schemas/vamsas.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!--
   3   Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
   4   Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   5
   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.
  10
  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.
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  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
  19 -->
  20 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
  21 <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">
  22         <xs:complexType name="VAMSAS">
  23                 <xs:sequence>
  24                         <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
  25                         <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
  26                 </xs:sequence>
  27         </xs:complexType>
  28         <xs:complexType name="mapListType">
  29                 <xs:annotation>
  30                         <xs:documentation>
  31                                 developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
  32                         </xs:documentation>
  33                         <xs:documentation>
  34                                 This effectively represents a java.util.MapList object
  35                         </xs:documentation>
  36                 </xs:annotation>
  37                 <xs:sequence>
  38                         <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
  39                                 <xs:annotation>
  40                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
  41                                 </xs:annotation>
  42                                 <xs:complexType>
  43                                         <xs:attribute name="start" type="xs:int" use="required"/>
  44                                         <xs:attribute name="end" type="xs:int" use="required"/>
  45                                 </xs:complexType>
  46                         </xs:element>
  47                         <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
  48                                 <xs:annotation>
  49                                         <xs:documentation> a region from start to end inclusive</xs:documentation>
  50                                 </xs:annotation>
  51                                 <xs:complexType>
  52                                         <xs:attribute name="start" type="xs:int" use="required"/>
  53                                         <xs:attribute name="end" type="xs:int" use="required"/>
  54                                 </xs:complexType>
  55                         </xs:element>
  56                 </xs:sequence>
  57                 <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
  58                         <xs:annotation>
  59                                 <xs:documentation>number of dictionary symbol widths involved in each
  60                                         mapped position on this sequence (for example, 3 for a dna sequence exon
  61                                         region that is being mapped to a protein sequence). This is optional,
  62                                         since the unit can be usually be inferred from the dictionary type of
  63                                         each sequence involved in the mapping. </xs:documentation>
  64                         </xs:annotation>
  65                 </xs:attribute>
  66                 <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
  67                         <xs:annotation>
  68                                 <xs:documentation>number of dictionary symbol widths involved in each
  69                                         mapped position on this sequence (for example, 3 for a dna sequence exon
  70                                         region that is being mapped to a protein sequence). This is optional,
  71                                         since the unit can be usually be inferred from the dictionary type of
  72                                         each sequence involved in the mapping. </xs:documentation>
  73                         </xs:annotation>
  74                 </xs:attribute>
  75         </xs:complexType>
  76         <xs:element name="Mapping">
  77                 <xs:complexType>
  78                         <xs:annotation>
  79                                 <xs:documentation>
  80                                         Represent the jalview.datamodel.Mapping object - it also provides
  81                                         a way of storing sequences that are mapped 'to' without adding them
  82                                         to the sequence set (which will mean they are then added to the alignment too).
  83                                 </xs:documentation>
  84                         </xs:annotation>
  85                         <xs:complexContent>
  86                                 <xs:extension base="vamsas:mapListType">
  87                                         <xs:sequence>
  88                                                 <xs:choice minOccurs="0" maxOccurs="1">
  89                                                         <xs:element ref="vamsas:Sequence"/>
  90                                                         <xs:element name="dseqFor">
  91                                                                 <xs:simpleType>
  92                                                                         <xs:restriction base="xs:string">
  93                                                                                 <xs:annotation>
  94                                                                                         <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
  95                                                                                 </xs:annotation>
  96                                                                         </xs:restriction>
  97                                                                 </xs:simpleType>
  98                                                         </xs:element>
  99                                                 </xs:choice>
 100                                         </xs:sequence>
 101                                 </xs:extension>
 102                         </xs:complexContent>
 103                 </xs:complexType>
 104         </xs:element>
 105         <xs:element name="AlcodonFrame">
 106                 <xs:complexType>
 107                         <xs:sequence>
 108                                 <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
 109                                         <xs:complexType>
 110                                                 <xs:attribute name="pos1" type="xs:integer"/>
 111                                                 <xs:attribute name="pos2" type="xs:integer"/>
 112                                                 <xs:attribute name="pos3" type="xs:integer"/>
 113                                         </xs:complexType>
 114                                 </xs:element>
 115                                 <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
 116                                         <xs:complexType>
 117                                                 <xs:sequence>
 118                                                         <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
 119                                                                 <xs:annotation>
 120                                                                         <xs:documentation>
 121                                                                                 a Mapping entry and an associated protein sequence
 122                                                                         </xs:documentation>
 123                                                                 </xs:annotation>
 124                                                         </xs:element>
 125                                                 </xs:sequence>
 126                                                 <xs:attribute name="dnasq" type="xs:string" use="required">
 127                                                         <xs:annotation>
 128                                                                 <xs:documentation>
 129                                                                         internal jalview id for the dnasq for this mapping.
