schemas/sifts/alignment.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <xsd:schema targetNamespace="http://www.ebi.ac.uk/pdbe/docs/sifts/eFamily.xsd"
   3         elementFormDefault="qualified" attributeFormDefault="unqualified"
   4         xmlns:data="http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd"
   5         xmlns:xsd="http://www.w3.org/2001/XMLSchema"
   6         xmlns="http://www.ebi.ac.uk/pdbe/docs/sifts/alignment.xsd" version="1.1">
   7         <xsd:import namespace="http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd"
   8                 schemaLocation="dataTypes.xsd"/>
   9         <xsd:element name="alignment">
  10                 <xsd:annotation>
  11                         <xsd:documentation>This section of the schema deals with alignments.  The alignment can be either a sequence alignment or a structural alignment.</xsd:documentation>
  12                 </xsd:annotation>
  13                 <xsd:complexType>
  14                         <xsd:sequence>
  15                                 <xsd:element name="alignObject" maxOccurs="unbounded">
  16                                         <xsd:annotation>
  17                                                 <xsd:documentation>description of object. id e.g. 1tim.A,8tim.B, P001228, ...; type: type of object e.g.: protein, dna. version: last time this object has been changed (sometimes not so easy to know ...)</xsd:documentation>
  18                                         </xsd:annotation>
  19                                         <xsd:complexType>
  20                                                 <xsd:sequence>
  21                                                         <xsd:element name="alignObjectDetail" minOccurs="0"
  22                                                                 maxOccurs="unbounded">
  23                                                                 <xsd:complexType mixed="true">
  24                                                                         <xsd:attributeGroup ref="data:detail"/>
  25                                                                 </xsd:complexType>
  26                                                         </xsd:element>
  27                                                         <xsd:element name="sequence" minOccurs="0">
  28                                                                 <xsd:complexType mixed="true">
  29                                                                         <xsd:attributeGroup ref="data:region"/>
  30                                                                 </xsd:complexType>
  31                                                         </xsd:element>
  32                                                 </xsd:sequence>
  33                                                 <xsd:attribute name="objectVersion" type="xsd:string" use="required"/>
  34                                                 <xsd:attribute name="intObjectId" type="xsd:string" use="required"/>
  35                                                 <xsd:attribute name="type" type="xsd:string" use="optional"/>
  36                                                 <xsd:attributeGroup ref="data:dbRef"/>
  37                                         </xsd:complexType>
  38                                 </xsd:element>
  39                                 <xsd:element name="score" minOccurs="0" maxOccurs="unbounded">
  40                                         <xsd:annotation>
  41                                                 <xsd:documentation>e.g.: number of identical residues, % id residues, aligmnent score, e-value, p-value, etc.</xsd:documentation>
  42                                         </xsd:annotation>
  43                                         <xsd:complexType>
  44                                                 <xsd:attribute name="methodName" type="xsd:string" use="required"/>
  45                                                 <xsd:attribute name="scoreValue" type="xsd:string" use="required"/>
  46                                         </xsd:complexType>
  47                                 </xsd:element>
  48                                 <xsd:element name="block" maxOccurs="unbounded">
  49                                         <xsd:complexType>
  50                                                 <xsd:sequence>
  51                                                         <xsd:element name="segment" maxOccurs="unbounded">
  52                                                                 <xsd:annotation>
  53                                                                         <xsd:documentation>the alignment given for a single object</xsd:documentation>
  54                                                                         <xsd:documentation>the alignment given for a single object</xsd:documentation>
  55                                                                 </xsd:annotation>
  56                                                                 <xsd:complexType>
  57                                                                         <xsd:sequence minOccurs="0">
  58                                                                                 <xsd:element name="cigar" type="data:cigarstring">
  59                                                                                         <xsd:annotation>
  60                                                                                                 <xsd:documentation>e.g. 2D23M4I</xsd:documentation>
  61                                                                                         </xsd:annotation>
  62                                                                                 </xsd:element>
  63                                                                         </xsd:sequence>
  64                                                                         <xsd:attributeGroup ref="data:region"/>
  65                                                                         <xsd:attribute name="intObjectId" use="required"/>
  66                                                                         <xsd:attribute name="strand" use="optional"/>
  67                                                                 </xsd:complexType>
  68                                                         </xsd:element>
  69                                                 </xsd:sequence>
  70                                                 <xsd:attribute name="blockScore" type="xsd:string" use="optional"/>
  71                                                 <xsd:attribute name="blockOrder" type="xsd:integer" use="required"/>
  72                                         </xsd:complexType>
  73                                 </xsd:element>
  74                                 <xsd:element name="geo3d" minOccurs="0" maxOccurs="unbounded">
  75                                         <xsd:annotation>
  76                                                 <xsd:documentation>geometrical operation to perform on 3D object</xsd:documentation>
  77                                         </xsd:annotation>
  78                                         <xsd:complexType>
  79                                                 <xsd:sequence>
  80                                                         <xsd:element name="vector">
  81                                                                 <xsd:complexType>
  82                                                                         <xsd:attribute name="x" type="xsd:float" use="required"/>
  83                                                                         <xsd:attribute name="y" type="xsd:float" use="required"/>
