 173                                                                                                                                                         Flag
 174                                                                                                                                                         set
 175                                                                                                                                                         if
 176                                                                                                                                                         the
 177                                                                                                                                                         structure
 178                                                                                                                                                         display
 179                                                                                                                                                         is
 180                                                                                                                                                         coloured
 181                                                                                                                                                         by
 182                                                                                                                                                         the
 183                                                                                                                                                         Jmol
 184                                                                                                                                                         state,
 185                                                                                                                                                         rather
 186                                                                                                                                                         than
 187                                                                                                                                                         by
 188                                                                                                                                                         one
 189                                                                                                                                                         or
 190                                                                                                                                                         more
 191                                                                                                                                                         linked
 192                                                                                                                                                         alignment
 193                                                                                                                                                         views.
 194                                                                                                                                                 </xs:documentation>
 195                                                                                                                                         </xs:annotation>
 196                                                                                                                                 </xs:attribute>
 197                                                                                                                                 <xs:attribute name="type" type="xs:string"
 198                                                                                                                                         use="optional">
 199                                                                                                                                         <xs:annotation>
 200                                                                                                                                                 <xs:documentation>
 201                                                                                                                                                         An
 202                                                                                                                                                         identifier
 203                                                                                                                                                         for
 204                                                                                                                                                         the
 205                                                                                                                                                         viewer
 206                                                                                                                                                         type,
 207                                                                                                                                                         currently
 208                                                                                                                                                         either
 209                                                                                                                                                         JMOL
 210                                                                                                                                                         or
 211                                                                                                                                                         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" type="xs:int"
 226                                                                 minOccurs="0" maxOccurs="unbounded" />
 227                                                         <xs:element name="rnaViewer" minOccurs="0" maxOccurs="unbounded">
 228                                                                 <xs:annotation>
 229                                                                         <xs:documentation>Reference to a viewer showing RNA structure
 230                                                                                 for this sequence. Schema supports one viewer showing multiple
 231                                                                                 annotations for multiple sequences, though currently only one
 232                                                                                 annotation for one sequence (gapped or trimmed) is used
 233                                                                         </xs:documentation>
 234                                                                 </xs:annotation>
 235                                                                 <xs:complexType>
 236                                                                         <xs:sequence>
 237                                                                                 <xs:element name="secondaryStructure" minOccurs="1"
 238                                                                                         maxOccurs="unbounded">
