1 <?xml version="1.0" encoding="UTF-8"?>
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3 Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
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4 Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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6 This program is free software; you can redistribute it and/or
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7 modify it under the terms of the GNU General Public License
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8 as published by the Free Software Foundation; either version 2
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9 of the License, or (at your option) any later version.
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11 This program is distributed in the hope that it will be useful,
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12 but WITHOUT ANY WARRANTY; without even the implied warranty of
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13 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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14 GNU General Public License for more details.
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16 You should have received a copy of the GNU General Public License
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17 along with this program; if not, write to the Free Software
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18 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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21 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
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22 xmlns:vamsas="www.vamsas.org"
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23 xmlns:jalview="www.jalview.org/colours"
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24 xmlns:jv="www.jalview.org"
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25 targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
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27 <xs:import schemaLocation="vamsasJvV1.xsd" namespace="www.vamsas.org"/>
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28 <xs:import schemaLocation="jalviewUserColours.xsd" namespace="www.jalview.org/colours"/>
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29 <xs:complexType name="JalviewModel">
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31 <xs:element name="creationDate" type="xs:dateTime"/>
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32 <xs:element name="version" type="xs:string"/>
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33 <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>
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35 <xs:element name="JSeq" maxOccurs="unbounded">
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38 <xs:element name="features" type="jv:feature" minOccurs="0" maxOccurs="unbounded"/>
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39 <xs:element name="pdbids" type="jv:pdbentry" minOccurs="0" maxOccurs="unbounded"/>
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42 <xs:attribute name="colour" type="xs:int" use="optional"/>
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43 <xs:attribute name="start" type="xs:int" use="required"/>
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44 <xs:attribute name="end" type="xs:int" use="required"/>
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45 <xs:attribute name="id" type="xs:int" use="required"/>
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48 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
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50 <xs:sequence minOccurs="1">
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51 <xs:element name="seq" maxOccurs="unbounded" type="xs:int"/>
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53 <xs:attribute name="start" type="xs:int"/>
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54 <xs:attribute name="end" type="xs:int"/>
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55 <xs:attribute name="name" type="xs:string"/>
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56 <xs:attribute name="colour" type="xs:string"/>
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57 <xs:attribute name="consThreshold" type="xs:int"/>
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58 <xs:attribute name="pidThreshold" type="xs:int"/>
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59 <xs:attribute name="outlineColour" type="xs:int"/>
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60 <xs:attribute name="displayBoxes" type="xs:boolean"/>
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61 <xs:attribute name="displayText" type="xs:boolean"/>
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62 <xs:attribute name="colourText" type="xs:boolean"/>
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65 <xs:element name="Viewport" maxOccurs="unbounded">
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67 <xs:attribute name="conservationSelected" type="xs:boolean"/>
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68 <xs:attribute name="pidSelected" type="xs:boolean"/>
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69 <xs:attribute name="bgColour" type="xs:string"/>
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70 <xs:attribute name="consThreshold" type="xs:int"/>
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71 <xs:attribute name="pidThreshold" type="xs:int"/>
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72 <xs:attribute name="title" type="xs:string"/>
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73 <xs:attribute name="showFullId" type="xs:boolean"/>
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74 <xs:attribute name="showText" type="xs:boolean"/>
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75 <xs:attribute name="showColourText" type="xs:boolean"/>
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76 <xs:attribute name="showBoxes" type="xs:boolean"/>
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77 <xs:attribute name="wrapAlignment" type="xs:boolean"/>
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78 <xs:attribute name="renderGaps" type="xs:boolean"/>
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79 <xs:attribute name="showSequenceFeatures" type="xs:boolean"/>
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80 <xs:attribute name="showAnnotation" type="xs:boolean"/>
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81 <xs:attribute name="showConservation" type="xs:boolean"/>
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82 <xs:attribute name="showQuality" type="xs:boolean"/>
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83 <xs:attribute name="showIdentity" type="xs:boolean"/>
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84 <xs:attribute name="xpos" type="xs:int"/>
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85 <xs:attribute name="ypos" type="xs:int"/>
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86 <xs:attribute name="width" type="xs:int"/>
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87 <xs:attribute name="height" type="xs:int"/>
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88 <xs:attribute name="startRes" type="xs:int"/>
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89 <xs:attribute name="startSeq" type="xs:int"/>
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90 <xs:attribute name="fontName" type="xs:string"/>
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91 <xs:attribute name="fontSize" type="xs:int"/>
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92 <xs:attribute name="fontStyle" type="xs:int"/>
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95 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
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97 <xs:sequence minOccurs="1">
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98 <xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
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100 <xs:attribute name="id" type="xs:string"/>
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103 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
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105 <xs:sequence minOccurs="0" maxOccurs="1">
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106 <xs:element name="title" type="xs:string"/>
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107 <xs:element name="newick" type="xs:string"/>
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109 <xs:attribute name="width" type="xs:int"/>
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110 <xs:attribute name="height" type="xs:int"/>
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111 <xs:attribute name="xpos" type="xs:int"/>
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112 <xs:attribute name="ypos" type="xs:int"/>
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113 <xs:attribute name="fontName" type="xs:string"/>
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114 <xs:attribute name="fontSize" type="xs:int"/>
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115 <xs:attribute name="fontStyle" type="xs:int"/>
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116 <xs:attribute name="threshold" type="xs:float"/>
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117 <xs:attribute name="showBootstrap" type="xs:boolean"/>
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118 <xs:attribute name="showDistances" type="xs:boolean"/>
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119 <xs:attribute name="markUnlinked" type="xs:boolean"/>
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120 <xs:attribute name="fitToWindow" type="xs:boolean"/>
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121 <xs:attribute name="currentTree" type="xs:boolean"/>
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125 <xs:element name="FeatureSettings" minOccurs="0" maxOccurs="1">
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128 <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
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130 <xs:attribute name="type" type="xs:string" use="required"/>
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131 <xs:attribute name="colour" type="xs:int" use="required"/>
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132 <xs:attribute name="display" type="xs:boolean" use="required"/>
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143 <xs:complexType name="feature">
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144 <xs:attribute name="begin" type="xs:int" use="required"/>
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145 <xs:attribute name="end" type="xs:int" use="required"/>
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146 <xs:attribute name="type" type="xs:string" use="required"/>
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147 <xs:attribute name="description" type="xs:string" use="optional"/>
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148 <xs:attribute name="status" type="xs:string" use="optional"/>
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151 <xs:complexType name="pdbentry">
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152 <xs:sequence minOccurs="0" maxOccurs="unbounded">
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153 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
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155 <xs:attribute name="name" type="xs:string" use="required"/>
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156 <xs:attribute name="value" type="xs:string" use="required"/>
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160 <xs:attribute name="id" type="xs:string" use="required"/>
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161 <xs:attribute name="type" type="xs:string" use="optional"/>
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