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 <!--
  14         Java JAXB binding classes are generated by running command line tool xjc:
  15             xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
  16         Note this also generates code for included schemas
  17 -->
  18 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
  19         xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours"
  20         xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset"
  21         targetNamespace="www.jalview.org" elementFormDefault="qualified"
  22         attributeFormDefault="unqualified">
  23         <xs:import namespace="www.vamsas.ac.uk/jalview/version2"
  24                 schemaLocation="vamsas.xsd" />
  25         <xs:import namespace="www.jalview.org/colours"
  26                 schemaLocation="JalviewUserColours.xsd" />
  27         <xs:import namespace="www.jalview.org/xml/wsparamset"
  28                 schemaLocation="JalviewWsParamSet.xsd" />
  29         <xs:element name="JalviewModel" type="jv:JalviewModel" />
  30         <xs:complexType name="JalviewModel">
  31                 <xs:sequence>
  32                         <xs:element name="creationDate" type="xs:dateTime" />
  33                         <xs:element name="version" type="xs:string" />
  34                         <xs:element name="vamsasModel" type="vamsas:VAMSAS" />
  35                         <xs:sequence>
  36                                 <xs:element name="JSeq" maxOccurs="unbounded" minOccurs="0">
  37                                         <xs:complexType>
  38                                                 <xs:sequence>
  39                                                         <xs:element name="features"
  40                                                                 type="jv:feature" minOccurs="0" maxOccurs="unbounded" />
  41                                                         <xs:element name="pdbids" minOccurs="0"
  42                                                                 maxOccurs="unbounded">
  43                                                                 <xs:complexType>
  44                                                                         <xs:complexContent>
  45                                                                                 <xs:extension
  46                                                                                         base="jv:pdbentry">
  47                                                                                         <xs:sequence>
  48                                                                                                 <xs:element
  49                                                                                                         name="structureState" minOccurs="0"
  50                                                                                                         maxOccurs="unbounded">
  51                                                                                                         <xs:complexType>
  52                                                                                                                 <xs:simpleContent>
  53                                                                                                                         <xs:extension
  54                                                                                                                                 base="xs:string">
  55                                                                                                                                 <xs:attributeGroup
  56                                                                                                                                         ref="jv:swingwindow" />
  57                                                                                                                                 <xs:attribute
  58                                                                                                                                         name="visible" type="xs:boolean" />
  59                                                                                                                                 <xs:attribute
  60                                                                                                                                         name="viewId" type="xs:string" use="optional">
  61                                                                                                                                         <xs:annotation>
  62                                                                                                                                                 <xs:documentation>
  63                                                                                                                                                         additional
  64                                                                                                                                                         identifier
  65                                                                                                                                                         which
  66                                                                                                                                                         properly
  67                                                                                                                                                         disambiguates
  68                                                                                                                                                         the
  69                                                                                                                                                         structure
  70                                                                                                                                                         view
  71                                                                                                                                                         from
  72                                                                                                                                                         any
  73                                                                                                                                                         other
  74                                                                                                                                                         view
  75                                                                                                                                                         with
  76                                                                                                                                                         the
  77                                                                                                                                                         same
  78                                                                                                                                                         attributes.
  79                                                                                                                                                         This
  80                                                                                                                                                         is
  81                                                                                                                                                         not
  82                                                                                                                                                         an
  83                                                                                                                                                         ID,
  84                                                                                                                                                         because
  85                                                                                                                                                         it
  86                                                                                                                                                         is
  87                                                                                                                                                         possible
  88                                                                                                                                                         to
  89                                                                                                                                                         have
  90                                                                                                                                                         many
  91                                                                                                                                                         references
  92                                                                                                                                                         to
  93                                                                                                                                                         the
  94                                                                                                                                                         same
  95                                                                                                                                                         physical
  96                                                                                                                                                         structure
  97                                                                                                                                                         view
  98                                                                                                                                                         from
  99                                                                                                                                                         different
 100                                                                                                                                                         sequences
 101                                                                                                                                                         in
 102                                                                                                                                                         an
 103                                                                                                                                                         alignment.
 104                                                                                                                                                         A
 105                                                                                                                                                         structureState
 106                                                                                                                                                         element
 107                                                                                                                                                         citing
 108                                                                                                                                                         the
 109                                                                                                                                                         same
 110                                                                                                                                                         viewId
 111                                                                                                                                                         will
 112                                                                                                                                                         appear
 113                                                                                                                                                         for
 114                                                                                                                                                         each
 115                                                                                                                                                         instance.
