1 <?xml version="1.0" encoding="UTF-8"?>
2 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
3 <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">
4 <xs:complexType name="VAMSAS">
6 <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
7 <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
10 <xs:complexType name="mapListType">
13 developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
16 This effectively represents a java.util.MapList object
20 <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
22 <xs:documentation> a region from start to end inclusive</xs:documentation>
25 <xs:attribute name="start" type="xs:int" use="required"/>
26 <xs:attribute name="end" type="xs:int" use="required"/>
29 <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
31 <xs:documentation> a region from start to end inclusive</xs:documentation>
34 <xs:attribute name="start" type="xs:int" use="required"/>
35 <xs:attribute name="end" type="xs:int" use="required"/>
39 <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
41 <xs:documentation>number of dictionary symbol widths involved in each
42 mapped position on this sequence (for example, 3 for a dna sequence exon
43 region that is being mapped to a protein sequence). This is optional,
44 since the unit can be usually be inferred from the dictionary type of
45 each sequence involved in the mapping. </xs:documentation>
48 <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
50 <xs:documentation>number of dictionary symbol widths involved in each
51 mapped position on this sequence (for example, 3 for a dna sequence exon
52 region that is being mapped to a protein sequence). This is optional,
53 since the unit can be usually be inferred from the dictionary type of
54 each sequence involved in the mapping. </xs:documentation>
58 <xs:element name="Mapping">
62 Represent the jalview.datamodel.Mapping object - it also provides
63 a way of storing sequences that are mapped 'to' without adding them
64 to the sequence set (which will mean they are then added to the alignment too).
68 <xs:extension base="vamsas:mapListType">
70 <xs:choice minOccurs="0" maxOccurs="1">
71 <xs:element ref="vamsas:Sequence"/>
72 <xs:element name="dseqFor">
74 <xs:restriction base="xs:string">
76 <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
87 <xs:element name="AlcodonFrame">
90 <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
94 specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
95 Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
98 <xs:attribute name="pos1" type="xs:integer" use="optional"/>
99 <xs:attribute name="pos2" type="xs:integer" use="optional"/>
100 <xs:attribute name="pos3" type="xs:integer" use="optional"/>
103 <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
106 <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
109 a Mapping entry and an associated protein sequence
114 <xs:attribute name="dnasq" type="xs:string" use="required">
117 internal jalview id for the dnasq for this mapping.
128 <xs:element name="Sequence">
131 <xs:extension base="vamsas:SequenceType">
133 <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
136 <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
138 <xs:attribute name="source" type="xs:string"/>
139 <xs:attribute name="version" type="xs:string"/>
140 <xs:attribute name="accessionId" type="xs:string"/>
144 <xs:attribute name="dsseqid" type="xs:string" use="optional">
147 dataset sequence id for this sequence. Will be created as union of sequences.
155 <xs:element name="Annotation">
158 <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
159 <xs:element name="label" type="xs:string"/>
160 <xs:element name="description" type="xs:string" minOccurs="0"/>
161 <xs:element name="thresholdLine" minOccurs="0">
163 <xs:attribute name="label" type="xs:string"/>
164 <xs:attribute name="value" type="xs:float"/>
165 <xs:attribute name="colour" type="xs:int"/>
169 <xs:attribute name="graph" type="xs:boolean" use="required"/>
170 <xs:attribute name="graphType" type="xs:int" use="optional"/>
171 <xs:attribute name="sequenceRef" type="xs:string" use="optional"/>
172 <xs:attribute name="graphColour" type="xs:int" use="optional"/>
173 <xs:attribute name="graphGroup" type="xs:int" use="optional"/>
174 <xs:attribute name="id" type="xs:string" use="optional"/>
175 <xs:attribute name="scoreOnly" type="xs:boolean" use="optional" default="false"/>
176 <xs:attribute name="score" type="xs:double" use="optional"/>
177 <xs:attribute name="visible" type="xs:boolean" use="optional"/>
180 <xs:element name="SequenceSet">
183 <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
184 <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
185 <xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
187 <xs:attribute name="key" type="xs:string"/>
188 <xs:attribute name="value" type="xs:string"/>
191 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
193 <xs:attribute name="gapChar" type="xs:string" use="required"/>
194 <xs:attribute name="datasetId" type="xs:string" use="optional">
197 reference to set where jalview will gather the dataset sequences for all sequences in the set.
203 <xs:element name="annotationElement">
206 <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
207 <xs:element name="description" type="xs:string" minOccurs="0"/>
208 <xs:element name="secondaryStructure" minOccurs="0">
210 <xs:restriction base="xs:string">
211 <xs:length value="1"/>
215 <xs:element name="value" type="xs:float" minOccurs="0"/>
217 <xs:attribute name="position" type="xs:int" use="required"/>
218 <xs:attribute name="colour" type="xs:int" use="optional"/>
221 <xs:complexType name="SequenceType">
223 <xs:element name="sequence" type="xs:string" minOccurs="0"/>
224 <xs:element name="name" type="xs:string" minOccurs="0"/>
226 <xs:attribute name="id" type="xs:string"/>
227 <xs:attribute name="description" type="xs:string"/>