X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fembl.xsd;fp=schemas%2Fembl.xsd;h=1baebfe75537c86a0202724efb30a2fead6c4e2d;hb=4d64932654de3f6ffe07db11d18f2d21f558c6e6;hp=0000000000000000000000000000000000000000;hpb=382f5ff058a4c2fed1e9874bb712b40f16ec1a4e;p=jalview.git

diff --git a/schemas/embl.xsd b/schemas/embl.xsd
new file mode 100644
index 0000000..1baebfe
--- /dev/null
+++ b/schemas/embl.xsd
@@ -0,0 +1,309 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- 
+    Retrieved for Jalview 14-Sep-2018 from ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.embl.xsd 
+	Modified to match ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.root.xsd with only ENA.embl.xsd included 
+	root element "ROOT" contains a <choice> of "entry" (single accession) or "entrySet" (one or more accessions) 
+	Java binding classes are generated by 
+		xjc schemas/embl.xsd -b schemas/embl_bindings.xml -d src -p jalview.xml.binding.embl 
+-->
+<xs:schema xmlns:ebi="http://www.ebi.ac.uk/embl/schema"
+	xmlns:xs="http://www.w3.org/2001/XMLSchema"
+	attributeFormDefault="unqualified" elementFormDefault="qualified"
+	version="1.1">
+	<xs:complexType name="XrefType">
+		<xs:annotation>
+			<xs:documentation>Database cross-reference.</xs:documentation>
+		</xs:annotation>
+		<xs:attribute name="db" type="xs:string" use="required" />
+		<xs:attribute name="id" type="xs:string" use="required" />
+		<xs:attribute name="secondaryId" type="xs:string"
+			use="optional" />
+	</xs:complexType>
+	<xs:complexType name="EntrySetType">
+		<xs:sequence minOccurs="1" maxOccurs="unbounded">
+			<xs:element name="entry" type="EntryType" />
+		</xs:sequence>
+	</xs:complexType>
+	<xs:complexType name="EntryType">
+		<xs:sequence>
+			<xs:element maxOccurs="unbounded" minOccurs="0"
+				name="secondaryAccession" type="xs:string" />
+			<xs:element maxOccurs="unbounded" minOccurs="0"
+				name="projectAccession" type="xs:string" />
+			<xs:element maxOccurs="1" minOccurs="1" name="description"
+				type="xs:string" />
+			<xs:element maxOccurs="1" minOccurs="0" name="comment"
+				type="xs:string" />
+			<xs:element maxOccurs="unbounded" minOccurs="0"
+				name="keyword" type="xs:string" />
+			<xs:element maxOccurs="unbounded" minOccurs="0"
+				name="reference">
+				<xs:annotation>
+					<xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+				</xs:annotation>
+				<xs:complexType>
+					<xs:sequence>
+						<xs:element maxOccurs="1" minOccurs="0" name="title"
+							type="xs:string" />
+						<xs:element maxOccurs="unbounded" minOccurs="0"
+							name="author" type="xs:string" />
+						<xs:element maxOccurs="unbounded" minOccurs="0"
+							name="applicant" type="xs:string">
+							<xs:annotation>
+								<xs:documentation>Patent applicant.</xs:documentation>
+							</xs:annotation>
+						</xs:element>
+						<xs:element maxOccurs="1" minOccurs="0"
+							name="consortium" type="xs:string" />
+						<xs:element maxOccurs="1" minOccurs="0"
+							name="submissionDate" type="xs:date">
+							<xs:annotation>
+								<xs:documentation>The submission date (used only for submission
+									references).</xs:documentation>
+							</xs:annotation>
+						</xs:element>
+						<xs:element maxOccurs="1" minOccurs="0" name="journal"
+							type="xs:string">
+							<xs:annotation>
+								<xs:documentation>The journal name (used only for article
+									references).</xs:documentation>
+							</xs:annotation>
+						</xs:element>
+						<xs:element maxOccurs="1" minOccurs="0" name="year"
+							type="xs:string">
+							<xs:annotation>
+								<xs:documentation>The publication year (used only for article
+									references).</xs:documentation>
+							</xs:annotation>
+						</xs:element>
+						<xs:element maxOccurs="1" minOccurs="0" name="volume"
+							type="xs:string">
+							<xs:annotation>
+								<xs:documentation>The volume number (used only for article
+									references).</xs:documentation>
+							</xs:annotation>
+						</xs:element>
+						<xs:element maxOccurs="1" minOccurs="0" name="issue"