 116                                                                                                                                                 </xs:documentation>
 117                                                                                                                                         </xs:annotation>
 118                                                                                                                                 </xs:attribute>
 119                                                                                                                                 <xs:attribute
 120                                                                                                                                         name="alignwithAlignPanel" type="xs:boolean"
 121                                                                                                                                         use="optional" default="true">
 122                                                                                                                                         <xs:annotation>
 123                                                                                                                                                 <xs:documentation>
 124                                                                                                                                                         Flag
 125                                                                                                                                                         set
 126                                                                                                                                                         if
 127                                                                                                                                                         the
 128                                                                                                                                                         alignment
 129                                                                                                                                                         panel
 130                                                                                                                                                         containing
 131                                                                                                                                                         this
 132                                                                                                                                                         JSeq
 133                                                                                                                                                         should
 134                                                                                                                                                         be
 135                                                                                                                                                         included
 136                                                                                                                                                         in
 137                                                                                                                                                         those
 138                                                                                                                                                         used
 139                                                                                                                                                         to
 140                                                                                                                                                         perform
 141                                                                                                                                                         a
 142                                                                                                                                                         structure
 143                                                                                                                                                         superposition
 144                                                                                                                                                         (since
 145                                                                                                                                                         Jalview
 146                                                                                                                                                         2.7).
 147                                                                                                                                                 </xs:documentation>
 148                                                                                                                                         </xs:annotation>
 149                                                                                                                                 </xs:attribute>
 150                                                                                                                                 <xs:attribute
 151                                                                                                                                         name="colourwithAlignPanel" type="xs:boolean"
 152                                                                                                                                         use="optional" default="false">
 153                                                                                                                                         <xs:annotation>
 154                                                                                                                                                 <xs:documentation>
 155                                                                                                                                                         Flag
 156                                                                                                                                                         set
 157                                                                                                                                                         if
 158                                                                                                                                                         the
 159                                                                                                                                                         alignment
 160                                                                                                                                                         panel
 161                                                                                                                                                         containing
 162                                                                                                                                                         this
 163                                                                                                                                                         JSeq
 164                                                                                                                                                         should
 165                                                                                                                                                         be
 166                                                                                                                                                         included
 167                                                                                                                                                         in
 168                                                                                                                                                         those
 169                                                                                                                                                         used
 170                                                                                                                                                         to
 171                                                                                                                                                         colour
 172                                                                                                                                                         its
 173                                                                                                                                                         associated
 174                                                                                                                                                         sequences
 175                                                                                                                                                         in
 176                                                                                                                                                         this
 177                                                                                                                                                         structureState(since
 178                                                                                                                                                         Jalview
 179                                                                                                                                                         2.7).
 180                                                                                                                                                 </xs:documentation>
 181                                                                                                                                         </xs:annotation>
 182                                                                                                                                 </xs:attribute>
 183                                                                                                                                 <xs:attribute
 184                                                                                                                                         name="colourByJmol" type="xs:boolean" use="optional"
 185                                                                                                                                         default="true">
 186                                                                                                                                         <xs:annotation>
 187                                                                                                                                                 <xs:documentation>
 188                                                                                                                                                         Flag
 189                                                                                                                                                         set
 190                                                                                                                                                         if
 191                                                                                                                                                         the
 192                                                                                                                                                         structure
 193                                                                                                                                                         display
 194                                                                                                                                                         is
 195                                                                                                                                                         coloured
 196                                                                                                                                                         by
 197                                                                                                                                                         the
 198                                                                                                                                                         Jmol
 199                                                                                                                                                         state,
 200                                                                                                                                                         rather
 201                                                                                                                                                         than
 202                                                                                                                                                         by
 203                                                                                                                                                         one
 204                                                                                                                                                         or
 205                                                                                                                                                         more
 206                                                                                                                                                         linked
 207                                                                                                                                                         alignment
 208                                                                                                                                                         views.
 209                                                                                                                                                 </xs:documentation>
 210                                                                                                                                         </xs:annotation>
 211                                                                                                                                 </xs:attribute>
 212                                                                                                                                 <xs:attribute
 213                                                                                                                                         name="type" type="xs:string" use="optional">
 214                                                                                                                                         <xs:annotation>
 215                                                                                                                                                 <xs:documentation>
 216                                                                                                                                                         An
 217                                                                                                                                                         identifier
 218                                                                                                                                                         for
 219                                                                                                                                                         the
 220                                                                                                                                                         viewer
 221                                                                                                                                                         type,
 222                                                                                                                                                         currently
 223                                                                                                                                                         either
 224                                                                                                                                                         JMOL
 225                                                                                                                                                         or
 226                                                                                                                                                         CHIMERA
 227                                                                                                                                                 </xs:documentation>
 228                                                                                                                                         </xs:annotation>
 229                                                                                                                                 </xs:attribute>
 230
 231                                                                                                                         </xs:extension>
 232                                                                                                                 </xs:simpleContent>
 233                                                                                                         </xs:complexType>
 234                                                                                                 </xs:element>
 235                                                                                         </xs:sequence>
 236                                                                                 </xs:extension>
 237                                                                         </xs:complexContent>
 238                                                                 </xs:complexType>
 239                                                         </xs:element>
 240                                                         <xs:element name="hiddenSequences"
 241                                                                 type="xs:int" minOccurs="0" maxOccurs="unbounded" />
 242                                                         <xs:element name="rnaViewer" minOccurs="0"
 243                                                                 maxOccurs="unbounded">
 244                                                                 <xs:annotation>
 245                                                                         <xs:documentation>
