schemas/jalview.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!--
   3   Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
   4   Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   5
   6   This program is free software; you can redistribute it and/or
   7   modify it under the terms of the GNU General Public License
   8   as published by the Free Software Foundation; either version 2
   9   of the License, or (at your option) any later version.
  10
  11   This program is distributed in the hope that it will be useful,
  12   but WITHOUT ANY WARRANTY; without even the implied warranty of
  13   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  14   GNU General Public License for more details.
  15
  16   You should have received a copy of the GNU General Public License
  17   along with this program; if not, write to the Free Software
  18   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  19 -->
  20 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours" xmlns:jv="www.jalview.org" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
  21                 <xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
  22         <xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
  23         <xs:complexType name="JalviewModel">
  24                 <xs:sequence>
  25                         <xs:element name="creationDate" type="xs:dateTime"/>
  26                         <xs:element name="version" type="xs:string"/>
  27                         <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>
  28                         <xs:sequence>
  29                                 <xs:element name="JSeq" maxOccurs="unbounded">
  30                                         <xs:complexType>
  31                                                 <xs:sequence>
  32                                                         <xs:element name="features" type="jv:feature" minOccurs="0" maxOccurs="unbounded"/>
  33                                                         <xs:element name="pdbids" minOccurs="0" maxOccurs="unbounded">
  34                                                                 <xs:complexType>
  35                                                                         <xs:complexContent>
  36                                                                                 <xs:extension base="jv:pdbentry">
  37                                                                                         <xs:sequence>
  38                                                                                                 <xs:element name="structureState" minOccurs="0" maxOccurs="unbounded">
  39                                                                                                         <xs:complexType>
  40                                                                                                                 <xs:simpleContent>
  41                                                                                                                         <xs:extension base="xs:string">
  42                                                                                                                                 <xs:attribute name="visible" type="xs:boolean"/>
  43                                                                                                                                 <xs:attribute name="xpos" type="xs:int"/>
  44                                                                                                                                 <xs:attribute name="ypos" type="xs:int"/>
  45                                                                                                                                 <xs:attribute name="width" type="xs:int"/>
  46                                                                                                                                 <xs:attribute name="height" type="xs:int"/>
  47                                                                                                                         </xs:extension>
  48                                                                                                                 </xs:simpleContent>
  49                                                                                                         </xs:complexType>
  50                                                                                                 </xs:element>
  51                                                                                         </xs:sequence>
  52                                                                                 </xs:extension>
  53                                                                         </xs:complexContent>
  54                                                                 </xs:complexType>
  55                                                         </xs:element>
  56                                                         <xs:element name="hiddenSequences" type="xs:int" minOccurs="0" maxOccurs="unbounded"/>
  57                                                 </xs:sequence>
  58                                                 <xs:attribute name="colour" type="xs:int" use="optional"/>
  59                                                 <xs:attribute name="start" type="xs:int" use="required"/>
  60                                                 <xs:attribute name="end" type="xs:int" use="required"/>
  61                                                 <xs:attribute name="id" type="xs:string" use="required"/>
  62                                                 <xs:attribute name="hidden" type="xs:boolean"/>
  63                                         </xs:complexType>
  64                                 </xs:element>
  65                                 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
  66                                         <xs:complexType>
  67                                                 <xs:sequence>
  68                                                         <xs:element name="seq" type="xs:string" maxOccurs="unbounded"/>
  69                                                 </xs:sequence>
  70                                                 <xs:attribute name="start" type="xs:int"/>
  71                                                 <xs:attribute name="end" type="xs:int"/>
  72                                                 <xs:attribute name="name" type="xs:string"/>
