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 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:jalview="www.jalview.org/colours" targetNamespace="www.jalview.org/colours">
  20         <xs:complexType name="JalviewUserColours">
  21                 <xs:sequence>
  22                         <xs:element name="Version" maxOccurs="1" minOccurs="0" type="xs:string">
  23                                 <xs:annotation>
  24                                 <xs:documentation>
  25                                 Jalview colour scheme document version.
  26                                 </xs:documentation>
  27                                 </xs:annotation>
  28                         </xs:element>
  29                         <xs:element name="colour" maxOccurs="unbounded" minOccurs="0">
  30                                 <xs:complexType>
  31                                     <xs:sequence>
  32                                             <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
  33                                                         <xs:annotation>
  34                                                                 <xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
  35                                                         </xs:annotation>
  36                                             </xs:element>
  37                                         </xs:sequence>
  38                                         <xs:attribute name="Name" type="xs:string">
  39                                                 <xs:annotation>
  40                                                         <xs:documentation>Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme</xs:documentation>
  41                                                 </xs:annotation>
  42                                         </xs:attribute>
  43                                         <xs:attribute name="RGB" type="xs:string" use="required"/>
  44                                         <xs:attribute name="minRGB" type="xs:string" use="optional"/>
  45                                         <xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
  46                                         <xs:attribute name="threshType" use="optional">
  47                                                 <xs:simpleType>
  48                                                         <xs:restriction base="xs:string">
  49                                                       <xs:enumeration value="NONE" />
  50                                                       <xs:enumeration value="ABOVE" />
  51                                                       <xs:enumeration value="BELOW" />
  52                                                     </xs:restriction>
  53                                             </xs:simpleType>
  54                                         </xs:attribute>
  55                                         <xs:attribute name="threshold" type="xs:float" use="optional"/>
  56                                         <xs:attribute name="max" type="xs:float" use="optional"/>
  57                                         <xs:attribute name="min" type="xs:float" use="optional"/>
  58                                         <xs:attribute name="colourByLabel" type="xs:boolean" use="optional"/>
  59                                         <xs:attribute name="autoScale" type="xs:boolean" use="optional"/>
  60                                 </xs:complexType>
  61                         </xs:element>
  62                         <xs:element name="filter" maxOccurs="unbounded" minOccurs="0" >
  63                             <xs:complexType>
  64                                         <xs:sequence>
  65                                                 <xs:element name="matcherSet" type="jalview:FeatureMatcherSet" />
  66                                         </xs:sequence>
  67                                         <xs:attribute name="featureType" type="xs:string" use="required"/>
  68                             </xs:complexType>
  69                         </xs:element>
  70                 </xs:sequence>
  71                 <xs:attribute name="schemeName" type="xs:string" use="optional"/>
  72         </xs:complexType>
  73
  74         <xs:complexType name="FeatureMatcherSet">
  75                 <xs:annotation>
  76                         <xs:documentation>A feature match condition, which may be simple or compound</xs:documentation>
  77                 </xs:annotation>
  78           <xs:choice>
  79             <xs:element name="matchCondition" type="jalview:FeatureMatcher" />
  80             <xs:element name="compoundMatcher">
  81                     <xs:complexType>
  82                           <xs:sequence>
  83                               <xs:element name="matcherSet" minOccurs="2" maxOccurs="2" type="jalview:FeatureMatcherSet" />
  84                           </xs:sequence>
  85                       <xs:attribute name="and" type="xs:boolean" use="required">
  86                                   <xs:annotation>
  87                                         <xs:documentation>If true, matchers are AND-ed, if false they are OR-ed</xs:documentation>
  88                                   </xs:annotation>
  89                       </xs:attribute>
  90                     </xs:complexType>
  91             </xs:element>
  92           </xs:choice>
  93         </xs:complexType>
  94
  95         <xs:complexType name="FeatureMatcher">
  96           <xs:sequence>
  97             <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
  98                         <xs:annotation>
  99                                 <xs:documentation>name of feature attribute to filter on, or attribute and sub-attribute</xs:documentation>
 100                         </xs:annotation>
 101             </xs:element>
 102             <xs:element name="condition" type="xs:string" />
 103             <xs:element name="value" type="xs:string" />
 104           </xs:sequence>
 105           <xs:attribute name="by">
 106                 <xs:simpleType>
 107                         <xs:restriction base="xs:string">
 108                       <xs:enumeration value="byLabel" />
 109                       <xs:enumeration value="byScore" />
 110                       <xs:enumeration value="byAttribute" />
 111                     </xs:restriction>
 112             </xs:simpleType>
 113           </xs:attribute>
 114         </xs:complexType>
 115
 116         <xs:simpleType name="NoValueColour">
 117                 <xs:annotation>
 118                         <xs:documentation>Graduated feature colour if no score (or attribute) value</xs:documentation>
 119                 </xs:annotation>
 120                 <xs:restriction base="xs:string">
 121               <xs:enumeration value="None" />
 122               <xs:enumeration value="Min" />
 123               <xs:enumeration value="Max" />
 124             </xs:restriction>
 125         </xs:simpleType>
 126 </xs:schema>