 246                                                                                 Reference to a viewer showing
 247                                                                                 RNA structure for this sequence.
 248                                                                                 Schema supports one viewer
 249                                                                                 showing multiple annotations for
 250                                                                                 multiple sequences, though
 251                                                                                 currently only one annotation
 252                                                                                 for one sequence (gapped or
 253                                                                                 trimmed) is used
 254                                                                         </xs:documentation>
 255                                                                 </xs:annotation>
 256                                                                 <xs:complexType>
 257                                                                         <xs:sequence>
 258                                                                                 <xs:element
 259                                                                                         name="secondaryStructure" minOccurs="1"
 260                                                                                         maxOccurs="unbounded">
 261                                                                                         <xs:complexType>
 262                                                                                                 <xs:attribute
 263                                                                                                         name="title" type="xs:string" />
 264                                                                                                 <xs:attribute
 265                                                                                                         name="annotationId" type="xs:string" use="required">
 266                                                                                                         <xs:annotation>
 267                                                                                                                 <xs:documentation>
 268                                                                                                                         id attribute
 269                                                                                                                         of
 270                                                                                                                         Annotation
 271                                                                                                                         in
 272                                                                                                                         vamsasModel
 273                                                                                                                         for the
 274                                                                                                                         secondary
 275                                                                                                                         structure
 276                                                                                                                         annotation
 277                                                                                                                         shown in the
 278                                                                                                                         viewer
 279                                                                                                                 </xs:documentation>
 280                                                                                                         </xs:annotation>
 281                                                                                                 </xs:attribute>
 282                                                                                                 <xs:attribute
 283                                                                                                         name="gapped" type="xs:boolean">
 284                                                                                                         <xs:annotation>
 285                                                                                                                 <xs:documentation>
 286                                                                                                                         if true the
 287                                                                                                                         RNA
 288                                                                                                                         structure is
 289                                                                                                                         shown with
 290                                                                                                                         gaps, if
 291                                                                                                                         false
 292                                                                                                                         without
 293                                                                                                                 </xs:documentation>
 294                                                                                                         </xs:annotation>
 295                                                                                                 </xs:attribute>
 296                                                                                                 <xs:attribute
 297                                                                                                         name="viewerState" type="xs:string">
 298                                                                                                         <xs:annotation>
 299                                                                                                                 <xs:documentation>
 300                                                                                                                         name of the
 301                                                                                                                         project jar
 302                                                                                                                         entry that
 303                                                                                                                         holds the
 304                                                                                                                         VARNA viewer
 305                                                                                                                         state for
 306                                                                                                                         the
 307                                                                                                                         structure
 308                                                                                                                 </xs:documentation>
 309                                                                                                         </xs:annotation>
 310                                                                                                 </xs:attribute>
 311                                                                                         </xs:complexType>
 312                                                                                 </xs:element>
 313                                                                         </xs:sequence>
 314                                                                         <xs:attributeGroup
 315                                                                                 ref="jv:swingwindow" />
 316                                                                         <xs:attribute name="title"
 317                                                                                 type="xs:string" />