+							type="xs:string">
+							<xs:annotation>
+								<xs:documentation>The issue number (used only for article
+									references).</xs:documentation>
+							</xs:annotation>
+						</xs:element>
+						<xs:element maxOccurs="1" minOccurs="0"
+							name="firstPage" type="xs:string">
+							<xs:annotation>
+								<xs:documentation>The first page (used only for article
+									references).</xs:documentation>
+							</xs:annotation>
+						</xs:element>
+						<xs:element maxOccurs="1" minOccurs="0" name="lastPage"
+							type="xs:string">
+							<xs:annotation>
+								<xs:documentation>The last page (used only for article
+									references).</xs:documentation>
+							</xs:annotation>
+						</xs:element>
+						<xs:element maxOccurs="1" minOccurs="0" name="comment"
+							type="xs:string" />
+						<xs:element maxOccurs="1" minOccurs="0"
+							name="referenceLocation" type="xs:string" />
+						<xs:element maxOccurs="unbounded" minOccurs="0"
+							name="xref" type="XrefType" />
+					</xs:sequence>
+					<xs:attribute name="type" use="required">
+						<xs:simpleType>
+							<xs:restriction base="xs:string">
+								<xs:enumeration value="submission" />
+								<xs:enumeration value="book" />
+								<xs:enumeration value="article" />
+								<xs:enumeration value="patent" />
+								<xs:enumeration value="thesis" />
+								<xs:enumeration value="unpublished" />
+							</xs:restriction>
+						</xs:simpleType>
+					</xs:attribute>
+					<xs:attribute name="number" type="xs:integer"
+						use="required" />
+					<xs:attribute name="location" type="xs:string" />
+				</xs:complexType>
+			</xs:element>
+			<xs:element maxOccurs="unbounded" minOccurs="0"
+				name="xref" type="XrefType" />
+			<xs:element maxOccurs="unbounded" minOccurs="0"
+				name="feature">
+				<xs:annotation>
+					<xs:documentation>Sequence feature.</xs:documentation>
+				</xs:annotation>
+				<xs:complexType>
+					<xs:sequence>
+						<xs:element maxOccurs="1" minOccurs="0" name="taxon">
+							<xs:complexType>
+								<xs:sequence>
+									<xs:element maxOccurs="1" minOccurs="0"
+										name="lineage">
+										<xs:complexType>
+											<xs:sequence>
+												<xs:element maxOccurs="unbounded" minOccurs="1"
+													name="taxon">
+													<xs:complexType>
+														<xs:attribute name="scientificName"
+															type="xs:string" use="required" />
+													</xs:complexType>
+												</xs:element>
+											</xs:sequence>
+										</xs:complexType>
+									</xs:element>
+								</xs:sequence>
+								<xs:attribute name="scientificName"
+									type="xs:string" use="required" />
+								<xs:attribute name="commonName" type="xs:string"
+									use="optional" />
+								<xs:attribute name="taxId" type="xs:integer"
+									use="optional" />
+							</xs:complexType>
+						</xs:element>
+						<xs:element maxOccurs="unbounded" minOccurs="0"
+							name="xref" type="XrefType" />
+						<xs:element maxOccurs="unbounded" minOccurs="0"
+							name="qualifier">
+							<xs:annotation>
+								<xs:documentation>Sequence feature qualifier.</xs:documentation>
+							</xs:annotation>
+							<xs:complexType>
+								<xs:sequence>
+									<xs:element maxOccurs="1" minOccurs="0" name="value"
+										type="xs:string" />
+								</xs:sequence>
+								<xs:attribute name="name" type="xs:string"
+									use="required" />
+							</xs:complexType>
+						</xs:element>
+					</xs:sequence>
+					<xs:attribute name="name" type="xs:string"
+						use="required" />
+					<xs:attribute name="location" type="xs:string"
+						use="required" />
+				</xs:complexType>
+			</xs:element>
+			<xs:element maxOccurs="1" minOccurs="0" name="assembly">
+				<xs:complexType>
+					<xs:sequence>
+						<xs:element maxOccurs="unbounded" minOccurs="1"
+							name="range">
+							<xs:complexType>
+								<xs:attribute name="begin" type="xs:integer"
+									use="required" />
+								<xs:attribute name="end" type="xs:integer"