 239                                                                                         <xs:complexType>
 240                                                                                                 <xs:attribute name="title" type="xs:string" />
 241                                                                                                 <xs:attribute name="annotationId" type="xs:string"
 242                                                                                                         use="required">
 243                                                                                                         <xs:annotation>
 244                                                                                                                 <xs:documentation>id attribute of Annotation in
 245                                                                                                                         vamsasModel for
 246                                                                                                                         the secondary structure annotation shown
 247                                                                                                                         in the viewer
 248                                                                                                                 </xs:documentation>
 249                                                                                                         </xs:annotation>
 250                                                                                                 </xs:attribute>
 251                                                                                                 <xs:attribute name="gapped" type="xs:boolean">
 252                                                                                                         <xs:annotation>
 253                                                                                                                 <xs:documentation>if true the RNA structure is shown with gaps, if false without
 254                                                                                                                 </xs:documentation>
 255                                                                                                         </xs:annotation>
 256                                                                                                 </xs:attribute>
 257                                                                                                 <xs:attribute name="viewerState" type="xs:string">
 258                                                                                                         <xs:annotation>
 259                                                                                                                 <xs:documentation>name of the project jar entry that holds
 260                                                                                                                         the VARNA viewer state for the structure
 261                                                                                                                 </xs:documentation>
 262                                                                                                         </xs:annotation>
 263                                                                                                 </xs:attribute>
 264                                                                                         </xs:complexType>
 265                                                                                 </xs:element>
 266                                                                         </xs:sequence>
 267                                                                         <xs:attributeGroup ref="jv:swingwindow" />
 268                                                                         <xs:attribute name="title" type="xs:string" />
 269                                                                         <xs:attribute name="viewId" type="xs:string">
 270                                                                                 <xs:annotation>
 271                                                                                         <xs:documentation>An id unique to the RNA viewer panel
 272                                                                                         </xs:documentation>
 273                                                                                 </xs:annotation>
 274                                                                         </xs:attribute>
 275                                                                         <xs:attribute name="dividerLocation" type="xs:int">
 276                                                                                 <xs:annotation>
 277                                                                                         <xs:documentation>horizontal position of split pane divider
 278                                                                                         </xs:documentation>
 279                                                                                 </xs:annotation>
 280                                                                         </xs:attribute>
 281                                                                         <xs:attribute name="selectedRna" type="xs:int">
 282                                                                                 <xs:annotation>
 283                                                                                         <xs:documentation>Index of the selected structure in the
 284                                                                                                 viewer panel
 285                                                                                         </xs:documentation>
 286                                                                                 </xs:annotation>
 287                                                                         </xs:attribute>
 288                                                                 </xs:complexType>
 289                                                         </xs:element>
 290                                                         <xs:element name="hmmerProfile" minOccurs="0" type="xs:string">
 291                                                                 <xs:annotation>
 292                                                                         <xs:documentation>name of the project jar entry that holds the HMM file with the profile for the sequence</xs:documentation>
 293                                                                 </xs:annotation>
 294                                                         </xs:element>
 295                                                 </xs:sequence>
 296                                                 <xs:attribute name="colour" type="xs:int" use="optional" />
 297                                                 <xs:attribute name="start" type="xs:int" use="required" />
 298                                                 <xs:attribute name="end" type="xs:int" use="required" />
 299                                                 <xs:attribute name="id" type="xs:string" use="required" />
 300                                                 <xs:attribute name="hidden" type="xs:boolean" />
 301                                                 <xs:attribute name="viewreference" type="xs:boolean" use="optional"/>
 302                                         </xs:complexType>
 303                                 </xs:element>
 304                                 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