 318                                                                         <xs:attribute name="viewId"
 319                                                                                 type="xs:string">
 320                                                                                 <xs:annotation>
 321                                                                                         <xs:documentation>
 322                                                                                                 An id unique to the RNA
 323                                                                                                 viewer panel
 324                                                                                         </xs:documentation>
 325                                                                                 </xs:annotation>
 326                                                                         </xs:attribute>
 327                                                                         <xs:attribute name="dividerLocation"
 328                                                                                 type="xs:int">
 329                                                                                 <xs:annotation>
 330                                                                                         <xs:documentation>
 331                                                                                                 horizontal position of
 332                                                                                                 split pane divider
 333                                                                                         </xs:documentation>
 334                                                                                 </xs:annotation>
 335                                                                         </xs:attribute>
 336                                                                         <xs:attribute name="selectedRna"
 337                                                                                 type="xs:int">
 338                                                                                 <xs:annotation>
 339                                                                                         <xs:documentation>
 340                                                                                                 Index of the selected
 341                                                                                                 structure in the viewer
 342                                                                                                 panel
 343                                                                                         </xs:documentation>
 344                                                                                 </xs:annotation>
 345                                                                         </xs:attribute>
 346                                                                 </xs:complexType>
 347                                                         </xs:element>
 348                                                 </xs:sequence>
 349                                                 <xs:attribute name="colour" type="xs:int" use="optional" />
 350                                                 <xs:attribute name="start" type="xs:int" use="required" />
 351                                                 <xs:attribute name="end" type="xs:int" use="required" />
 352                                                 <xs:attribute name="id" type="xs:string" use="required" />
 353                                                 <xs:attribute name="hidden" type="xs:boolean" />
 354                                                 <xs:attribute name="viewreference" type="xs:boolean" use="optional"/>
 355                                         </xs:complexType>
 356                                 </xs:element>
 357                                 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
 358                                         <xs:complexType>
 359                                                 <xs:sequence>
 360                                                         <xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
 361                                                         <xs:element name="annotationColours" type="jv:AnnotationColourScheme"
 362                                                                 minOccurs="0" maxOccurs="1" />
 363                                                 </xs:sequence>
 364                                                 <xs:attribute name="start" type="xs:int" />
 365                                                 <xs:attribute name="end" type="xs:int" />
 366                                                 <xs:attribute name="name" type="xs:string" />
 367                                                 <xs:attribute name="colour" type="xs:string" />
 368                                                 <xs:attribute name="consThreshold" type="xs:int" />
 369                                                 <xs:attribute name="pidThreshold" type="xs:int" />
 370                                                 <xs:attribute name="outlineColour" type="xs:int" />
 371                                                 <xs:attribute name="displayBoxes" type="xs:boolean" />
 372                                                 <xs:attribute name="displayText" type="xs:boolean" />
 373                                                 <xs:attribute name="colourText" type="xs:boolean" />
 374                                                 <xs:attribute name="textCol1" type="xs:int" />
 375                                                 <xs:attribute name="textCol2" type="xs:int" />
 376                                                 <xs:attribute name="textColThreshold" type="xs:int" />
 377                                                 <xs:attribute name="showUnconserved" type="xs:boolean"
 378                                                         use="optional" />
 379                                                 <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
 380                                                         use="optional" default="true" />
 381                                                 <xs:attribute name="showConsensusHistogram" type="xs:boolean"
 382                                                         use="optional" default="true" />
 383                                                 <xs:attribute name="showSequenceLogo" type="xs:boolean"
 384                                                         use="optional" default="false" />
 385                                                 <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
 386                                                         use="optional" default="false" />
 387                                                 <xs:attribute name="id" type="xs:string" use="optional">
 388                                                         <xs:annotation>
 389                                                                 <xs:documentation>
 390                                                                         Optional sequence group ID (only
 391                                                                         needs to be
 392                                                                         unique for this
 393                                                                         alignment)
 394                                                                 </xs:documentation>
 395                                                         </xs:annotation>
 396                                                 </xs:attribute>
 397                                         </xs:complexType>
 398                                 </xs:element>
 399                                 <xs:element name="Viewport" maxOccurs="unbounded"
 400                                         minOccurs="0">
 401                                         <xs:complexType>
 402                                                 <xs:sequence>
 403                                                         <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
 404                                                                 minOccurs="0" maxOccurs="1">
 405                                                         </xs:element>
 406                                                         <xs:element name="hiddenColumns" minOccurs="0"
 407                                                                 maxOccurs="unbounded">
 408                                                                 <xs:complexType>
 409                                                                         <xs:attribute name="start" type="xs:int" />
