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