  84                                                                         <xsd:attribute name="z" type="xsd:float" use="required"/>
  85                                                                 </xsd:complexType>
  86                                                         </xsd:element>
  87                                                         <xsd:element name="matrix" maxOccurs="unbounded">
  88                                                                 <xsd:complexType>
  89                                                                         <xsd:sequence>
  90                                                                                 <xsd:element name="max11">
  91                                                                                         <xsd:complexType>
  92                                                                                                 <xsd:attribute name="coord" type="xsd:float"
  93                                                                                                 use="required"/>
  94                                                                                         </xsd:complexType>
  95                                                                                 </xsd:element>
  96                                                                                 <xsd:element name="max12">
  97                                                                                         <xsd:complexType>
  98                                                                                                 <xsd:attribute name="coord" type="xsd:float"
  99                                                                                                 use="required"/>
 100                                                                                         </xsd:complexType>
 101                                                                                 </xsd:element>
 102                                                                                 <xsd:element name="max13">
 103                                                                                         <xsd:complexType>
 104                                                                                                 <xsd:attribute name="coord" type="xsd:float"
 105                                                                                                 use="required"/>
 106                                                                                         </xsd:complexType>
 107                                                                                 </xsd:element>
 108                                                                                 <xsd:element name="max21">
 109                                                                                         <xsd:complexType>
 110                                                                                                 <xsd:attribute name="coord" type="xsd:float"
 111                                                                                                 use="required"/>
 112                                                                                         </xsd:complexType>
 113                                                                                 </xsd:element>
 114                                                                                 <xsd:element name="max22">
 115                                                                                         <xsd:complexType>
 116                                                                                                 <xsd:attribute name="coord" type="xsd:float"
 117                                                                                                 use="required"/>
 118                                                                                         </xsd:complexType>
 119                                                                                 </xsd:element>
 120                                                                                 <xsd:element name="max23">
 121                                                                                         <xsd:complexType>
 122                                                                                                 <xsd:attribute name="coord" type="xsd:float"
 123                                                                                                 use="required"/>
 124                                                                                         </xsd:complexType>
 125                                                                                 </xsd:element>
 126                                                                                 <xsd:element name="max31">
 127                                                                                         <xsd:complexType>
 128                                                                                                 <xsd:attribute name="coord" type="xsd:float"
 129                                                                                                 use="required"/>
 130                                                                                         </xsd:complexType>
 131                                                                                 </xsd:element>
 132                                                                                 <xsd:element name="max32">
 133                                                                                         <xsd:complexType>
 134                                                                                                 <xsd:attribute name="coord" type="xsd:float"
 135                                                                                                 use="required"/>
 136                                                                                         </xsd:complexType>
 137                                                                                 </xsd:element>
 138                                                                                 <xsd:element name="max33">
 139                                                                                         <xsd:complexType>
 140                                                                                                 <xsd:attribute name="coord" type="xsd:float"
 141                                                                                                 use="required"/>
 142                                                                                         </xsd:complexType>
 143                                                                                 </xsd:element>
 144                                                                         </xsd:sequence>
 145                                                                 </xsd:complexType>
 146                                                         </xsd:element>
 147                                                 </xsd:sequence>
 148                                                 <xsd:attribute name="intObjectId" type="xsd:string" use="required"/>
 149                                         </xsd:complexType>
 150                                 </xsd:element>
 151                         </xsd:sequence>
 152                         <xsd:attribute name="alignType" type="xsd:string" use="required"/>
 153                 </xsd:complexType>
 154         </xsd:element>
 155 </xsd:schema>