schemas/jalviewJvV1.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!--
   3   Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   4   Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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 -->
  19 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
  20                                  xmlns:vamsas="www.vamsas.org"
  21                                  xmlns:jalview="www.jalview.org/colours"
  22                                  xmlns:jv="www.jalview.org"
  23                                  targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
  24
  25         <xs:import schemaLocation="vamsasJvV1.xsd" namespace="www.vamsas.org"/>
  26         <xs:import schemaLocation="jalviewUserColours.xsd" namespace="www.jalview.org/colours"/>
  27         <xs:complexType name="JalviewModel">
  28                 <xs:sequence>
  29                         <xs:element name="creationDate" type="xs:dateTime"/>
  30                         <xs:element name="version" type="xs:string"/>
  31                         <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>
  32                         <xs:sequence>
  33                                 <xs:element name="JSeq" maxOccurs="unbounded">
  34                                         <xs:complexType>
  35                                                 <xs:sequence>
  36                                                          <xs:element name="features" type="jv:feature" minOccurs="0" maxOccurs="unbounded"/>
  37                                                          <xs:element name="pdbids" type="jv:pdbentry" minOccurs="0" maxOccurs="unbounded"/>
  38                                               </xs:sequence>
  39
  40                                                     <xs:attribute name="colour" type="xs:int" use="optional"/>
  41                                                         <xs:attribute name="start" type="xs:int" use="required"/>
  42                                                         <xs:attribute name="end" type="xs:int" use="required"/>
  43                                                         <xs:attribute name="id" type="xs:int" use="required"/>
  44                                                 </xs:complexType>
  45                                 </xs:element>
  46                                 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
  47                                         <xs:complexType>
  48                                                 <xs:sequence minOccurs="1">
  49                                                         <xs:element name="seq" maxOccurs="unbounded" type="xs:int"/>
  50                                                 </xs:sequence>
  51                                                 <xs:attribute name="start" type="xs:int"/>
  52                                                 <xs:attribute name="end" type="xs:int"/>
  53                                                 <xs:attribute name="name" type="xs:string"/>
  54                                                 <xs:attribute name="colour" type="xs:string"/>
  55                                                 <xs:attribute name="consThreshold" type="xs:int"/>
  56                                                 <xs:attribute name="pidThreshold" type="xs:int"/>
  57                                                 <xs:attribute name="outlineColour" type="xs:int"/>
  58                                                 <xs:attribute name="displayBoxes" type="xs:boolean"/>
  59                                                 <xs:attribute name="displayText" type="xs:boolean"/>
  60                                                 <xs:attribute name="colourText" type="xs:boolean"/>
  61                                         </xs:complexType>
  62                                 </xs:element>
  63                                 <xs:element name="Viewport" maxOccurs="unbounded">
  64                                         <xs:complexType>
  65                                                 <xs:attribute name="conservationSelected" type="xs:boolean"/>
  66                                                 <xs:attribute name="pidSelected" type="xs:boolean"/>
  67                                                 <xs:attribute name="bgColour" type="xs:string"/>
  68                                                 <xs:attribute name="consThreshold" type="xs:int"/>
  69                                                 <xs:attribute name="pidThreshold" type="xs:int"/>
  70                                                 <xs:attribute name="title" type="xs:string"/>
  71                                                 <xs:attribute name="showFullId" type="xs:boolean"/>
  72                                                 <xs:attribute name="showText" type="xs:boolean"/>
  73                                                 <xs:attribute name="showColourText" type="xs:boolean"/>
  74                                                 <xs:attribute name="showBoxes" type="xs:boolean"/>
  75                                                 <xs:attribute name="wrapAlignment" type="xs:boolean"/>
  76                                                 <xs:attribute name="renderGaps" type="xs:boolean"/>
  77                                                 <xs:attribute name="showSequenceFeatures" type="xs:boolean"/>
  78                                                 <xs:attribute name="showAnnotation" type="xs:boolean"/>
  79                                                 <xs:attribute name="showConservation" type="xs:boolean"/>
  80                                                 <xs:attribute name="showQuality" type="xs:boolean"/>
  81                                                 <xs:attribute name="showIdentity" type="xs:boolean"/>
  82                                                 <xs:attribute name="xpos" type="xs:int"/>
