From: amwaterhouse <Andrew Waterhouse> Date: Fri, 20 May 2005 08:16:59 +0000 (+0000) Subject: xml schemas X-Git-Tag: Release_2_0~268 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=37c1bc52d964f50df6604d50a381a8f5dae8a5aa;p=jalview.git xml schemas --- diff --git a/schemas/JalviewState.xsd b/schemas/JalviewState.xsd new file mode 100755 index 0000000..e0274c6 --- /dev/null +++ b/schemas/JalviewState.xsd @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="www.jalview.org"> + <xs:complexType name="JalviewState"> + <xs:sequence> + <xs:element name="creationDate" type="xs:dateTime"/> + <xs:element name="file" maxOccurs="unbounded" type="xs:string"/> + </xs:sequence> + </xs:complexType> +</xs:schema> \ No newline at end of file diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd new file mode 100755 index 0000000..77d701c --- /dev/null +++ b/schemas/jalview.xsd @@ -0,0 +1,136 @@ +<?xml version="1.0" encoding="UTF-8"?> +<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" + xmlns:vamsas="www.vamsas.org" + xmlns:jalview="www.jalview.org" + targetNamespace="www.jalview.org" + elementFormDefault="qualified" + attributeFormDefault="unqualified"> + +<xs:import schemaLocation="vamsas.xsd" namespace="www.vamsas.org" /> + +<xs:complexType name="JalviewModel"> + + <xs:sequence> + + <xs:element name="creationDate" type="xs:dateTime"/> + + <xs:element name="vamsasModel" type="vamsas:VAMSAS"/> + + <xs:sequence> + + <xs:element name="JSeq" maxOccurs="unbounded"> + + <xs:complexType> + + <xs:attribute name="colour" type="xs:int" use="optional"/> + + <xs:attribute name="start" type="xs:int" use="required"/> + + <xs:attribute name="end" type="xs:int" use="required"/> + + <xs:attribute name="id" type="xs:int" use="required"/> + + </xs:complexType> + + </xs:element> + + <xs:element name="JGroup" maxOccurs="unbounded"> + + <xs:complexType> + + <xs:sequence minOccurs="1"> + + <xs:element name="seq" maxOccurs="unbounded" type="xs:int"/> + + </xs:sequence> + + <xs:attribute name="start" type="xs:int"/> + + <xs:attribute name="end" type="xs:int"/> + + <xs:attribute name="name" type="xs:string"/> + + <xs:attribute name="colour" type="xs:string"/> + + <xs:attribute name="consThreshold" type="xs:int"/> + + <xs:attribute name="pidThreshold" type="xs:int"/> + + <xs:attribute name="outlineColour" type="xs:int"/> + + <xs:attribute name="displayBoxes" type="xs:boolean"/> + + <xs:attribute name="displayText" type="xs:boolean"/> + + <xs:attribute name="colourText" type="xs:boolean"/> + + </xs:complexType> + + </xs:element> + + <xs:element name="Viewport" maxOccurs="unbounded"> + + <xs:complexType> + <xs:attribute name="conservationSelected" type="xs:boolean"/> + + <xs:attribute name="pidSelected" type="xs:boolean"/> + + <xs:attribute name="bgColour" type="xs:string"/> + + <xs:attribute name="consThreshold" type="xs:int"/> + + <xs:attribute name="pidThreshold" type="xs:int"/> + + <xs:attribute name="title" type="xs:string"/> + + <xs:attribute name="showFullId" type="xs:boolean"/> + + <xs:attribute name="showText" type="xs:boolean"/> + + <xs:attribute name="showColourText" type="xs:boolean"/> + + <xs:attribute name="showBoxes" type="xs:boolean"/> + + <xs:attribute name="wrapAlignment" type="xs:boolean"/> + + <xs:attribute name="renderGaps" type="xs:boolean"/> + + <xs:attribute name="showSequenceFeatures" type="xs:boolean"/> + + <xs:attribute name="showAnnotation" type="xs:boolean"/> + + <xs:attribute name="showConservation" type="xs:boolean"/> + + <xs:attribute name="showQuality" type="xs:boolean"/> + + <xs:attribute name="showIdentity" type="xs:boolean"/> + + <xs:attribute name="xpos" type="xs:int"/> + + <xs:attribute name="ypos" type="xs:int"/> + + <xs:attribute name="width" type="xs:int"/> + + <xs:attribute name="height" type="xs:int"/> + + <xs:attribute name="startRes" type="xs:int"/> + <xs:attribute name="startSeq" type="xs:int"/> + <xs:attribute name="fontName" type="xs:string"/> + <xs:attribute name="fontSize" type="xs:int"/> + <xs:attribute name="fontStyle" type="xs:int"/> + + + </xs:complexType> + + </xs:element> + + </xs:sequence> + + </xs:sequence> + +</xs:complexType> + + + + +</xs:schema> diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd new file mode 100755 index 0000000..08a70af --- /dev/null +++ b/schemas/vamsas.xsd @@ -0,0 +1,73 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by lj (jl) --> +<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.org" targetNamespace="www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified"> + <xs:complexType name="VAMSAS"> + <xs:sequence> + <xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded"> + <xs:complexType> + <xs:sequence> + <xs:element name="Annotation" minOccurs="0"> + <xs:complexType> + <xs:sequence> + <xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/> + <xs:element name="label" type="xs:string"/> + <xs:element name="description" type="xs:string"/> + </xs:sequence> + <xs:attribute name="graph" type="xs:boolean" use="required"/> + </xs:complexType> + </xs:element> + <xs:element ref="vamsas:SequenceSet"/> + </xs:sequence> + </xs:complexType> + </xs:element> + <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/> + <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/> + </xs:sequence> + </xs:complexType> + <xs:element name="SequenceSet"> + <xs:complexType> + <xs:sequence> + <xs:element name="Sequence" type="vamsas:SequenceType" maxOccurs="unbounded"/> + <xs:element name="Annotation" minOccurs="0" maxOccurs="unbounded"> + <xs:complexType> + <xs:sequence> + <xs:element name="description" type="xs:string" minOccurs="0"/> + <xs:element name="status" type="xs:string" minOccurs="0"/> + <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/> + </xs:sequence> + <xs:attribute name="type" type="xs:string" use="required"/> + <xs:attribute name="end" type="xs:string" use="required"/> + <xs:attribute name="begin" type="xs:string" use="required"/> + <xs:attribute name="seqRef" type="xs:string" use="required"/> + </xs:complexType> + </xs:element> + </xs:sequence> + <xs:attribute name="gapChar" type="xs:string" use="required"/> + <xs:attribute name="aligned" type="xs:boolean" use="optional"/> + </xs:complexType> + </xs:element> + <xs:element name="annotationElement"> + <xs:complexType> + <xs:sequence> + <xs:element name="displayCharacter" type="xs:string"/> + <xs:element name="description" type="xs:string"/> + <xs:element name="secondaryStructure"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:length value="1"/> + </xs:restriction> + </xs:simpleType> + </xs:element> + <xs:element name="value" type="xs:float"/> + </xs:sequence> + <xs:attribute name="position" type="xs:int" use="required"/> + </xs:complexType> + </xs:element> + <xs:complexType name="SequenceType"> + <xs:sequence> + <xs:element name="sequence" type="xs:string"/> + <xs:element name="name" type="xs:string"/> + </xs:sequence> + <xs:attribute name="id" type="xs:string"/> + </xs:complexType> +</xs:schema>