X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2FJalviewUserColours.xsd;h=50f0479886fc310bbae4f20bbf64a97dad77edbc;hb=b4f40b3f92e17f4373ecf047b393f579bc88164d;hp=27f57da793a98efeed6a4c3e83d9793453d03dec;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/schemas/JalviewUserColours.xsd b/schemas/JalviewUserColours.xsd
index 27f57da..50f0479 100755
--- a/schemas/JalviewUserColours.xsd
+++ b/schemas/JalviewUserColours.xsd
@@ -1,34 +1,140 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-  Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
-  Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+  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 program 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 2
-  of the License, or (at your option) any later version.
+  This file is part of Jalview.
   
-  This program 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.
+  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 this program; if not, write to the Free Software
-  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+  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="colour" maxOccurs="unbounded">
+			<xs:element name="Version" maxOccurs="1" minOccurs="0" type="xs:string">
+				<xs:annotation>
+				<xs:documentation>
+				Jalview colour scheme document version.
+				</xs:documentation>
+				</xs:annotation>
+			</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="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="colourByLabel" type="xs:boolean" 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>