 305                                         <xs:complexType>
 306                                                 <xs:sequence>
 307                                                         <xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
 308                                                         <xs:element name="annotationColours" type="jv:AnnotationColourScheme"
 309                                                                 minOccurs="0" maxOccurs="1" />
 310                                                 </xs:sequence>
 311                                                 <xs:attribute name="start" type="xs:int" />
 312                                                 <xs:attribute name="end" type="xs:int" />
 313                                                 <xs:attribute name="name" type="xs:string" />
 314                                                 <xs:attribute name="colour" type="xs:string" />
 315                                                 <xs:attribute name="consThreshold" type="xs:int" />
 316                                                 <xs:attribute name="pidThreshold" type="xs:int" />
 317                                                 <xs:attribute name="outlineColour" type="xs:int" />
 318                                                 <xs:attribute name="displayBoxes" type="xs:boolean" />
 319                                                 <xs:attribute name="displayText" type="xs:boolean" />
 320                                                 <xs:attribute name="colourText" type="xs:boolean" />
 321                                                 <xs:attribute name="textCol1" type="xs:int" />
 322                                                 <xs:attribute name="textCol2" type="xs:int" />
 323                                                 <xs:attribute name="textColThreshold" type="xs:int" />
 324                                                 <xs:attribute name="showUnconserved" type="xs:boolean"
 325                                                         use="optional" />
 326                                                 <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
 327                                                         use="optional" default="true" />
 328                                                 <xs:attribute name="showConsensusHistogram" type="xs:boolean"
 329                                                         use="optional" default="true" />
 330                                                 <xs:attribute name="showSequenceLogo" type="xs:boolean"
 331                                                         use="optional" default="false" />
 332                                                 <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
 333                                                         use="optional" default="false" />
 334                                                 <xs:attribute name="id" type="xs:string" use="optional">
 335                                                         <xs:annotation>
 336                                                                 <xs:documentation>
 337                                                                         Optional sequence group ID (only
 338                                                                         needs to be
 339                                                                         unique for this
 340                                                                         alignment)
 341                                                                 </xs:documentation>
 342                                                         </xs:annotation>
 343                                                 </xs:attribute>
 344                                         </xs:complexType>
 345                                 </xs:element>
 346                                 <xs:element name="Viewport" maxOccurs="unbounded"
 347                                         minOccurs="0">
 348                                         <xs:complexType>
 349                                                 <xs:sequence>
 350                                                         <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
 351                                                                 minOccurs="0" maxOccurs="1">
 352                                                         </xs:element>
 353                                                         <xs:element name="hiddenColumns" minOccurs="0"
 354                                                                 maxOccurs="unbounded">
 355                                                                 <xs:complexType>
 356                                                                         <xs:attribute name="start" type="xs:int" />
 357                                                                         <xs:attribute name="end" type="xs:int" />
 358                                                                 </xs:complexType>
 359                                                         </xs:element>
 360                                                         <xs:element name="calcIdParam" minOccurs="0"
 361                                                                 maxOccurs="unbounded">
 362                                                                 <xs:complexType>
 363                                                                         <xs:complexContent>
 364                                                                                 <xs:extension base="jvws:WebServiceParameterSet">
 365                                                                                         <xs:attribute name="calcId" type="xs:string"
 366                                                                                                 use="required">
 367                                                                                                 <xs:annotation>
 368                                                                                                         <xs:documentation>handle for the calculation which uses
 369                                                                                                                 this parameter set
 370                                                                                                         </xs:documentation>
 371                                                                                                 </xs:annotation>
 372                                                                                         </xs:attribute>
 373                                                                                         <xs:attribute name="needsUpdate" type="xs:boolean"
 374                                                                                                 use="optional" default="false">
 375                                                                                                 <xs:annotation>
 376                                                                                                         <xs:documentation>should the calculation be performed
 377                                                                                                                 immediately after loading in order to refresh results
 378                                                                                                         </xs:documentation>
 379                                                                                                 </xs:annotation>
 380                                                                                         </xs:attribute>
 381                                                                                         <xs:attribute name="autoUpdate" type="xs:boolean"