  83                                                 <xs:attribute name="ypos" type="xs:int"/>
  84                                                 <xs:attribute name="width" type="xs:int"/>
  85                                                 <xs:attribute name="height" type="xs:int"/>
  86                                                 <xs:attribute name="startRes" type="xs:int"/>
  87                                                 <xs:attribute name="startSeq" type="xs:int"/>
  88                                                 <xs:attribute name="fontName" type="xs:string"/>
  89                                                 <xs:attribute name="fontSize" type="xs:int"/>
  90                                                 <xs:attribute name="fontStyle" type="xs:int"/>
  91                                         </xs:complexType>
  92                                 </xs:element>
  93                                 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
  94                                         <xs:complexType>
  95                                                 <xs:sequence minOccurs="1">
  96                                                         <xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
  97                                                 </xs:sequence>
  98                                                 <xs:attribute name="id" type="xs:string"/>
  99                                         </xs:complexType>
 100                                 </xs:element>
 101                                 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
 102                                         <xs:complexType>
 103                                                 <xs:sequence minOccurs="0" maxOccurs="1">
 104                                                         <xs:element name="title" type="xs:string"/>
 105                                                         <xs:element name="newick" type="xs:string"/>
 106                                                 </xs:sequence>
 107                                                 <xs:attribute name="width" type="xs:int"/>
 108                                                 <xs:attribute name="height" type="xs:int"/>
 109                                                 <xs:attribute name="xpos" type="xs:int"/>
 110                                                 <xs:attribute name="ypos" type="xs:int"/>
 111                                                 <xs:attribute name="fontName" type="xs:string"/>
 112                                                 <xs:attribute name="fontSize" type="xs:int"/>
 113                                                 <xs:attribute name="fontStyle" type="xs:int"/>
 114                                                 <xs:attribute name="threshold" type="xs:float"/>
 115                                                 <xs:attribute name="showBootstrap" type="xs:boolean"/>
 116                                                 <xs:attribute name="showDistances" type="xs:boolean"/>
 117                                                 <xs:attribute name="markUnlinked" type="xs:boolean"/>
 118                                                 <xs:attribute name="fitToWindow" type="xs:boolean"/>
 119                                                 <xs:attribute name="currentTree" type="xs:boolean"/>
 120                                         </xs:complexType>
 121                                 </xs:element>
 122
 123                                 <xs:element name="FeatureSettings" minOccurs="0" maxOccurs="1">
 124                                                 <xs:complexType>
 125                                 <xs:sequence>
 126                                         <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
 127                                                 <xs:complexType>
 128                                                         <xs:attribute name="type" type="xs:string" use="required"/>
 129                                                         <xs:attribute name="colour" type="xs:int" use="required"/>
 130                                                         <xs:attribute name="display" type="xs:boolean" use="required"/>
 131                                                 </xs:complexType>
 132                                         </xs:element>
 133                                 </xs:sequence>
 134                                 </xs:complexType>
 135                                 </xs:element>
 136
 137                         </xs:sequence>
 138                 </xs:sequence>
 139         </xs:complexType>
 140
 141         <xs:complexType name="feature">
 142                 <xs:attribute name="begin" type="xs:int" use="required"/>
 143                 <xs:attribute name="end" type="xs:int" use="required"/>
 144                 <xs:attribute name="type" type="xs:string" use="required"/>
 145                 <xs:attribute name="description" type="xs:string" use="optional"/>
 146                 <xs:attribute name="status" type="xs:string" use="optional"/>
 147         </xs:complexType>
 148
 149         <xs:complexType name="pdbentry">
 150                 <xs:sequence minOccurs="0" maxOccurs="unbounded">
 151                         <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
 152                                 <xs:complexType>
 153                                         <xs:attribute name="name" type="xs:string" use="required"/>
 154                                         <xs:attribute name="value" type="xs:string" use="required"/>
 155                                 </xs:complexType>
 156                         </xs:element>
 157                 </xs:sequence>
 158                 <xs:attribute name="id" type="xs:string" use="required"/>
 159                 <xs:attribute name="type" type="xs:string" use="optional"/>
 160         </xs:complexType>
 161
 162 </xs:schema>