1 <?xml version="1.0" encoding="UTF-8"?>
3 Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
4 Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
6 This program is free software; you can redistribute it and/or
7 modify it under the terms of the GNU General Public License
8 as published by the Free Software Foundation; either version 2
9 of the License, or (at your option) any later version.
11 This program is distributed in the hope that it will be useful,
12 but WITHOUT ANY WARRANTY; without even the implied warranty of
13 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 GNU General Public License for more details.
16 You should have received a copy of the GNU General Public License
17 along with this program; if not, write to the Free Software
18 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
21 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
22 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">
23 <xs:complexType name="VAMSAS">
25 <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
26 <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
29 <xs:complexType name="mapListType">
32 developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
35 This effectively represents a java.util.MapList object
39 <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
41 <xs:documentation> a region from start to end inclusive</xs:documentation>
44 <xs:attribute name="start" type="xs:int" use="required"/>
45 <xs:attribute name="end" type="xs:int" use="required"/>
48 <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
50 <xs:documentation> a region from start to end inclusive</xs:documentation>
53 <xs:attribute name="start" type="xs:int" use="required"/>
54 <xs:attribute name="end" type="xs:int" use="required"/>
58 <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
60 <xs:documentation>number of dictionary symbol widths involved in each
61 mapped position on this sequence (for example, 3 for a dna sequence exon
62 region that is being mapped to a protein sequence). This is optional,
63 since the unit can be usually be inferred from the dictionary type of
64 each sequence involved in the mapping. </xs:documentation>
67 <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
69 <xs:documentation>number of dictionary symbol widths involved in each
70 mapped position on this sequence (for example, 3 for a dna sequence exon
71 region that is being mapped to a protein sequence). This is optional,
72 since the unit can be usually be inferred from the dictionary type of
73 each sequence involved in the mapping. </xs:documentation>
77 <xs:element name="Mapping">
81 Represent the jalview.datamodel.Mapping object - it also provides
82 a way of storing sequences that are mapped 'to' without adding them
83 to the sequence set (which will mean they are then added to the alignment too).
87 <xs:extension base="vamsas:mapListType">
89 <xs:choice minOccurs="0" maxOccurs="1">
90 <xs:element ref="vamsas:Sequence"/>
91 <xs:element name="dseqFor">
93 <xs:restriction base="xs:string">
95 <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
106 <xs:element name="AlcodonFrame">
109 <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
113 specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
114 Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
117 <xs:attribute name="pos1" type="xs:integer" use="optional"/>
118 <xs:attribute name="pos2" type="xs:integer" use="optional"/>
119 <xs:attribute name="pos3" type="xs:integer" use="optional"/>
122 <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
125 <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
128 a Mapping entry and an associated protein sequence
133 <xs:attribute name="dnasq" type="xs:string" use="required">
136 internal jalview id for the dnasq for this mapping.
147 <xs:element name="Sequence">
150 <xs:extension base="vamsas:SequenceType">
152 <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
155 <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
157 <xs:attribute name="source" type="xs:string"/>
158 <xs:attribute name="version" type="xs:string"/>
159 <xs:attribute name="accessionId" type="xs:string"/>
163 <xs:attribute name="dsseqid" type="xs:string" use="optional">
166 dataset sequence id for this sequence. Will be created as union of sequences.
174 <xs:element name="Annotation">
177 <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
178 <xs:element name="label" type="xs:string"/>
179 <xs:element name="description" type="xs:string" minOccurs="0"/>
180 <xs:element name="thresholdLine" minOccurs="0">
182 <xs:attribute name="label" type="xs:string"/>
183 <xs:attribute name="value" type="xs:float"/>
184 <xs:attribute name="colour" type="xs:int"/>
188 <xs:attribute name="graph" type="xs:boolean" use="required"/>
189 <xs:attribute name="graphType" type="xs:int" use="optional"/>
190 <xs:attribute name="sequenceRef" type="xs:string" use="optional"/>
191 <xs:attribute name="graphColour" type="xs:int" use="optional"/>
192 <xs:attribute name="graphGroup" type="xs:int" use="optional"/>
193 <xs:attribute name="id" type="xs:string" use="optional"/>
194 <xs:attribute name="scoreOnly" type="xs:boolean" use="optional" default="false"/>
195 <xs:attribute name="score" type="xs:double" use="optional"/>
196 <xs:attribute name="visible" type="xs:boolean" use="optional"/>
199 <xs:element name="SequenceSet">
202 <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
203 <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
204 <xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
206 <xs:attribute name="key" type="xs:string"/>
207 <xs:attribute name="value" type="xs:string"/>
210 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
212 <xs:attribute name="gapChar" type="xs:string" use="required"/>
213 <xs:attribute name="datasetId" type="xs:string" use="optional">
216 reference to set where jalview will gather the dataset sequences for all sequences in the set.
222 <xs:element name="annotationElement">
225 <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
226 <xs:element name="description" type="xs:string" minOccurs="0"/>
227 <xs:element name="secondaryStructure" minOccurs="0">
229 <xs:restriction base="xs:string">
230 <xs:length value="1"/>
234 <xs:element name="value" type="xs:float" minOccurs="0"/>
236 <xs:attribute name="position" type="xs:int" use="required"/>
237 <xs:attribute name="colour" type="xs:int" use="optional"/>
240 <xs:complexType name="SequenceType">
242 <xs:element name="sequence" type="xs:string" minOccurs="0"/>
243 <xs:element name="name" type="xs:string" minOccurs="0"/>
245 <xs:attribute name="id" type="xs:string"/>
246 <xs:attribute name="description" type="xs:string"/>