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

<!-- 	document	: rnastructAlignmentML schema definition
	version 		: 0.1
	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>
	released 	: no
	buglevel	: uses the latest (not yet released) version 1.1 BioTypes
	todo		: sequence element should use types from sequenceML
-->
<xs:schema 
	xmlns:xs="http://www.w3.org/2001/XMLSchema" 
	xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes"
	xmlns:cr="http://schemas.bioservices.net/2006/01/crossrefs"
	targetNamespace="http://hobit.sourceforge.net/xsds/20060201/rnastructAlignmentML"
	xmlns:rsa="http://hobit.sourceforge.net/xsds/20060201/rnastructAlignmentML"
	elementFormDefault="qualified" 
	attributeFormDefault="unqualified">
	
	<!-- RNAStructAlignmentML is based on BioTypes 1.1 and Crossrefs 0.1 -->
	<xs:import namespace="http://schemas.bioservices.net/2006/01/biotypes" schemaLocation="http://bibiserv.techfak.uni-bielefeld.de/xsd/net/bioservices/schemas/2005/biotypes.xsd" />
	<xs:import namespace="http://schemas.bioservices.net/2006/01/crossrefs" schemaLocation="http://schemas.bioservices.net/2006/01/crossrefs_0.1.xsd" />
	
	<!--                    	-->
	<!-- ELEMENTS -->
	<!--                   	-->
	<xs:element name="rnastructAlignmentML" nillable="true">
		<xs:annotation>
			<xs:documentation>
				This is the root element for rnastructAlignmentML. Represents a unsorted list of structure alignments.
			</xs:documentation>
		</xs:annotation>
		<xs:complexType>
			<xs:sequence> 
				<xs:element name="rnastructurealignment" type="rsa:rnastructurealignmentWithProgramType" minOccurs="1" maxOccurs="unbounded" />
			</xs:sequence>
			<xs:attribute name="version" type="xs:string" fixed="0.1"/>
		</xs:complexType>
	</xs:element>
	
	<!--             	-->
	<!-- TYPES 	-->
	<!--             	-->
	<xs:complexType name="rnastructurealignmentWithProgramType">
		<xs:complexContent>
			<xs:extension base="rsa:rnastructurealignmentType">
				<xs:sequence>
					<xs:element name="program" type="rsa:programType" minOccurs="0" maxOccurs="1" />
				</xs:sequence>
			</xs:extension>
		</xs:complexContent>
	</xs:complexType>
	
	<xs:complexType name="rnastructurealignmentType">
		<xs:annotation>
			<xs:documentation>represents a rna structure alignment</xs:documentation>
		</xs:annotation>
		<xs:sequence maxOccurs="1">
			<xs:element name="sequence" type="rsa:sequenceType" minOccurs="2" maxOccurs="unbounded" />
			<xs:element name="comment" type="xs:string" minOccurs="0" maxOccurs="1" />
			<xs:element name="consensusstructure" type="rsa:structureType" minOccurs="0" maxOccurs="1"/>
		</xs:sequence>
		<xs:attribute name="score" type="xs:int"/>
		<xs:attribute name="id" type="xs:ID" use="optional" />
	</xs:complexType>
	
	<xs:complexType name="sequenceType">
		<xs:sequence maxOccurs="1">
			<xs:element name="name" type="xs:string" minOccurs="0" maxOccurs="1"/>
			<xs:element name="synonyms" type="xs:string" minOccurs="0" maxOccurs="unbounded">
				<xs:annotation>
					<xs:documentation>Synonyms for this element</xs:documentation>
				</xs:annotation>
			</xs:element>
			<xs:element name="description" type="xs:string" minOccurs="0" maxOccurs="1"/>
			<xs:choice maxOccurs="1">
				<xs:element name="alignedNucleicAcidSequence" type="rsa:alignedNucleotideSequence"/>
				<xs:element name="alignedFreeSequence" type="rsa:alignedFreeSequence"/>
				<xs:element name="emptySequence" fixed=""/>
			</xs:choice>
			<xs:element name="structure" type="rsa:structureType" minOccurs="1" maxOccurs="1"/>
			<xs:element minOccurs="0" ref="cr:crossRefs" />
			<xs:element name="comment" type="xs:string" minOccurs="0" maxOccurs="1"/>
		</xs:sequence>
		<xs:attribute name="seqID" type="xs:string" use="required"/>
		<xs:anyAttribute processContents="lax"/>
	</xs:complexType>

	<!-- Types, currently not within BioTypes -->
	<xs:simpleType name="alignedFreeSequence">
		<xs:annotation>
			<xs:documentation>inherit gappedFreeSequenceType from hobitTypes; does not allow gaps</xs:documentation>
		</xs:annotation>
		<xs:restriction base="xs:string">
			<xs:whiteSpace value="replace"/>
			<xs:pattern value="[A-Z\-]{0,}"/>
		</xs:restriction>
	</xs:simpleType>
	
	<xs:complexType name="alignedNucleotideSequence">
		<xs:annotation>
			<xs:documentation>An aligned nucleic acid sequence.</xs:documentation>
		</xs:annotation>
		<xs:simpleContent>
			<xs:extension base="bt:gappedAmbiguousNucleotideSequence">
				<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
			</xs:extension>
		</xs:simpleContent>
	</xs:complexType>
	
	<xs:complexType name="programType" mixed="true">
		<xs:attribute name="command" type="xs:string" use="optional" />
		<xs:attribute name="version" type="xs:string" use="optional" />
		<xs:attribute name="date" type="xs:date" use="optional" />
		<xs:anyAttribute processContents="lax"/>
	</xs:complexType>
	
	<xs:complexType name="structureType">
		<xs:simpleContent>
			<xs:extension base="bt:gappedRnaSecondaryStructureSequence">
				<xs:attribute name="energy" type="xs:double" use="optional" />
				<xs:attribute name="probability" type="rsa:probability" 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>