 410                                                                         <xs:attribute name="end" type="xs:int" />
 411                                                                 </xs:complexType>
 412                                                         </xs:element>
 413                                                         <xs:element name="calcIdParam" minOccurs="0"
 414                                                                 maxOccurs="unbounded">
 415                                                                 <xs:complexType>
 416                                                                         <xs:complexContent>
 417                                                                                 <xs:extension base="jvws:WebServiceParameterSet">
 418                                                                                         <xs:attribute name="calcId" type="xs:string"
 419                                                                                                 use="required">
 420                                                                                                 <xs:annotation>
 421                                                                                                         <xs:documentation>handle for the calculation which uses
 422                                                                                                                 this parameter set
 423                                                                                                         </xs:documentation>
 424                                                                                                 </xs:annotation>
 425                                                                                         </xs:attribute>
 426                                                                                         <xs:attribute name="needsUpdate" type="xs:boolean"
 427                                                                                                 use="optional" default="false">
 428                                                                                                 <xs:annotation>
 429                                                                                                         <xs:documentation>should the calculation be performed
 430                                                                                                                 immediately after loading in order to refresh results
 431                                                                                                         </xs:documentation>
 432                                                                                                 </xs:annotation>
 433                                                                                         </xs:attribute>
 434                                                                                         <xs:attribute name="autoUpdate" type="xs:boolean"
 435                                                                                                 use="required">
 436                                                                                                 <xs:annotation>
 437                                                                                                         <xs:documentation>should the calculation be automatically
 438                                                                                                                 performed on edits
 439                                                                                                         </xs:documentation>
 440                                                                                                 </xs:annotation>
 441                                                                                         </xs:attribute>
 442                                                                                 </xs:extension>
 443                                                                         </xs:complexContent>
 444                                                                 </xs:complexType>
 445                                                         </xs:element>
 446                                                         <xs:element name="overview" minOccurs="0">
 447                                                           <xs:complexType>
 448                                                                 <xs:attributeGroup ref="jv:swingwindow" />
 449                                                                 <xs:attribute name="showHidden" type="xs:boolean" />
 450                                                                 <xs:attribute name="residueColour" type="xs:int" />
 451                                                                 <xs:attribute name="gapColour" type="xs:int" />
 452                                                                 <xs:attribute name="hiddenColour" type="xs:int" />
 453                                                                 <xs:attribute name="title" type="xs:string" />
 454                                                           </xs:complexType>
 455                                                         </xs:element>
 456                                                 </xs:sequence>
 457                                                 <xs:attributeGroup ref="jv:swingwindow" />
 458                                                 <xs:attribute name="conservationSelected" type="xs:boolean" />
 459                                                 <xs:attribute name="pidSelected" type="xs:boolean" />
 460                                                 <xs:attribute name="bgColour" type="xs:string" />
 461                                                 <xs:attribute name="consThreshold" type="xs:int" />
 462                                                 <xs:attribute name="pidThreshold" type="xs:int" />
 463                                                 <xs:attribute name="title" type="xs:string" />
 464                                                 <xs:attribute name="showFullId" type="xs:boolean" />
 465                                                 <xs:attribute name="rightAlignIds" type="xs:boolean" />
 466                                                 <xs:attribute name="showText" type="xs:boolean" />
 467                                                 <xs:attribute name="showColourText" type="xs:boolean" />
 468                                                 <xs:attribute name="showUnconserved" type="xs:boolean"
 469                                                         use="optional" default="false" />
 470                                                 <xs:attribute name="showBoxes" type="xs:boolean" />
 471                                                 <xs:attribute name="wrapAlignment" type="xs:boolean" />
 472                                                 <xs:attribute name="renderGaps" type="xs:boolean" />
 473                                                 <xs:attribute name="showSequenceFeatures" type="xs:boolean" />
 474                                                 <xs:attribute name="showNPfeatureTooltip" type="xs:boolean"
 475                                                         use="optional" />
 476                                                 <xs:attribute name="showDbRefTooltip" type="xs:boolean"
 477                                                         use="optional" />
 478                                                 <xs:attribute name="followHighlight" type="xs:boolean"
 479                                                         use="optional" default="true" />
 480                                                 <xs:attribute name="followSelection" type="xs:boolean"
 481                                                         use="optional" default="true" />
 482                                                 <xs:attribute name="showAnnotation" type="xs:boolean" />
 483                                                 <xs:attribute name="centreColumnLabels" type="xs:boolean"
 484                                                         use="optional" default="false" />
 485                                                 <xs:attribute name="showGroupConservation" type="xs:boolean"
 486                                                         use="optional" default="false" />
 487                                                 <xs:attribute name="showGroupConsensus" type="xs:boolean"
 488                                                         use="optional" default="false" />
 489                                                 <xs:attribute name="showConsensusHistogram" type="xs:boolean"
 490                                                         use="optional" default="true" />
