schemas/jalviewJvV1.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>\r
   2 <!--\r
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
   4  * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
   5  * \r
   6  * This file is part of Jalview.\r
   7  * \r
   8  * Jalview is free software: you can redistribute it and/or\r
   9  * modify it under the terms of the GNU General Public License \r
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
  11  * \r
  12  * Jalview is distributed in the hope that it will be useful, but \r
  13  * WITHOUT ANY WARRANTY; without even the implied warranty \r
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
  15  * PURPOSE.  See the GNU General Public License for more details.\r
  16  * \r
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  18 -->\r
  19 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"\r
  20                                  xmlns:vamsas="www.vamsas.org"\r
  21                                  xmlns:jalview="www.jalview.org/colours"\r
  22                                  xmlns:jv="www.jalview.org" \r
  23                                  targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">\r
  24                                  \r
  25         <xs:import schemaLocation="vamsasJvV1.xsd" namespace="www.vamsas.org"/>\r
  26         <xs:import schemaLocation="jalviewUserColours.xsd" namespace="www.jalview.org/colours"/>\r
  27         <xs:complexType name="JalviewModel">\r
  28                 <xs:sequence>\r
  29                         <xs:element name="creationDate" type="xs:dateTime"/>\r
  30                         <xs:element name="version" type="xs:string"/>\r
  31                         <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>\r
  32                         <xs:sequence>\r
  33                                 <xs:element name="JSeq" maxOccurs="unbounded">\r
  34                                         <xs:complexType>\r
  35                                                 <xs:sequence>\r
  36                                                          <xs:element name="features" type="jv:feature" minOccurs="0" maxOccurs="unbounded"/>\r
  37                                                          <xs:element name="pdbids" type="jv:pdbentry" minOccurs="0" maxOccurs="unbounded"/>\r
  38                                               </xs:sequence>\r
  39                                               \r
  40                                                     <xs:attribute name="colour" type="xs:int" use="optional"/>\r
  41                                                         <xs:attribute name="start" type="xs:int" use="required"/>\r
  42                                                         <xs:attribute name="end" type="xs:int" use="required"/>\r
  43                                                         <xs:attribute name="id" type="xs:int" use="required"/>\r
  44                                                 </xs:complexType>\r
  45                                 </xs:element>\r
  46                                 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">\r
  47                                         <xs:complexType>\r
  48                                                 <xs:sequence minOccurs="1">\r
  49                                                         <xs:element name="seq" maxOccurs="unbounded" type="xs:int"/>\r
  50                                                 </xs:sequence>\r
  51                                                 <xs:attribute name="start" type="xs:int"/>\r
  52                                                 <xs:attribute name="end" type="xs:int"/>\r
  53                                                 <xs:attribute name="name" type="xs:string"/>\r
  54                                                 <xs:attribute name="colour" type="xs:string"/>\r
  55                                                 <xs:attribute name="consThreshold" type="xs:int"/>\r
  56                                                 <xs:attribute name="pidThreshold" type="xs:int"/>\r
  57                                                 <xs:attribute name="outlineColour" type="xs:int"/>\r
  58                                                 <xs:attribute name="displayBoxes" type="xs:boolean"/>\r
  59                                                 <xs:attribute name="displayText" type="xs:boolean"/>\r
  60                                                 <xs:attribute name="colourText" type="xs:boolean"/>\r
  61                                         </xs:complexType>\r
  62                                 </xs:element>\r
  63                                 <xs:element name="Viewport" maxOccurs="unbounded">\r
  64                                         <xs:complexType>\r
  65                                                 <xs:attribute name="conservationSelected" type="xs:boolean"/>\r
  66                                                 <xs:attribute name="pidSelected" type="xs:boolean"/>\r
  67                                                 <xs:attribute name="bgColour" type="xs:string"/>\r
  68                                                 <xs:attribute name="consThreshold" type="xs:int"/>\r
  69                                                 <xs:attribute name="pidThreshold" type="xs:int"/>\r
  70                                                 <xs:attribute name="title" type="xs:string"/>\r
  71                                                 <xs:attribute name="showFullId" type="xs:boolean"/>\r
  72                                                 <xs:attribute name="showText" type="xs:boolean"/>\r
  73                                                 <xs:attribute name="showColourText" type="xs:boolean"/>\r
  74                                                 <xs:attribute name="showBoxes" type="xs:boolean"/>\r
  75                                                 <xs:attribute name="wrapAlignment" type="xs:boolean"/>\r
  76                                                 <xs:attribute name="renderGaps" type="xs:boolean"/>\r
  77                                                 <xs:attribute name="showSequenceFeatures" type="xs:boolean"/>\r
  78                                                 <xs:attribute name="showAnnotation" type="xs:boolean"/>\r
  79                                                 <xs:attribute name="showConservation" type="xs:boolean"/>\r
  80                                                 <xs:attribute name="showQuality" type="xs:boolean"/>\r
