JAL-1198 JAL-1197 migrated to IA 2012 and new VM
[jalview.git] / 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