 491                                                 <xs:attribute name="showSequenceLogo" type="xs:boolean"
 492                                                         use="optional" default="false" />
 493                                                 <xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
 494                                                         use="optional" default="false" />
 495                                                 <xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
 496                                                         use="optional" default="true" />
 497                                                 <xs:attribute name="startRes" type="xs:int" />
 498                                                 <xs:attribute name="startSeq" type="xs:int" />
 499                                                 <xs:attribute name="charWidth" type="xs:int" />
 500                                                 <xs:attribute name="charHeight" type="xs:int" />
 501                                                 <xs:attribute name="fontName" type="xs:string" />
 502                                                 <xs:attribute name="fontSize" type="xs:int" />
 503                                                 <xs:attribute name="fontStyle" type="xs:int" />
 504                                                 <xs:attribute name="idWidth" type="xs:int" />
 505                                                 <xs:attribute name="idWidthManuallyAdjusted" type="xs:boolean" />
 506                                                 <xs:attribute name="scaleProteinAsCdna" type="xs:boolean" use="optional" default="true" />
 507                                                 <xs:attribute name="viewName" type="xs:string" />
 508                                                 <xs:attribute name="sequenceSetId" type="xs:string" />
 509                                                 <xs:attribute name="gatheredViews" type="xs:boolean" />
 510                                                 <xs:attribute name="textCol1" type="xs:int" />
 511                                                 <xs:attribute name="textCol2" type="xs:int" />
 512                                                 <xs:attribute name="textColThreshold" type="xs:int" />
 513                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 514                                                         <xs:annotation>
 515                                                                 <xs:documentation>
 516                                                                         unique id used by jalview to
 517                                                                         synchronize
 518                                                                         between stored and
 519                                                                         instantiated views
 520                                                                 </xs:documentation>
 521                                                         </xs:annotation>
 522                                                 </xs:attribute>
 523                                                 <xs:attribute name="complementId" type="xs:string"
 524                                                         use="optional">
 525                                                         <xs:annotation>
 526                                                                 <xs:documentation>
 527                                                                         The viewport id of this viewport's
 528                                                                         (cdna/protein) coding complement, if any
 529                                                                 </xs:documentation>
 530                                                         </xs:annotation>
 531                                                 </xs:attribute>
 532                                                 <xs:attribute name="showComplementFeatures" type="xs:boolean" use="optional" default="false" />
 533                                                 <xs:attribute name="showComplementFeaturesOnTop" type="xs:boolean" use="optional" default="false" />
 534                                         </xs:complexType>
 535                                 </xs:element>
 536                                 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
 537                                         <xs:complexType>
 538                                                 <xs:sequence>
 539                                                         <xs:element name="UserColourScheme" type="jalview:JalviewUserColours" />
 540                                                 </xs:sequence>
 541                                                 <xs:attribute name="id" type="xs:string" />
 542                                         </xs:complexType>
 543                                 </xs:element>
 544                                 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
 545                                         <xs:complexType>
 546                                                 <xs:sequence minOccurs="0">
 547                                                         <xs:element name="title" type="xs:string" />
 548                                                         <xs:element name="newick" type="xs:string" />
 549                                                 </xs:sequence>
 550                                                 <xs:attribute name="fontName" type="xs:string" />
 551                                                 <xs:attribute name="fontSize" type="xs:int" />
 552                                                 <xs:attribute name="fontStyle" type="xs:int" />
 553                                                 <xs:attribute name="threshold" type="xs:float" />
 554                                                 <xs:attribute name="showBootstrap" type="xs:boolean" />
 555                                                 <xs:attribute name="showDistances" type="xs:boolean" />
 556                                                 <xs:attribute name="markUnlinked" type="xs:boolean" />
 557                                                 <xs:attribute name="fitToWindow" type="xs:boolean" />
 558                                                 <xs:attribute name="currentTree" type="xs:boolean" />
 559                                                 <xs:attribute name="columnWise" type="xs:boolean" use="optional" default="false"><xs:annotation><xs:documentation>Set for trees associated with columns of an alignment, sequence or annotation row</xs:documentation></xs:annotation></xs:attribute>
 560                                                 <xs:attribute name="columnReference" type="xs:string" use="optional"><xs:annotation><xs:documentation>Refers to annotation row the tree is provided by</xs:documentation></xs:annotation></xs:attribute>
 561                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 562                                                         <xs:annotation>
 563                                                                 <xs:documentation>
 564                                                                         Tree ID added for binding tree
 565                                                                         visualization
 566                                                                         settings to vamsas
 567                                                                         document trees in jalview 2.4.1
 568                                                                 </xs:documentation>
 569                                                         </xs:annotation>
 570                                                 </xs:attribute>
 571                                                 <xs:attributeGroup ref="jv:swingwindow" />
 572                                                 <xs:attribute name="linkToAllViews" use="optional" default="false" type="xs:boolean" />
 573                                         </xs:complexType>
 574                                 </xs:element>
 575                                 <xs:element name="PcaViewer" minOccurs="0" maxOccurs="unbounded">
 576                                         <xs:complexType>
 577                                                 <xs:sequence>
 578                                                         <xs:element name="sequencePoint" minOccurs="1" maxOccurs="unbounded">
 579                                                                 <xs:complexType>
 580                                                                         <xs:attribute name="sequenceRef" type="xs:string" />
 581                                                                         <xs:attributeGroup ref="jv:position" />