  81                                                 <xs:attribute name="showIdentity" type="xs:boolean"/>\r
  82                                                 <xs:attribute name="xpos" type="xs:int"/>\r
  83                                                 <xs:attribute name="ypos" type="xs:int"/>\r
  84                                                 <xs:attribute name="width" type="xs:int"/>\r
  85                                                 <xs:attribute name="height" type="xs:int"/>\r
  86                                                 <xs:attribute name="startRes" type="xs:int"/>\r
  87                                                 <xs:attribute name="startSeq" type="xs:int"/>\r
  88                                                 <xs:attribute name="fontName" type="xs:string"/>\r
  89                                                 <xs:attribute name="fontSize" type="xs:int"/>\r
  90                                                 <xs:attribute name="fontStyle" type="xs:int"/>\r
  91                                         </xs:complexType>\r
  92                                 </xs:element>\r
  93                                 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">\r
  94                                         <xs:complexType>\r
  95                                                 <xs:sequence minOccurs="1">\r
  96                                                         <xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>\r
  97                                                 </xs:sequence>\r
  98                                                 <xs:attribute name="id" type="xs:string"/>\r
  99                                         </xs:complexType>\r
 100                                 </xs:element>\r
 101                                 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">\r
 102                                         <xs:complexType>\r
 103                                                 <xs:sequence minOccurs="0" maxOccurs="1">\r
 104                                                         <xs:element name="title" type="xs:string"/>\r
 105                                                         <xs:element name="newick" type="xs:string"/>\r
 106                                                 </xs:sequence>\r
 107                                                 <xs:attribute name="width" type="xs:int"/>\r
 108                                                 <xs:attribute name="height" type="xs:int"/>\r
 109                                                 <xs:attribute name="xpos" type="xs:int"/>\r
 110                                                 <xs:attribute name="ypos" type="xs:int"/>\r
 111                                                 <xs:attribute name="fontName" type="xs:string"/>\r
 112                                                 <xs:attribute name="fontSize" type="xs:int"/>\r
 113                                                 <xs:attribute name="fontStyle" type="xs:int"/>\r
 114                                                 <xs:attribute name="threshold" type="xs:float"/>\r
 115                                                 <xs:attribute name="showBootstrap" type="xs:boolean"/>\r
 116                                                 <xs:attribute name="showDistances" type="xs:boolean"/>\r
 117                                                 <xs:attribute name="markUnlinked" type="xs:boolean"/>\r
 118                                                 <xs:attribute name="fitToWindow" type="xs:boolean"/>\r
 119                                                 <xs:attribute name="currentTree" type="xs:boolean"/>\r
 120                                         </xs:complexType>\r
 121                                 </xs:element>\r
 122                                 \r
 123                                 <xs:element name="FeatureSettings" minOccurs="0" maxOccurs="1">\r
 124                                                 <xs:complexType>\r
 125                                 <xs:sequence>\r
 126                                         <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">\r
 127                                                 <xs:complexType>\r
 128                                                         <xs:attribute name="type" type="xs:string" use="required"/>\r
 129                                                         <xs:attribute name="colour" type="xs:int" use="required"/>\r
 130                                                         <xs:attribute name="display" type="xs:boolean" use="required"/>\r
 131                                                 </xs:complexType>\r
 132                                         </xs:element>\r
 133                                 </xs:sequence>\r
 134                                 </xs:complexType>\r
 135                                 </xs:element>\r
 136                                 \r
 137                         </xs:sequence>\r
 138                 </xs:sequence>\r
 139         </xs:complexType>\r
 140         \r
 141         <xs:complexType name="feature">\r
 142                 <xs:attribute name="begin" type="xs:int" use="required"/>\r
 143                 <xs:attribute name="end" type="xs:int" use="required"/>\r
 144                 <xs:attribute name="type" type="xs:string" use="required"/>\r
 145                 <xs:attribute name="description" type="xs:string" use="optional"/>\r
 146                 <xs:attribute name="status" type="xs:string" use="optional"/>\r
 147         </xs:complexType>\r
 148                 \r
 149         <xs:complexType name="pdbentry">\r
 150                 <xs:sequence minOccurs="0" maxOccurs="unbounded">\r
 151                         <xs:element name="property" minOccurs="0" maxOccurs="unbounded">\r
 152                                 <xs:complexType>\r
 153                                         <xs:attribute name="name" type="xs:string" use="required"/>\r
 154                                         <xs:attribute name="value" type="xs:string" use="required"/>\r
 155                                 </xs:complexType>\r
 156                         </xs:element>\r
 157                 </xs:sequence>\r
 158                 <xs:attribute name="id" type="xs:string" use="required"/>\r
 159                 <xs:attribute name="type" type="xs:string" use="optional"/>\r
 160         </xs:complexType>\r
 161         \r
 162 </xs:schema>\r