 382                                                                                                 use="required">
 383                                                                                                 <xs:annotation>
 384                                                                                                         <xs:documentation>should the calculation be automatically
 385                                                                                                                 performed on edits
 386                                                                                                         </xs:documentation>
 387                                                                                                 </xs:annotation>
 388                                                                                         </xs:attribute>
 389                                                                                 </xs:extension>
 390                                                                         </xs:complexContent>
 391                                                                 </xs:complexType>
 392                                                         </xs:element>
 393                                                 </xs:sequence>
 394                                                 <xs:attributeGroup ref="jv:swingwindow" />
 395                                                 <xs:attribute name="conservationSelected" type="xs:boolean" />
 396                                                 <xs:attribute name="pidSelected" type="xs:boolean" />
 397                                                 <xs:attribute name="bgColour" type="xs:string" />
 398                                                 <xs:attribute name="consThreshold" type="xs:int" />
 399                                                 <xs:attribute name="pidThreshold" type="xs:int" />
 400                                                 <xs:attribute name="title" type="xs:string" />
 401                                                 <xs:attribute name="showFullId" type="xs:boolean" />
 402                                                 <xs:attribute name="rightAlignIds" type="xs:boolean" />
 403                                                 <xs:attribute name="showText" type="xs:boolean" />
 404                                                 <xs:attribute name="showColourText" type="xs:boolean" />
 405                                                 <xs:attribute name="showUnconserved" type="xs:boolean"
 406                                                         use="optional" default="false" />
 407                                                 <xs:attribute name="showBoxes" type="xs:boolean" />
 408                                                 <xs:attribute name="wrapAlignment" type="xs:boolean" />
 409                                                 <xs:attribute name="renderGaps" type="xs:boolean" />
 410                                                 <xs:attribute name="showSequenceFeatures" type="xs:boolean" />
 411                                                 <xs:attribute name="showNPfeatureTooltip" type="xs:boolean"
 412                                                         use="optional" />
 413                                                 <xs:attribute name="showDbRefTooltip" type="xs:boolean"
 414                                                         use="optional" />
 415                                                 <xs:attribute name="followHighlight" type="xs:boolean"
 416                                                         use="optional" default="true" />
 417                                                 <xs:attribute name="followSelection" type="xs:boolean"
 418                                                         use="optional" default="true" />
 419                                                 <xs:attribute name="showAnnotation" type="xs:boolean" />
 420                                                 <xs:attribute name="centreColumnLabels" type="xs:boolean"
 421                                                         use="optional" default="false" />
 422                                                 <xs:attribute name="showGroupConservation" type="xs:boolean"
 423                                                         use="optional" default="false" />
 424                                                 <xs:attribute name="showGroupConsensus" type="xs:boolean"
 425                                                         use="optional" default="false" />
 426                                                 <xs:attribute name="showConsensusHistogram" type="xs:boolean"
 427                                                         use="optional" default="true" />
 428                                                 <xs:attribute name="showSequenceLogo" type="xs:boolean"
 429                                                         use="optional" default="false" />
 430                                                 <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
 431                                                         use="optional" default="false" />
 432                                                 <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
 433                                                         use="optional" default="true" />
 434                                                 <xs:attribute name="startRes" type="xs:int" />
 435                                                 <xs:attribute name="startSeq" type="xs:int" />
 436                                                 <xs:attribute name="fontName" type="xs:string" />
 437                                                 <xs:attribute name="fontSize" type="xs:int" />
 438                                                 <xs:attribute name="fontStyle" type="xs:int" />
 439                                                 <xs:attribute name="scaleProteinAsCdna" type="xs:boolean" use="optional" default="true" />
 440                                                 <xs:attribute name="viewName" type="xs:string" />
 441                                                 <xs:attribute name="sequenceSetId" type="xs:string" />
 442                                                 <xs:attribute name="gatheredViews" type="xs:boolean" />
 443                                                 <xs:attribute name="textCol1" type="xs:int" />
 444                                                 <xs:attribute name="textCol2" type="xs:int" />
 445                                                 <xs:attribute name="textColThreshold" type="xs:int" />
 446                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 447                                                         <xs:annotation>
 448                                                                 <xs:documentation>
 449                                                                         unique id used by jalview to
 450                                                                         synchronize
 451                                                                         between stored and
 452                                                                         instantiated views
 453                                                                 </xs:documentation>
 454                                                         </xs:annotation>
 455                                                 </xs:attribute>
 456                                                 <xs:attribute name="complementId" type="xs:string"
 457                                                         use="optional">
 458                                                         <xs:annotation>
 459                                                                 <xs:documentation>
