1 <?xml version="1.0" encoding="UTF-8"?>
3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
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.
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.
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.
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">
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">
30 <xs:element name="creationDate" type="xs:dateTime"/>
31 <xs:element name="version" type="xs:string"/>
32 <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>
34 <xs:element name="JSeq" maxOccurs="unbounded">
37 <xs:element name="features" type="jv:feature" minOccurs="0" maxOccurs="unbounded"/>
38 <xs:element name="pdbids" type="jv:pdbentry" minOccurs="0" maxOccurs="unbounded"/>
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"/>
47 <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
49 <xs:sequence minOccurs="1">
50 <xs:element name="seq" maxOccurs="unbounded" type="xs:int"/>
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"/>
64 <xs:element name="Viewport" maxOccurs="unbounded">
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"/>
94 <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
96 <xs:sequence minOccurs="1">
97 <xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
99 <xs:attribute name="id" type="xs:string"/>
102 <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
104 <xs:sequence minOccurs="0" maxOccurs="1">
105 <xs:element name="title" type="xs:string"/>
106 <xs:element name="newick" type="xs:string"/>
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"/>
124 <xs:element name="FeatureSettings" minOccurs="0" maxOccurs="1">
127 <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
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"/>
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"/>
150 <xs:complexType name="pdbentry">
151 <xs:sequence minOccurs="0" maxOccurs="unbounded">
152 <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
154 <xs:attribute name="name" type="xs:string" use="required"/>
155 <xs:attribute name="value" type="xs:string" use="required"/>
159 <xs:attribute name="id" type="xs:string" use="required"/>
160 <xs:attribute name="type" type="xs:string" use="optional"/>