<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+
+ This file is part of Jalview.
+
+ Jalview is free software: you can redistribute it and/or
+ modify it under the terms of the GNU General Public License
+ as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+ Jalview is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY; without even the implied warranty
+ of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
-<!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by lj (jl) -->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="www.jalview.org/colours">
+<!--
+ Java JAXB binding classes are generated by running command line tool xjc:
+ xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
+ Note this also generates code for included schemas
+-->
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:jalview="www.jalview.org/colours" targetNamespace="www.jalview.org/colours">
+ <xs:element name="JalviewUserColours" type="jalview:JalviewUserColours" />
<xs:complexType name="JalviewUserColours">
<xs:sequence>
<xs:element name="Version" maxOccurs="1" minOccurs="0" type="xs:string">
</xs:element>
<xs:element name="colour" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
- <xs:attribute name="Name" type="xs:string"/>
+ <xs:sequence>
+ <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
+ <xs:annotation>
+ <xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="Name" type="xs:string">
+ <xs:annotation>
+ <xs:documentation>Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
<xs:attribute name="RGB" type="xs:string" use="required"/>
<xs:attribute name="minRGB" type="xs:string" use="optional"/>
- <xs:attribute name="threshType" type="xs:string" use="optional">
- <xs:annotation>
- <xs:documentation>loosely specified enumeration: NONE,ABOVE, or BELOW</xs:documentation>
- </xs:annotation>
- </xs:attribute>
+ <xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
+ <xs:attribute name="threshType" use="optional" type="jalview:ThresholdType" />
<xs:attribute name="threshold" type="xs:float" use="optional"/>
<xs:attribute name="max" type="xs:float" use="optional"/>
<xs:attribute name="min" type="xs:float" use="optional"/>
<xs:attribute name="autoScale" type="xs:boolean" use="optional"/>
</xs:complexType>
</xs:element>
+ <xs:element name="filter" maxOccurs="unbounded" minOccurs="0" >
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="matcherSet" type="jalview:FeatureMatcherSet" />
+ </xs:sequence>
+ <xs:attribute name="featureType" type="xs:string" use="required"/>
+ </xs:complexType>
+ </xs:element>
</xs:sequence>
<xs:attribute name="schemeName" type="xs:string" use="optional"/>
</xs:complexType>
+
+ <xs:complexType name="FeatureMatcherSet">
+ <xs:annotation>
+ <xs:documentation>A feature match condition, which may be simple or compound</xs:documentation>
+ </xs:annotation>
+ <xs:choice>
+ <xs:element name="matchCondition" type="jalview:FeatureMatcher" />
+ <xs:element name="compoundMatcher">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="matcherSet" minOccurs="2" maxOccurs="2" type="jalview:FeatureMatcherSet" />
+ </xs:sequence>
+ <xs:attribute name="and" type="xs:boolean" use="required">
+ <xs:annotation>
+ <xs:documentation>If true, matchers are AND-ed, if false they are OR-ed</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ </xs:element>
+ </xs:choice>
+ </xs:complexType>
+
+ <xs:complexType name="FeatureMatcher">
+ <xs:sequence>
+ <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
+ <xs:annotation>
+ <xs:documentation>name of feature attribute to filter on, or attribute and sub-attribute</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="condition" type="xs:string" />
+ <xs:element name="value" type="xs:string" />
+ </xs:sequence>
+ <xs:attribute name="by" type="jalview:FilterBy" />
+ </xs:complexType>
+
+ <xs:simpleType name="ThresholdType">
+ <xs:annotation>
+ <xs:documentation>Whether filter has a threshold, and if so is it
+ above or below
+ </xs:documentation>
+ </xs:annotation>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="NONE" />
+ <xs:enumeration value="ABOVE" />
+ <xs:enumeration value="BELOW" />
+ </xs:restriction>
+ </xs:simpleType>
+
+ <xs:simpleType name="FilterBy">
+ <xs:annotation>
+ <xs:documentation>Filter may apply to label, score or some feature attribute</xs:documentation>
+ </xs:annotation>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="byLabel" />
+ <xs:enumeration value="byScore" />
+ <xs:enumeration value="byAttribute" />
+ </xs:restriction>
+ </xs:simpleType>
+
+ <xs:simpleType name="NoValueColour">
+ <xs:annotation>
+ <xs:documentation>Graduated feature colour if no score (or attribute) value</xs:documentation>
+ </xs:annotation>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="None" />
+ <xs:enumeration value="Min" />
+ <xs:enumeration value="Max" />
+ </xs:restriction>
+ </xs:simpleType>
</xs:schema>
git://source.jalview.org / jalview.git / blobdiff