JAL-2629 JAL-2937 respect 'align automatically' option for HMMSearch
[jalview.git] / 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>