 460                                                                         The viewport id of this viewport's
 461                                                                         (cdna/protein) coding complement, if any
 462                                                                 </xs:documentation>
 463                                                         </xs:annotation>
 464                                                 </xs:attribute>
 465                                         </xs:complexType>
 466                                 </xs:element>
 467                                 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
 468                                         <xs:complexType>
 469                                                 <xs:sequence>
 470                                                         <xs:element name="UserColourScheme" type="jalview:JalviewUserColours" />
 471                                                 </xs:sequence>
 472                                                 <xs:attribute name="id" type="xs:string" />
 473                                         </xs:complexType>
 474                                 </xs:element>
 475                                 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
 476                                         <xs:complexType>
 477                                                 <xs:sequence minOccurs="0">
 478                                                         <xs:element name="title" type="xs:string" />
 479                                                         <xs:element name="newick" type="xs:string" />
 480                                                 </xs:sequence>
 481                                                 <xs:attribute name="fontName" type="xs:string" />
 482                                                 <xs:attribute name="fontSize" type="xs:int" />
 483                                                 <xs:attribute name="fontStyle" type="xs:int" />
 484                                                 <xs:attribute name="threshold" type="xs:float" />
 485                                                 <xs:attribute name="showBootstrap" type="xs:boolean" />
 486                                                 <xs:attribute name="showDistances" type="xs:boolean" />
 487                                                 <xs:attribute name="markUnlinked" type="xs:boolean" />
 488                                                 <xs:attribute name="fitToWindow" type="xs:boolean" />
 489                                                 <xs:attribute name="currentTree" type="xs:boolean" />
 490                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 491                                                         <xs:annotation>
 492                                                                 <xs:documentation>
 493                                                                         Tree ID added for binding tree
 494                                                                         visualization
 495                                                                         settings to vamsas
 496                                                                         document trees in jalview 2.4.1
 497                                                                 </xs:documentation>
 498                                                         </xs:annotation>
 499                                                 </xs:attribute>
 500                                                 <xs:attributeGroup ref="jv:swingwindow" />
 501                                         </xs:complexType>
 502                                 </xs:element>
 503                                 <xs:element name="FeatureSettings" minOccurs="0">
 504                                         <xs:complexType>
 505                                                 <xs:sequence>
 506                                                         <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
 507                                                                 <xs:complexType>
 508                                                                         <xs:sequence>
 509                                                                             <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
 510                                                                                         <xs:annotation>
 511                                                                                                 <xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
 512                                                                                         </xs:annotation>
 513                                                                             </xs:element>
 514                                                                                 <xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
 515                                                                                         <xs:annotation>
 516                                                                                                 <xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
 517                                                                                         </xs:annotation>
 518                                                                                 </xs:element>
 519                                                                         </xs:sequence>
 520                                                                         <xs:attribute name="type" type="xs:string" use="required" />
 521                                                                         <xs:attribute name="colour" type="xs:int" use="required" />
 522                                                                         <xs:attribute name="display" type="xs:boolean"
 523                                                                                 use="required" />
 524                                                                         <xs:attribute name="order" type="xs:float" use="optional" />
 525                                                                         <xs:attribute name="mincolour" type="xs:int" use="optional">
 526                                                                                 <xs:annotation>
 527                                                                                         <xs:documentation>
 528                                                                                                 Optional minimum colour
 529                                                                                                 for graduated
 530                                                                                                 feature
 531                                                                                                 colour
 532                                                                                         </xs:documentation>
 533                                                                                 </xs:annotation>
 534                                                                         </xs:attribute>
 535                                                                         <xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
 536                                                                         <xs:attribute name="threshold" type="xs:float"
 537                                                                                 use="optional">
 538                                                                                 <xs:annotation>
 539                                                                                         <xs:documentation>
