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" type="jalview:ThresholdType" />
  47                                         <xs:attribute name="threshold" type="xs:float" use="optional"/>
  48                                         <xs:attribute name="max" type="xs:float" use="optional"/>
  49                                         <xs:attribute name="min" type="xs:float" use="optional"/>
  50                                         <xs:attribute name="colourByLabel" type="xs:boolean" use="optional"/>
  51                                         <xs:attribute name="autoScale" type="xs:boolean" use="optional"/>
  52                                 </xs:complexType>
  53                         </xs:element>
  54                         <xs:element name="filter" maxOccurs="unbounded" minOccurs="0" >
  55                             <xs:complexType>
  56                                         <xs:sequence>
  57                                                 <xs:element name="matcherSet" type="jalview:FeatureMatcherSet" />
  58                                         </xs:sequence>
  59                                         <xs:attribute name="featureType" type="xs:string" use="required"/>
  60                             </xs:complexType>
  61                         </xs:element>
  62                 </xs:sequence>
  63                 <xs:attribute name="schemeName" type="xs:string" use="optional"/>
  64         </xs:complexType>
  65
  66         <xs:complexType name="FeatureMatcherSet">
  67                 <xs:annotation>
  68                         <xs:documentation>A feature match condition, which may be simple or compound</xs:documentation>
  69                 </xs:annotation>
  70           <xs:choice>
  71             <xs:element name="matchCondition" type="jalview:FeatureMatcher" />
  72             <xs:element name="compoundMatcher">
  73                     <xs:complexType>
  74                           <xs:sequence>
  75                               <xs:element name="matcherSet" minOccurs="2" maxOccurs="2" type="jalview:FeatureMatcherSet" />
  76                           </xs:sequence>
  77                       <xs:attribute name="and" type="xs:boolean" use="required">
  78                                   <xs:annotation>
  79                                         <xs:documentation>If true, matchers are AND-ed, if false they are OR-ed</xs:documentation>
  80                                   </xs:annotation>
  81                       </xs:attribute>
  82                     </xs:complexType>
  83             </xs:element>
  84           </xs:choice>
  85         </xs:complexType>
  86
  87         <xs:complexType name="FeatureMatcher">
  88           <xs:sequence>
  89             <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
  90                         <xs:annotation>
  91                                 <xs:documentation>name of feature attribute to filter on, or attribute and sub-attribute</xs:documentation>
  92                         </xs:annotation>
  93             </xs:element>
  94             <xs:element name="condition" type="xs:string" />
  95             <xs:element name="value" type="xs:string" />
  96           </xs:sequence>
  97           <xs:attribute name="by" type="jalview:FilterBy" />
  98         </xs:complexType>
  99
 100         <xs:simpleType name="ThresholdType">
 101                 <xs:annotation>
 102                         <xs:documentation>Whether filter has a threshold, and if so is it
 103                                 above or below
 104                         </xs:documentation>
 105                 </xs:annotation>
 106                 <xs:restriction base="xs:string">
 107                         <xs:enumeration value="NONE" />
 108                         <xs:enumeration value="ABOVE" />
 109                         <xs:enumeration value="BELOW" />
 110                 </xs:restriction>
 111         </xs:simpleType>
 112
 113         <xs:simpleType name="FilterBy">
 114                 <xs:annotation>
 115                         <xs:documentation>Filter may apply to label, score or some feature attribute</xs:documentation>
 116                 </xs:annotation>
 117                 <xs:restriction base="xs:string">
 118               <xs:enumeration value="byLabel" />
 119               <xs:enumeration value="byScore" />
 120               <xs:enumeration value="byAttribute" />
 121             </xs:restriction>
 122         </xs:simpleType>
 123
 124         <xs:simpleType name="NoValueColour">
 125                 <xs:annotation>
 126                         <xs:documentation>Graduated feature colour if no score (or attribute) value</xs:documentation>
 127                 </xs:annotation>
 128                 <xs:restriction base="xs:string">
 129               <xs:enumeration value="None" />
 130               <xs:enumeration value="Min" />
 131               <xs:enumeration value="Max" />
 132             </xs:restriction>
 133         </xs:simpleType>
 134 </xs:schema>