schemas/jalviewJvV1.xsd

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