+									use="required" />
+								<xs:attribute name="primaryBegin" type="xs:integer"
+									use="optional" />
+								<xs:attribute name="primaryEnd" type="xs:integer"
+									use="optional" />
+								<xs:attribute name="accession" type="xs:string"
+									use="required" />
+								<xs:attribute name="version" type="xs:integer"
+									use="required" />
+								<xs:attribute default="false" name="complement"
+									type="xs:boolean" use="optional" />
+							</xs:complexType>
+						</xs:element>
+					</xs:sequence>
+				</xs:complexType>
+			</xs:element>
+			<xs:element maxOccurs="1" minOccurs="0" name="contig">
+				<xs:complexType>
+					<xs:sequence>
+						<xs:choice maxOccurs="unbounded" minOccurs="0">
+							<xs:element maxOccurs="1" minOccurs="1" name="range">
+								<xs:complexType>
+									<xs:attribute name="begin" type="xs:integer"
+										use="required" />
+									<xs:attribute name="end" type="xs:integer"
+										use="required" />
+									<xs:attribute name="primaryBegin"
+										type="xs:integer" use="optional" />
+									<xs:attribute name="primaryEnd" type="xs:integer"
+										use="optional" />
+									<xs:attribute name="accession" type="xs:string"
+										use="required" />
+									<xs:attribute name="version" type="xs:integer"
+										use="required" />
+									<xs:attribute default="false" name="complement"
+										type="xs:boolean" use="optional" />
+								</xs:complexType>
+							</xs:element>
+							<xs:element maxOccurs="1" minOccurs="1" name="gap">
+								<xs:complexType>
+									<xs:attribute name="begin" type="xs:integer"
+										use="required" />
+									<xs:attribute name="end" type="xs:integer"
+										use="required" />
+									<xs:attribute name="length" type="xs:integer"
+										use="required" />
+									<xs:attribute default="false" name="unknownLength"
+										type="xs:boolean" use="optional" />
+								</xs:complexType>
+							</xs:element>
+						</xs:choice>
+					</xs:sequence>
+				</xs:complexType>
+			</xs:element>
+			<xs:element maxOccurs="1" minOccurs="0" name="sequence"
+				type="xs:string" />
+		</xs:sequence>
+		<xs:attribute name="accession" type="xs:string"
+			use="required" />
+		<xs:attribute name="version" type="xs:integer"
+			use="required" />
+		<xs:attribute name="entryVersion" type="xs:integer">
+			<xs:annotation>
+				<xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+			</xs:annotation>
+		</xs:attribute>
+		<xs:attribute name="dataClass" type="xs:string"
+			use="required" />
+		<xs:attribute name="taxonomicDivision" type="xs:string"
+			use="required" />
+		<xs:attribute name="moleculeType" type="xs:string"
+			use="required" />
+		<xs:attribute name="sequenceLength" type="xs:integer"
+			use="required" />
+		<xs:attribute name="topology" use="required">
+			<xs:simpleType>
+				<xs:restriction base="xs:string">
+					<xs:enumeration value="circular" />
+					<xs:enumeration value="linear" />
+				</xs:restriction>
+			</xs:simpleType>
+		</xs:attribute>
+		<xs:attribute name="firstPublic" type="xs:date">
+			<xs:annotation>
+				<xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+			</xs:annotation>
+		</xs:attribute>
+		<xs:attribute name="firstPublicRelease" type="xs:integer">
+			<xs:annotation>
+				<xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+			</xs:annotation>
+		</xs:attribute>
+		<xs:attribute name="lastUpdated" type="xs:date">
+			<xs:annotation>
+				<xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+			</xs:annotation>
+		</xs:attribute>
+		<xs:attribute name="lastUpdatedRelease" type="xs:integer">
+			<xs:annotation>
+				<xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+			</xs:annotation>
+		</xs:attribute>
+	</xs:complexType>
+	<xs:element name="ROOT">
+		<xs:complexType>
+			<xs:choice>
+				<xs:element name="entrySet" type="EntrySetType" />
+				<xs:element name="entry" type="EntryType" />
+			</xs:choice>
+		</xs:complexType>
+	</xs:element>
+</xs:schema>