 582                                                                 </xs:complexType>
 583                                                         </xs:element>
 584                                                         <xs:element name="axis" minOccurs="3" maxOccurs="3">
 585                                                                 <xs:annotation>
 586                                                                         <xs:documentation>
 587                                                                                 endpoints of X, Y and Z axes in that order
 588                                                                         </xs:documentation>
 589                                                                 </xs:annotation>
 590                                                                 <xs:complexType>
 591                                                                         <xs:attributeGroup ref="jv:position" />
 592                                                                 </xs:complexType>
 593                                                         </xs:element>
 594                                                         <xs:element name="seqPointMin">
 595                                                                 <xs:complexType>
 596                                                                         <xs:attributeGroup ref="jv:position" />
 597                                                                 </xs:complexType>
 598                                                         </xs:element>
 599                                                         <xs:element name="seqPointMax">
 600                                                                 <xs:complexType>
 601                                                                         <xs:attributeGroup ref="jv:position" />
 602                                                                 </xs:complexType>
 603                                                         </xs:element>
 604                                                         <xs:element name="pcaData" type="jv:PcaDataType" />
 605                                                 </xs:sequence>
 606                                                 <xs:attribute name="title" type="xs:string" />
 607                                                 <xs:attribute name="scoreModelName" type="xs:string" />
 608                                                 <xs:attribute name="xDim" type="xs:int" />
 609                                                 <xs:attribute name="yDim" type="xs:int" />
 610                                                 <xs:attribute name="zDim" type="xs:int" />
 611                                                 <xs:attribute name="bgColour" type="xs:int" />
 612                                                 <xs:attribute name="scaleFactor" type="xs:float" />
 613                                                 <xs:attribute name="showLabels" type="xs:boolean" />
 614                                                 <xs:attribute name="linkToAllViews" type="xs:boolean" />
 615                                                 <xs:attributeGroup ref="jv:SimilarityParams" />
 616                                                 <xs:attributeGroup ref="jv:swingwindow" />
 617                                         </xs:complexType>
 618                                 </xs:element>
 619                                 <xs:element name="FeatureSettings" minOccurs="0">
 620                                         <xs:complexType>
 621                                                 <xs:sequence>
 622                                                         <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
 623                                                                 <xs:complexType>
 624                                                                         <xs:sequence>
 625                                                                             <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
 626                                                                                         <xs:annotation>
 627                                                                                                 <xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
 628                                                                                         </xs:annotation>
 629                                                                             </xs:element>
 630                                                                                 <xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
 631                                                                                         <xs:annotation>
 632                                                                                                 <xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
 633                                                                                         </xs:annotation>
 634                                                                                 </xs:element>
 635                                                                         </xs:sequence>
 636                                                                         <xs:attribute name="type" type="xs:string" use="required" />
 637                                                                         <xs:attribute name="colour" type="xs:int" use="required" />
 638                                                                         <xs:attribute name="display" type="xs:boolean"
 639                                                                                 use="required" />
 640                                                                         <xs:attribute name="order" type="xs:float" use="optional" />
 641                                                                         <xs:attribute name="mincolour" type="xs:int" use="optional">
 642                                                                                 <xs:annotation>
 643                                                                                         <xs:documentation>
 644                                                                                                 Optional minimum colour
 645                                                                                                 for graduated
 646                                                                                                 feature
 647                                                                                                 colour
 648                                                                                         </xs:documentation>
 649                                                                                 </xs:annotation>
 650                                                                         </xs:attribute>
 651                                                                         <xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
 652                                                                         <xs:attribute name="threshold" type="xs:float"
 653                                                                                 use="optional">
 654                                                                                 <xs:annotation>
 655                                                                                         <xs:documentation>
 656                                                                                                 threshold value for
 657                                                                                                 graduated feature colour
 658                                                                                         </xs:documentation>
 659                                                                                 </xs:annotation>
 660                                                                         </xs:attribute>
 661                                                                         <xs:attribute name="threshstate" type="xs:int"
 662                                                                                 use="optional">
 663                                                                                 <xs:annotation>
 664                                                                                         <xs:documentation>
 665                                                                                                 threshold type for
 666                                                                                                 graduated feature colour
 667                                                                                         </xs:documentation>