 130                                                                 </xs:documentation>
 131                                                         </xs:annotation>
 132                                                 </xs:attribute>
 133                                         </xs:complexType>
 134
 135                                 </xs:element>
 136
 137                         </xs:sequence>
 138                 </xs:complexType>
 139         </xs:element>
 140         <xs:element name="Sequence">
 141                 <xs:complexType>
 142                         <xs:complexContent>
 143                                 <xs:extension base="vamsas:SequenceType">
 144                                         <xs:sequence>
 145                                                 <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
 146                                                         <xs:complexType>
 147                                                                 <xs:sequence>
 148                                                                         <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
 149                                                                 </xs:sequence>
 150                                                                 <xs:attribute name="source" type="xs:string"/>
 151                                                                 <xs:attribute name="version" type="xs:string"/>
 152                                                                 <xs:attribute name="accessionId" type="xs:string"/>
 153                                                         </xs:complexType>
 154                                                 </xs:element>
 155                                         </xs:sequence>
 156                                         <xs:attribute name="dsseqid" type="xs:string" use="optional">
 157                                                 <xs:annotation>
 158                                                         <xs:documentation>
 159                                                                 dataset sequence id for this sequence. Will be created as union of sequences.
 160                                                         </xs:documentation>
 161                                                 </xs:annotation>
 162                                         </xs:attribute>
 163                                 </xs:extension>
 164                         </xs:complexContent>
 165                 </xs:complexType>
 166         </xs:element>
 167         <xs:element name="Annotation">
 168                 <xs:complexType>
 169                         <xs:sequence>
 170                                 <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
 171                                 <xs:element name="label" type="xs:string"/>
 172                                 <xs:element name="description" type="xs:string" minOccurs="0"/>
 173                                 <xs:element name="thresholdLine" minOccurs="0">
 174                                         <xs:complexType>
 175                                                 <xs:attribute name="label" type="xs:string"/>
 176                                                 <xs:attribute name="value" type="xs:float"/>
 177                                                 <xs:attribute name="colour" type="xs:int"/>
 178                                         </xs:complexType>
 179                                 </xs:element>
 180                         </xs:sequence>
 181                         <xs:attribute name="graph" type="xs:boolean" use="required"/>
 182                         <xs:attribute name="graphType" type="xs:int" use="optional"/>
 183                         <xs:attribute name="sequenceRef" type="xs:string" use="optional"/>
 184                         <xs:attribute name="graphColour" type="xs:int" use="optional"/>
 185                         <xs:attribute name="graphGroup" type="xs:int" use="optional"/>
 186                         <xs:attribute name="id" type="xs:string" use="optional"/>
 187                         <xs:attribute name="scoreOnly" type="xs:boolean" use="optional" default="false"/>
 188                         <xs:attribute name="score" type="xs:double" use="optional"/>
 189                         <xs:attribute name="visible" type="xs:boolean" use="optional"/>
 190                 </xs:complexType>
 191         </xs:element>
 192         <xs:element name="SequenceSet">
 193                 <xs:complexType>
 194                         <xs:sequence>
 195                                 <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
 196                                 <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
 197                                 <xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
 198                                         <xs:complexType>
 199                                                 <xs:attribute name="key" type="xs:string"/>
 200                                                 <xs:attribute name="value" type="xs:string"/>
 201                                         </xs:complexType>
 202                                 </xs:element>
 203                                 <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
 204                         </xs:sequence>
 205                         <xs:attribute name="gapChar" type="xs:string" use="required"/>
 206                         <xs:attribute name="datasetId" type="xs:string" use="optional">
 207                                 <xs:annotation>
 208                                         <xs:documentation>
 209                                                 reference to set where jalview will gather the dataset sequences for all sequences in the set.
 210                                         </xs:documentation>
 211                                 </xs:annotation>
 212                         </xs:attribute>
 213                 </xs:complexType>
 214         </xs:element>
 215         <xs:element name="annotationElement">
 216                 <xs:complexType>
 217                         <xs:sequence>
 218                                 <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
 219                                 <xs:element name="description" type="xs:string" minOccurs="0"/>
 220                                 <xs:element name="secondaryStructure" minOccurs="0">
 221                                         <xs:simpleType>
 222                                                 <xs:restriction base="xs:string">
 223                                                         <xs:length value="1"/>
 224                                                 </xs:restriction>
 225                                         </xs:simpleType>
 226                                 </xs:element>
 227                                 <xs:element name="value" type="xs:float" minOccurs="0"/>
 228                         </xs:sequence>
 229                         <xs:attribute name="position" type="xs:int" use="required"/>
 230                         <xs:attribute name="colour" type="xs:int" use="optional"/>
 231                 </xs:complexType>
 232         </xs:element>
 233         <xs:complexType name="SequenceType">
 234                 <xs:sequence>
 235                         <xs:element name="sequence" type="xs:string" minOccurs="0"/>
 236                         <xs:element name="name" type="xs:string" minOccurs="0"/>
 237                 </xs:sequence>
 238                 <xs:attribute name="id" type="xs:string"/>
 239                 <xs:attribute name="description" type="xs:string"/>
 240         </xs:complexType>
 241 </xs:schema>