 540                                                                                                 threshold value for
 541                                                                                                 graduated feature colour
 542                                                                                         </xs:documentation>
 543                                                                                 </xs:annotation>
 544                                                                         </xs:attribute>
 545                                                                         <xs:attribute name="threshstate" type="xs:int"
 546                                                                                 use="optional">
 547                                                                                 <xs:annotation>
 548                                                                                         <xs:documentation>
 549                                                                                                 threshold type for
 550                                                                                                 graduated feature colour
 551                                                                                         </xs:documentation>
 552                                                                                 </xs:annotation>
 553                                                                         </xs:attribute>
 554                                                                         <xs:attribute name="max" type="xs:float" use="optional" />
 555                                                                         <xs:attribute name="min" type="xs:float" use="optional" />
 556                                                                         <xs:attribute name="colourByLabel" type="xs:boolean"
 557                                                                                 use="optional" />
 558                                                                         <xs:attribute name="autoScale" type="xs:boolean"
 559                                                                                 use="optional" />
 560                                                                 </xs:complexType>
 561                                                         </xs:element>
 562                                                         <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
 563                                                                 <xs:complexType>
 564                                                                         <xs:attribute name="name" type="xs:string" use="required" />
 565                                                                         <xs:attribute name="display" type="xs:boolean"
 566                                                                                 use="required" />
 567                                                                 </xs:complexType>
 568                                                         </xs:element>
 569                                                 </xs:sequence>
 570                                         </xs:complexType>
 571                                 </xs:element>
 572                         </xs:sequence>
 573                 </xs:sequence>
 574         </xs:complexType>
 575         <xs:complexType name="feature">
 576                 <xs:sequence>
 577                         <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 578                                 <xs:complexType>
 579                                         <xs:attribute name="key" type="xs:string" use="required" />
 580                                         <xs:attribute name="key2" type="xs:string" use="optional">
 581                                                 <xs:annotation>
 582                                                         <xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
 583                                                 </xs:annotation>
 584                                         </xs:attribute>
 585                                         <xs:attribute name="value" type="xs:string" use="required" />
 586                                 </xs:complexType>
 587                         </xs:element>
 588                 </xs:sequence>
 589                 <xs:attribute name="begin" type="xs:int" use="required" />
 590                 <xs:attribute name="end" type="xs:int" use="required" />
 591                 <xs:attribute name="type" type="xs:string" use="required" />
 592                 <xs:attribute name="description" type="xs:string" use="optional" />
 593                 <xs:attribute name="status" type="xs:string" use="optional" />
 594                 <xs:attribute name="featureGroup" type="xs:string" use="optional" />
 595                 <xs:attribute name="score" type="xs:float" use="optional" />
 596         </xs:complexType>
 597         <xs:complexType name="pdbentry">
 598                 <xs:sequence minOccurs="0" maxOccurs="unbounded">
 599                         <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
 600                                 <xs:complexType>
 601                                         <xs:attribute name="name" type="xs:string" use="required" />
 602                                         <xs:attribute name="value" type="xs:string" use="required" />
 603                                 </xs:complexType>
 604                         </xs:element>
 605                 </xs:sequence>
 606                 <xs:attribute name="id" type="xs:string" use="required" />
 607                 <xs:attribute name="type" type="xs:string" use="optional" />
 608                 <xs:attribute name="file" type="xs:string" />
 609         </xs:complexType>
 610         <!-- <xs:complexType name="reportWindow"> <xs:annotation> <xs:documentation>Generic
 611                 type for windows containing mime-typed data associated with other jalview
 612                 windows</xs:documentation> </xs:annotation> <xs:sequence> </xs:sequence>
 613                 <xs:attribute name="id" type="xs:string" use="required"/> <xs:attribute name="type"
 614                 type="xs:string" use="optional"/> <xs:attribute name="file" type="xs:string"
 615                 use="optional"/> </xs:complexType> -->
 616         <xs:attributeGroup name="swingwindow">
 617                 <xs:annotation>
 618                         <xs:documentation>
 619                                 base attributes for windows displayed in Jalview
 620                                 desktop.
 621                         </xs:documentation>
 622                 </xs:annotation>
 623                 <xs:attribute name="width" type="xs:int" />
 624                 <xs:attribute name="height" type="xs:int" />
 625                 <xs:attribute name="xpos" type="xs:int" />
 626                 <xs:attribute name="ypos" type="xs:int" />
 627         </xs:attributeGroup>
 628         <xs:complexType name="AnnotationColourScheme">
 629                 <xs:attribute name="aboveThreshold" type="xs:int" />
 630                 <xs:attribute name="annotation" type="xs:string" />
 631                 <xs:attribute name="minColour" type="xs:int" />
 632                 <xs:attribute name="maxColour" type="xs:int" />
 633                 <xs:attribute name="colourScheme" type="xs:string" />
 634                 <xs:attribute name="threshold" type="xs:float" />
 635                 <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
 636                 <xs:attribute name="predefinedColours" type="xs:boolean"
 637                         use="optional" />
 638         </xs:complexType>
 639
 640 </xs:schema>