schemas/JalviewUserColours.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!--
   3   Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   4   Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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 -->
  19 <!--
  20         Java JAXB binding classes are generated by running command line tool xjc:
  21             xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
  22         Note this also generates code for included schemas
  23 -->
  24 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:jalview="www.jalview.org/colours" targetNamespace="www.jalview.org/colours">
  25         <xs:element name="JalviewUserColours" type="jalview:JalviewUserColours" />
  26         <xs:complexType name="JalviewUserColours">
  27                 <xs:sequence>
  28                         <xs:element name="Version" maxOccurs="1" minOccurs="0" type="xs:string">
  29                                 <xs:annotation>
  30                                 <xs:documentation>
  31                                 Jalview colour scheme document version.
  32                                 </xs:documentation>
  33                                 </xs:annotation>
  34                         </xs:element>
  35                         <xs:element name="colour" maxOccurs="unbounded" minOccurs="0">
  36                                 <xs:complexType>
  37                                     <xs:sequence>
  38                                             <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
  39                                                         <xs:annotation>
  40                                                                 <xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
  41                                                         </xs:annotation>
  42                                             </xs:element>
  43                                         </xs:sequence>
  44                                         <xs:attribute name="Name" type="xs:string">
  45                                                 <xs:annotation>
  46                                                         <xs:documentation>Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme</xs:documentation>
  47                                                 </xs:annotation>
  48                                         </xs:attribute>
  49                                         <xs:attribute name="RGB" type="xs:string" use="required"/>
  50                                         <xs:attribute name="minRGB" type="xs:string" use="optional"/>
  51                                         <xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
  52                                         <xs:attribute name="threshType" use="optional" type="jalview:ThresholdType" />
  53                                         <xs:attribute name="threshold" type="xs:float" use="optional"/>
  54                                         <xs:attribute name="max" type="xs:float" use="optional"/>
  55                                         <xs:attribute name="min" type="xs:float" use="optional"/>
  56                                         <xs:attribute name="colourByLabel" type="xs:boolean" use="optional"/>
  57                                         <xs:attribute name="autoScale" type="xs:boolean" use="optional"/>
  58                                 </xs:complexType>
  59                         </xs:element>
  60                         <xs:element name="filter" maxOccurs="unbounded" minOccurs="0" >
  61                             <xs:complexType>
  62                                         <xs:sequence>
  63                                                 <xs:element name="matcherSet" type="jalview:FeatureMatcherSet" />
  64                                         </xs:sequence>
  65                                         <xs:attribute name="featureType" type="xs:string" use="required"/>
  66                             </xs:complexType>
  67                         </xs:element>
  68                 </xs:sequence>
  69                 <xs:attribute name="schemeName" type="xs:string" use="optional"/>
  70         </xs:complexType>
  71
  72         <xs:complexType name="FeatureMatcherSet">
  73                 <xs:annotation>
  74                         <xs:documentation>A feature match condition, which may be simple or compound</xs:documentation>
  75                 </xs:annotation>
  76           <xs:choice>
  77             <xs:element name="matchCondition" type="jalview:FeatureMatcher" />
  78             <xs:element name="compoundMatcher">
  79                     <xs:complexType>
  80                           <xs:sequence>
  81                               <xs:element name="matcherSet" minOccurs="2" maxOccurs="2" type="jalview:FeatureMatcherSet" />
  82                           </xs:sequence>
  83                       <xs:attribute name="and" type="xs:boolean" use="required">
  84                                   <xs:annotation>
  85                                         <xs:documentation>If true, matchers are AND-ed, if false they are OR-ed</xs:documentation>
  86                                   </xs:annotation>
  87                       </xs:attribute>
  88                     </xs:complexType>
  89             </xs:element>
  90           </xs:choice>
  91         </xs:complexType>
  92
  93         <xs:complexType name="FeatureMatcher">
  94           <xs:sequence>
  95             <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
  96                         <xs:annotation>
  97                                 <xs:documentation>name of feature attribute to filter on, or attribute and sub-attribute</xs:documentation>
  98                         </xs:annotation>
  99             </xs:element>
 100             <xs:element name="condition" type="xs:string" />
 101             <xs:element name="value" type="xs:string" />
 102           </xs:sequence>
 103           <xs:attribute name="by" type="jalview:FilterBy" />
 104         </xs:complexType>
 105
 106         <xs:simpleType name="ThresholdType">
 107                 <xs:annotation>
 108                         <xs:documentation>Whether filter has a threshold, and if so is it
 109                                 above or below
 110                         </xs:documentation>
 111                 </xs:annotation>
 112                 <xs:restriction base="xs:string">
 113                         <xs:enumeration value="NONE" />
 114                         <xs:enumeration value="ABOVE" />
 115                         <xs:enumeration value="BELOW" />
 116                 </xs:restriction>
 117         </xs:simpleType>
 118
 119         <xs:simpleType name="FilterBy">
 120                 <xs:annotation>
 121                         <xs:documentation>Filter may apply to label, score or some feature attribute</xs:documentation>
 122                 </xs:annotation>
 123                 <xs:restriction base="xs:string">
 124               <xs:enumeration value="byLabel" />
 125               <xs:enumeration value="byScore" />
 126               <xs:enumeration value="byAttribute" />
 127             </xs:restriction>
 128         </xs:simpleType>
 129
 130         <xs:simpleType name="NoValueColour">
 131                 <xs:annotation>
 132                         <xs:documentation>Graduated feature colour if no score (or attribute) value</xs:documentation>
 133                 </xs:annotation>
 134                 <xs:restriction base="xs:string">
 135               <xs:enumeration value="None" />
 136               <xs:enumeration value="Min" />
 137               <xs:enumeration value="Max" />
 138             </xs:restriction>
 139         </xs:simpleType>
 140 </xs:schema>