  73                                                 <xs:attribute name="colour" type="xs:string"/>
  74                                                 <xs:attribute name="consThreshold" type="xs:int"/>
  75                                                 <xs:attribute name="pidThreshold" type="xs:int"/>
  76                                                 <xs:attribute name="outlineColour" type="xs:int"/>
  77                                                 <xs:attribute name="displayBoxes" type="xs:boolean"/>
  78                                                 <xs:attribute name="displayText" type="xs:boolean"/>
  79                                                 <xs:attribute name="colourText" type="xs:boolean"/>
  80                                                 <xs:attribute name="textCol1" type="xs:int"/>
  81                                                 <xs:attribute name="textCol2" type="xs:int"/>
  82                                                 <xs:attribute name="textColThreshold" type="xs:int"/>
  83                                         </xs:complexType>
  84                                 </xs:element>
  85                                 <xs:element name="Viewport" maxOccurs="unbounded">
  86                                         <xs:complexType>
  87                                                 <xs:sequence>
  88                                                         <xs:element name="AnnotationColours" minOccurs="0">
  89                                                                 <xs:complexType>
  90                                                                         <xs:attribute name="aboveThreshold" type="xs:int"/>
  91                                                                         <xs:attribute name="annotation" type="xs:string"/>
  92                                                                         <xs:attribute name="minColour" type="xs:int"/>
  93                                                                         <xs:attribute name="maxColour" type="xs:int"/>
  94                                                                         <xs:attribute name="colourScheme" type="xs:string"/>
  95                                                                         <xs:attribute name="threshold" type="xs:float"/>
  96                                                                 </xs:complexType>
  97                                                         </xs:element>
  98                                                         <xs:element name="hiddenColumns" minOccurs="0" maxOccurs="unbounded">
  99                                                                 <xs:complexType>
 100                                                                         <xs:attribute name="start" type="xs:int"/>
 101                                                                         <xs:attribute name="end" type="xs:int"/>
 102                                                                 </xs:complexType>
 103                                                         </xs:element>
 104                                                 </xs:sequence>
 105                                                 <xs:attribute name="conservationSelected" type="xs:boolean"/>
 106                                                 <xs:attribute name="pidSelected" type="xs:boolean"/>
 107                                                 <xs:attribute name="bgColour" type="xs:string"/>
 108                                                 <xs:attribute name="consThreshold" type="xs:int"/>
 109                                                 <xs:attribute name="pidThreshold" type="xs:int"/>
 110                                                 <xs:attribute name="title" type="xs:string"/>
 111                                                 <xs:attribute name="showFullId" type="xs:boolean"/>
 112                                                 <xs:attribute name="rightAlignIds" type="xs:boolean"/>
 113                                                 <xs:attribute name="showText" type="xs:boolean"/>
 114                                                 <xs:attribute name="showColourText" type="xs:boolean"/>
 115                                                 <xs:attribute name="showBoxes" type="xs:boolean"/>
 116                                                 <xs:attribute name="wrapAlignment" type="xs:boolean"/>
 117                                                 <xs:attribute name="renderGaps" type="xs:boolean"/>
 118                                                 <xs:attribute name="showSequenceFeatures" type="xs:boolean"/>
 119                                                 <xs:attribute name="showAnnotation" type="xs:boolean"/>
 120                                                 <xs:attribute name="xpos" type="xs:int"/>
 121                                                 <xs:attribute name="ypos" type="xs:int"/>
 122                                                 <xs:attribute name="width" type="xs:int"/>
 123                                                 <xs:attribute name="height" type="xs:int"/>
 124                                                 <xs:attribute name="startRes" type="xs:int"/>
 125                                                 <xs:attribute name="startSeq" type="xs:int"/>
 126                                                 <xs:attribute name="fontName" type="xs:string"/>
 127                                                 <xs:attribute name="fontSize" type="xs:int"/>
 128                                                 <xs:attribute name="fontStyle" type="xs:int"/>
 129                                                 <xs:attribute name="viewName" type="xs:string"/>
 130                                                 <xs:attribute name="sequenceSetId" type="xs:string"/>
 131                                                 <xs:attribute name="gatheredViews" type="xs:boolean"/>
 132                                                 <xs:attribute name="textCol1" type="xs:int"/>
 133                                                 <xs:attribute name="textCol2" type="xs:int"/>
 134                                                 <xs:attribute name="textColThreshold" type="xs:int"/>
 135                                         </xs:complexType>
 136                                 </xs:element>
 137                                 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
 138                                         <xs:complexType>
