<?xml version="1.0" encoding="UTF-8"?>

<!-- 	document	: rnastructML schema definition
	version 		: 2.0
	date 		: 2006-02-01
	author		: Kai Loewenthal <kloewent@techfak.uni-bielefeld.de>
			  Sven Hartmeier <shartmei@techfak.uni-bielefeld.de>
			  Jan Krueger <jkrueger.techfak.uni-bielefeld.de>
-->
<xs:schema 
	xmlns:xs="http://www.w3.org/2001/XMLSchema" 
	xmlns:bt="http://schemas.bioservices.net/2005/biotypes"
	xmlns:ht="http://hobit.sourceforge.net/xsds/20060403/hobitTypes"
	targetNamespace="http://hobit.sourceforge.net/xsds/20060201/rnastructML"
	xmlns:rna="http://hobit.sourceforge.net/xsds/20060201/rnastructML"
	elementFormDefault="qualified" 
	attributeFormDefault="unqualified">
	
	<!-- RNAStructAlignmentML is based on BioTypes 1.1 and HobitTypes -->
	<xs:import namespace="http://schemas.bioservices.net/2005/biotypes" schemaLocation="http://bibiserv.techfak.uni-bielefeld.de/xsd/net/bioservices/schemas/2005/biotypes.xsd" />
	<xs:import namespace="http://hobit.sourceforge.net/xsds/20060403/hobitTypes" schemaLocation="http://bibiserv.techfak.uni-bielefeld.de/xsd/net/sourceforge/hobit/20060403/hobitTypes.xsd" />
	
	
	
	<!--                    	-->
	<!-- ELEMENTS -->
	<!--                   	-->
	<xs:element name="rnastructML" nillable="true">
		<xs:annotation>
			<xs:documentation>
				RNAStructML is a format for storing rna secondary structure information. 
				One widely accepted usage for rnatools, such as 
				RNAshapes {http://bibiserv.techfak.uni-bielefeld.de/rnashapes}, 
				RNAfold {http://www.tbi.univie.ac.at/~ivo/RNA/} and 
				Mfold {http://www.bioinfo.rpi.edu/applications/mfold/old/rna/form1.cgi}
				is the proprosal of rna secondary structures, based on thermodynamic principles.
				RNAStructML is based on SequenceML and uses DotBracket strings for storing 
				the structure information.
			</xs:documentation>
		</xs:annotation>
		<xs:complexType>
			<xs:sequence> 
				<xs:element name="rnastructure" type ="rna:rnastructureWithProgramType" minOccurs="1" maxOccurs="unbounded" />
			</xs:sequence>
			<xs:attribute name="version" type="bt:version" use="optional" />
		</xs:complexType>
	</xs:element>
	
	<!--             	-->
	<!-- TYPES 	-->
	<!--             	-->
	<xs:complexType name="rnastructureWithProgramType">
		<xs:complexContent>
			<xs:extension base="rna:rnastructureType">
				<xs:sequence>
					<xs:element name="program" type="ht:programType" minOccurs="0" maxOccurs="1" />
				</xs:sequence>
			</xs:extension>
		</xs:complexContent>
	</xs:complexType>
	
	<xs:complexType name="rnastructureType">
		<xs:sequence maxOccurs="1">
			<xs:element name="sequence" type="rna:sequenceType" minOccurs="0" maxOccurs="1" />
			<xs:element name="comment" type="xs:string" minOccurs="0" maxOccurs="1" />
			<xs:sequence minOccurs="1" maxOccurs="unbounded">
				<xs:choice>
					<xs:element name="shape" type="rna:shapeType" />
					<xs:element name="structure" type="rna:structureType" />
				</xs:choice>
			</xs:sequence>
		</xs:sequence>
		<xs:anyAttribute processContents="lax"/>
	</xs:complexType>
	
	<xs:complexType name="sequenceType">
		<xs:sequence minOccurs="1" maxOccurs="1">
			<xs:element minOccurs="0" maxOccurs="1" name="name" type="xs:string" />
			<xs:element minOccurs="0" maxOccurs="unbounded" name="synonyms" type="xs:string">
				<xs:annotation>
					<xs:documentation>Synonyms for this element</xs:documentation>
				</xs:annotation>
			</xs:element>
			<xs:element minOccurs="0" name="description" type="xs:string" />
			<xs:choice>
				<xs:element name="nucleicAcidSequence" type="bt:ambiguousNucleotideSequence" />
				<xs:element name="freeSequence" type="bt:sequence" />
				<xs:element name="emptySequence" fixed=""/>
			</xs:choice>
			
			<xs:element maxOccurs="1" minOccurs="0" name="comment" type="xs:string" />
		</xs:sequence>
		<xs:attribute name="seqID" type="bt:accessionNumber" use="required" />
		<xs:anyAttribute processContents="lax"/>
	</xs:complexType>
	

	
	<xs:complexType name="shapeType">
		<xs:simpleContent>
			<xs:extension base="bt:rnaSecondaryStructureSequenceClass">  
				<xs:attribute name="probability" type="rna:probability" use="optional" />
				<xs:attribute name="id" type="xs:ID" use="optional" />
				<xs:anyAttribute processContents="lax"/>
			</xs:extension>
		</xs:simpleContent>
	</xs:complexType>
	
	<xs:complexType name="structureType">
		<xs:simpleContent>
			<xs:extension base="bt:rnaSecondaryStructureSequence">
				<xs:attribute name="energy" type="xs:double" use="optional" />
				<xs:attribute name="probability" type="rna:probability" use="optional"/>
				<xs:attribute name="shaperef" type="xs:IDREF" use="optional" />
				<xs:anyAttribute processContents="lax"/>
			</xs:extension>
		</xs:simpleContent>
	</xs:complexType>
	
	<xs:simpleType name="probability">
		<xs:restriction base="xs:double">
			<xs:maxInclusive value="1.0" />
			<xs:minInclusive value="0.0" />
		</xs:restriction>
	</xs:simpleType>
</xs:schema>

