1 <?xml version="1.0" encoding="UTF-8"?>
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
6 This file is part of Jalview.
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.
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.
17 You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:jalview="www.jalview.org/colours" targetNamespace="www.jalview.org/colours">
20 <xs:element name="JalviewUserColours" type="jalview:JalviewUserColours" />
21 <xs:complexType name="JalviewUserColours">
23 <xs:element name="Version" maxOccurs="1" minOccurs="0" type="xs:string">
26 Jalview colour scheme document version.
30 <xs:element name="colour" maxOccurs="unbounded" minOccurs="0">
33 <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
35 <xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
39 <xs:attribute name="Name" type="xs:string">
41 <xs:documentation>Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme</xs:documentation>
44 <xs:attribute name="RGB" type="xs:string" use="required"/>
45 <xs:attribute name="minRGB" type="xs:string" use="optional"/>
46 <xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
47 <xs:attribute name="threshType" use="optional" type="jalview:ThresholdType" />
48 <xs:attribute name="threshold" type="xs:float" use="optional"/>
49 <xs:attribute name="max" type="xs:float" use="optional"/>
50 <xs:attribute name="min" type="xs:float" use="optional"/>
51 <xs:attribute name="colourByLabel" type="xs:boolean" use="optional"/>
52 <xs:attribute name="autoScale" type="xs:boolean" use="optional"/>
55 <xs:element name="filter" maxOccurs="unbounded" minOccurs="0" >
58 <xs:element name="matcherSet" type="jalview:FeatureMatcherSet" />
60 <xs:attribute name="featureType" type="xs:string" use="required"/>
64 <xs:attribute name="schemeName" type="xs:string" use="optional"/>
67 <xs:complexType name="FeatureMatcherSet">
69 <xs:documentation>A feature match condition, which may be simple or compound</xs:documentation>
72 <xs:element name="matchCondition" type="jalview:FeatureMatcher" />
73 <xs:element name="compoundMatcher">
76 <xs:element name="matcherSet" minOccurs="2" maxOccurs="2" type="jalview:FeatureMatcherSet" />
78 <xs:attribute name="and" type="xs:boolean" use="required">
80 <xs:documentation>If true, matchers are AND-ed, if false they are OR-ed</xs:documentation>
88 <xs:complexType name="FeatureMatcher">
90 <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
92 <xs:documentation>name of feature attribute to filter on, or attribute and sub-attribute</xs:documentation>
95 <xs:element name="condition" type="xs:string" />
96 <xs:element name="value" type="xs:string" />
98 <xs:attribute name="by" type="jalview:FilterBy" />
101 <xs:simpleType name="ThresholdType">
103 <xs:documentation>Whether filter has a threshold, and if so is it
107 <xs:restriction base="xs:string">
108 <xs:enumeration value="NONE" />
109 <xs:enumeration value="ABOVE" />
110 <xs:enumeration value="BELOW" />
114 <xs:simpleType name="FilterBy">
116 <xs:documentation>Filter may apply to label, score or some feature attribute</xs:documentation>
118 <xs:restriction base="xs:string">
119 <xs:enumeration value="byLabel" />
120 <xs:enumeration value="byScore" />
121 <xs:enumeration value="byAttribute" />
125 <xs:simpleType name="NoValueColour">
127 <xs:documentation>Graduated feature colour if no score (or attribute) value</xs:documentation>
129 <xs:restriction base="xs:string">
130 <xs:enumeration value="None" />
131 <xs:enumeration value="Min" />
132 <xs:enumeration value="Max" />