 668                                                                                 </xs:annotation>
 669                                                                         </xs:attribute>
 670                                                                         <xs:attribute name="max" type="xs:float" use="optional" />
 671                                                                         <xs:attribute name="min" type="xs:float" use="optional" />
 672                                                                         <xs:attribute name="colourByLabel" type="xs:boolean"
 673                                                                                 use="optional" />
 674                                                                         <xs:attribute name="autoScale" type="xs:boolean"
 675                                                                                 use="optional" />
 676                                                                 </xs:complexType>
 677                                                         </xs:element>
 678                                                         <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
 679                                                                 <xs:complexType>
 680                                                                         <xs:attribute name="name" type="xs:string" use="required" />
 681                                                                         <xs:attribute name="display" type="xs:boolean"
 682                                                                                 use="required" />
 683                                                                 </xs:complexType>
 684                                                         </xs:element>
 685                                                 </xs:sequence>
 686                                         </xs:complexType>
 687                                 </xs:element>
 688                         </xs:sequence>
 689                 </xs:sequence>
 690         </xs:complexType>
 691         <xs:complexType name="feature">
 692                 <xs:sequence>
 693                         <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 694                                 <xs:complexType>
 695                                         <xs:attribute name="key" type="xs:string" use="required" />
 696                                         <xs:attribute name="key2" type="xs:string" use="optional">
 697                                                 <xs:annotation>
 698                                                         <xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
 699                                                 </xs:annotation>
 700                                         </xs:attribute>
 701                                         <xs:attribute name="value" type="xs:string" use="required" />
 702                                 </xs:complexType>
 703                         </xs:element>
 704                 </xs:sequence>
 705                 <xs:attribute name="begin" type="xs:int" use="required" />
 706                 <xs:attribute name="end" type="xs:int" use="required" />
 707                 <xs:attribute name="type" type="xs:string" use="required" />
 708                 <xs:attribute name="description" type="xs:string" use="optional" />
 709                 <xs:attribute name="status" type="xs:string" use="optional" />
 710                 <xs:attribute name="featureGroup" type="xs:string" use="optional" />
 711                 <xs:attribute name="score" type="xs:float" use="optional" />
 712         </xs:complexType>
 713         <xs:complexType name="pdbentry">
 714                 <xs:sequence minOccurs="0" maxOccurs="unbounded">
 715                         <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
 716                                 <xs:complexType>
 717                                         <xs:attribute name="name" type="xs:string" use="required" />
 718                                         <xs:attribute name="value" type="xs:string" use="required" />
 719                                 </xs:complexType>
 720                         </xs:element>
 721                 </xs:sequence>
 722                 <xs:attribute name="id" type="xs:string" use="required" />
 723                 <xs:attribute name="type" type="xs:string" use="optional" />
 724                 <xs:attribute name="file" type="xs:string" />
 725         </xs:complexType>
 726         <!-- <xs:complexType name="reportWindow"> <xs:annotation> <xs:documentation>Generic
 727                 type for windows containing mime-typed data associated with other jalview
 728                 windows</xs:documentation> </xs:annotation> <xs:sequence> </xs:sequence>
 729                 <xs:attribute name="id" type="xs:string" use="required"/> <xs:attribute name="type"
 730                 type="xs:string" use="optional"/> <xs:attribute name="file" type="xs:string"
 731                 use="optional"/> </xs:complexType> -->
 732         <xs:attributeGroup name="swingwindow">
 733                 <xs:annotation>
 734                         <xs:documentation>
 735                                 base attributes for windows displayed in Jalview
 736                                 desktop.
 737                         </xs:documentation>
 738                 </xs:annotation>
 739                 <xs:attribute name="width" type="xs:int" />
 740                 <xs:attribute name="height" type="xs:int" />
 741                 <xs:attribute name="xpos" type="xs:int" />
 742                 <xs:attribute name="ypos" type="xs:int" />
 743         </xs:attributeGroup>
 744         <xs:complexType name="AnnotationColourScheme">
 745                 <xs:attribute name="aboveThreshold" type="xs:int" />
 746                 <xs:attribute name="annotation" type="xs:string" />
 747                 <xs:attribute name="minColour" type="xs:int" />
 748                 <xs:attribute name="maxColour" type="xs:int" />
 749                 <xs:attribute name="colourScheme" type="xs:string" />
 750                 <xs:attribute name="threshold" type="xs:float" />
 751                 <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
 752                 <xs:attribute name="predefinedColours" type="xs:boolean"
 753                         use="optional" />
 754         </xs:complexType>
 755         <xs:attributeGroup name="SimilarityParams">
 756                 <xs:annotation>
 757                         <xs:documentation>
 758                                 parameters that condition a similarity score calculation
 759                         </xs:documentation>
 760                 </xs:annotation>
 761                 <xs:attribute name="includeGaps" type="xs:boolean" />
 762                 <xs:attribute name="matchGaps" type="xs:boolean" />
 763                 <xs:attribute name="includeGappedColumns" type="xs:boolean" />
 764                 <xs:attribute name="denominateByShortestLength" type="xs:boolean" />
 765         </xs:attributeGroup>
 766         <xs:attributeGroup name="position">
 767                 <xs:attribute name="xPos" type="xs:float" />
 768                 <xs:attribute name="yPos" type="xs:float" />
 769                 <xs:attribute name="zPos" type="xs:float" />
 770         </xs:attributeGroup>
 771         <xs:complexType name="PcaDataType">
 772                 <xs:annotation>
 773                         <xs:documentation>
 774                                 The results of a PCA calculation
 775                         </xs:documentation>
 776                 </xs:annotation>
 777                 <xs:sequence>
 778                         <xs:element name="pairwiseMatrix" type="jv:DoubleMatrix" />
 779                         <xs:element name="tridiagonalMatrix" type="jv:DoubleMatrix" />
 780                         <xs:element name="eigenMatrix" type="jv:DoubleMatrix" />
 781                 </xs:sequence>
 782         </xs:complexType>
 783         <xs:complexType name="DoubleVector">
 784                 <xs:sequence>
 785                         <xs:element name="v" type="xs:double" minOccurs="0" maxOccurs="unbounded" />
 786                 </xs:sequence>
 787         </xs:complexType>
 788         <xs:complexType name="DoubleMatrix">
 789                 <xs:sequence>
 790                         <xs:element name="row" type="jv:DoubleVector" minOccurs="0" maxOccurs="unbounded" />
 791                         <xs:element name="D" minOccurs="0" type="jv:DoubleVector" />
 792                         <xs:element name="E" minOccurs="0" type="jv:DoubleVector" />
 793                 </xs:sequence>
 794                 <xs:attribute name="rows"  type="xs:int" />
 795                 <xs:attribute name="columns" type="xs:int" />
 796         </xs:complexType>
 797 </xs:schema>