 139                                                 <xs:sequence>
 140                                                         <xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
 141                                                 </xs:sequence>
 142                                                 <xs:attribute name="id" type="xs:string"/>
 143                                         </xs:complexType>
 144                                 </xs:element>
 145                                 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
 146                                         <xs:complexType>
 147                                                 <xs:sequence minOccurs="0">
 148                                                         <xs:element name="title" type="xs:string"/>
 149                                                         <xs:element name="newick" type="xs:string"/>
 150                                                 </xs:sequence>
 151                                                 <xs:attribute name="width" type="xs:int"/>
 152                                                 <xs:attribute name="height" type="xs:int"/>
 153                                                 <xs:attribute name="xpos" type="xs:int"/>
 154                                                 <xs:attribute name="ypos" type="xs:int"/>
 155                                                 <xs:attribute name="fontName" type="xs:string"/>
 156                                                 <xs:attribute name="fontSize" type="xs:int"/>
 157                                                 <xs:attribute name="fontStyle" type="xs:int"/>
 158                                                 <xs:attribute name="threshold" type="xs:float"/>
 159                                                 <xs:attribute name="showBootstrap" type="xs:boolean"/>
 160                                                 <xs:attribute name="showDistances" type="xs:boolean"/>
 161                                                 <xs:attribute name="markUnlinked" type="xs:boolean"/>
 162                                                 <xs:attribute name="fitToWindow" type="xs:boolean"/>
 163                                                 <xs:attribute name="currentTree" type="xs:boolean"/>
 164                                         </xs:complexType>
 165                                 </xs:element>
 166                                 <xs:element name="FeatureSettings" minOccurs="0">
 167                                         <xs:complexType>
 168                                                 <xs:sequence>
 169                                                         <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
 170                                                                 <xs:complexType>
 171                                                                         <xs:attribute name="type" type="xs:string" use="required"/>
 172                                                                         <xs:attribute name="colour" type="xs:int" use="required"/>
 173                                                                         <xs:attribute name="display" type="xs:boolean" use="required"/>
 174                                                                         <xs:attribute name="order" type="xs:float" use="optional"/>
 175                                                                 </xs:complexType>
 176                                                         </xs:element>
 177                                                         <xs:element name="group" minOccurs="0" maxOccurs="unbounded">
 178                                                                 <xs:complexType>
 179                                                                         <xs:attribute name="name" type="xs:string" use="required"/>
 180                                                                         <xs:attribute name="display" type="xs:boolean" use="required"/>
 181                                                                 </xs:complexType>
 182                                                         </xs:element>
 183                                                 </xs:sequence>
 184                                         </xs:complexType>
 185                                 </xs:element>
 186                         </xs:sequence>
 187                 </xs:sequence>
 188         </xs:complexType>
 189         <xs:complexType name="feature">
 190                 <xs:sequence>
 191                         <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 192                                 <xs:complexType>
 193                                         <xs:attribute name="key" type="xs:string" use="required"/>
 194                                         <xs:attribute name="value" type="xs:string" use="required"/>
 195                                 </xs:complexType>
 196                         </xs:element>
 197                 </xs:sequence>
 198                 <xs:attribute name="begin" type="xs:int" use="required"/>
 199                 <xs:attribute name="end" type="xs:int" use="required"/>
 200                 <xs:attribute name="type" type="xs:string" use="required"/>
 201                 <xs:attribute name="description" type="xs:string" use="optional"/>
 202                 <xs:attribute name="status" type="xs:string" use="optional"/>
 203                 <xs:attribute name="featureGroup" type="xs:string" use="optional"/>
 204                 <xs:attribute name="score" type="xs:float" use="optional"/>
 205         </xs:complexType>
 206         <xs:complexType name="pdbentry">
 207                 <xs:sequence minOccurs="0" maxOccurs="unbounded">
 208                         <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
 209                                 <xs:complexType>
 210                                         <xs:attribute name="name" type="xs:string" use="required"/>
 211                                         <xs:attribute name="value" type="xs:string" use="required"/>
 212                                 </xs:complexType>
 213                         </xs:element>
 214                 </xs:sequence>
 215                 <xs:attribute name="id" type="xs:string" use="required"/>
 216                 <xs:attribute name="type" type="xs:string" use="optional"/>
 217                 <xs:attribute name="file" type="xs:string"/>
 218         </xs:complexType>
 219 </xs:schema>